Read the Docs build information Build id: 1014372 Project: giottoteam-giotto Version: suite Commit: b9d0a818c42c9f6734cbcdf0b2579adb0d045337 Date: 2022-07-14T19:39:56.351981Z State: finished Success: True [rtd-command-info] start-time: 2022-07-14T19:39:58.314819Z, end-time: 2022-07-14T19:41:17.639294Z, duration: 79, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/sistia01/Giotto.git . Cloning into '.'... Updating files: 8% (707/8334) Updating files: 9% (751/8334) Updating files: 10% (834/8334) Updating files: 10% (903/8334) Updating files: 11% (917/8334) Updating files: 12% (1001/8334) Updating files: 13% (1084/8334) Updating files: 14% (1167/8334) Updating files: 15% (1251/8334) Updating files: 16% (1334/8334) Updating files: 17% (1417/8334) Updating files: 18% (1501/8334) Updating files: 19% (1584/8334) Updating files: 20% (1667/8334) Updating files: 21% (1751/8334) Updating files: 21% (1768/8334) Updating files: 22% (1834/8334) Updating files: 23% (1917/8334) Updating files: 23% (1948/8334) Updating files: 24% (2001/8334) Updating files: 25% (2084/8334) Updating files: 26% (2167/8334) Updating files: 27% (2251/8334) Updating files: 28% (2334/8334) Updating files: 29% (2417/8334) Updating files: 30% (2501/8334) Updating files: 31% (2584/8334) Updating files: 32% (2667/8334) Updating files: 33% (2751/8334) Updating files: 34% (2834/8334) Updating files: 35% (2917/8334) Updating files: 36% (3001/8334) Updating files: 37% (3084/8334) Updating files: 38% (3167/8334) Updating files: 39% (3251/8334) Updating files: 40% (3334/8334) Updating files: 41% (3417/8334) Updating files: 42% (3501/8334) Updating files: 43% (3584/8334) Updating files: 44% (3667/8334) Updating files: 45% (3751/8334) Updating files: 46% (3834/8334) Updating files: 47% (3917/8334) Updating files: 48% (4001/8334) Updating files: 49% (4084/8334) Updating files: 50% (4167/8334) Updating files: 51% (4251/8334) Updating files: 52% (4334/8334) Updating files: 53% (4418/8334) Updating files: 54% (4501/8334) Updating files: 55% (4584/8334) Updating files: 55% (4596/8334) Updating files: 56% (4668/8334) Updating files: 57% (4751/8334) Updating files: 57% (4794/8334) Updating files: 58% (4834/8334) Updating files: 59% (4918/8334) Updating files: 60% (5001/8334) Updating files: 61% (5084/8334) Updating files: 62% (5168/8334) Updating files: 63% (5251/8334) Updating files: 64% (5334/8334) Updating files: 65% (5418/8334) Updating files: 66% (5501/8334) Updating files: 67% (5584/8334) Updating files: 68% (5668/8334) Updating files: 69% (5751/8334) Updating files: 70% (5834/8334) Updating files: 70% (5847/8334) Updating files: 71% (5918/8334) Updating files: 72% (6001/8334) Updating files: 73% (6084/8334) Updating files: 73% (6091/8334) Updating files: 73% (6164/8334) Updating files: 74% (6168/8334) Updating files: 75% (6251/8334) Updating files: 75% (6252/8334) Updating files: 76% (6334/8334) Updating files: 77% (6418/8334) Updating files: 78% (6501/8334) Updating files: 79% (6584/8334) Updating files: 80% (6668/8334) Updating files: 81% (6751/8334) Updating files: 82% (6834/8334) Updating files: 83% (6918/8334) Updating files: 84% (7001/8334) Updating files: 85% (7084/8334) Updating files: 86% (7168/8334) Updating files: 87% (7251/8334) Updating files: 88% (7334/8334) Updating files: 89% (7418/8334) Updating files: 90% (7501/8334) Updating files: 91% (7584/8334) Updating files: 92% (7668/8334) Updating files: 93% (7751/8334) Updating files: 94% (7834/8334) Updating files: 95% (7918/8334) Updating files: 96% (8001/8334) Updating files: 97% (8084/8334) Updating files: 98% (8168/8334) Updating files: 99% (8251/8334) Updating files: 100% (8334/8334) Updating files: 100% (8334/8334), done. [rtd-command-info] start-time: 2022-07-14T19:41:18.006218Z, end-time: 2022-07-14T19:41:32.019509Z, duration: 14, exit-code: 0 git checkout --force origin/suite Note: switching to 'origin/suite'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at b9d0a818 finalized datasets [rtd-command-info] start-time: 2022-07-14T19:41:32.213231Z, end-time: 2022-07-14T19:41:32.429472Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-07-14T19:41:41.491755Z, end-time: 2022-07-14T19:41:46.053848Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2022-07-14T19:41:46.288958Z, end-time: 2022-07-14T19:41:48.116064Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (22.1.2) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 26.3 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 63.2.0 Uninstalling setuptools-63.2.0: Successfully uninstalled setuptools-63.2.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-07-14T19:41:48.296689Z, end-time: 2022-07-14T19:41:56.825218Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 20.8 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 118.1 MB/s eta 0:00:00 Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 kB 185.4 MB/s eta 0:00:00 Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx Downloading Sphinx-5.0.2-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 181.9 MB/s eta 0:00:00 Collecting sphinx-rtd-theme Downloading sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 181.0 MB/s eta 0:00:00 Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.8-py2.py3-none-any.whl (11 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 kB 256.7 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting docutils>=0.11 Downloading docutils-0.19-py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 107.7 MB/s eta 0:00:00 Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 kB 251.0 MB/s eta 0:00:00 Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 kB 214.6 MB/s eta 0:00:00 Collecting importlib-metadata>=4.4 Downloading importlib_metadata-4.12.0-py3-none-any.whl (21 kB) Collecting imagesize Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting sphinxcontrib-htmlhelp>=2.0.0 Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.5/100.5 kB 219.0 MB/s eta 0:00:00 Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting babel>=1.3 Downloading Babel-2.10.3-py3-none-any.whl (9.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 164.4 MB/s eta 0:00:00 Collecting sphinxcontrib-serializinghtml>=1.1.5 Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 215.3 MB/s eta 0:00:00 Collecting requests>=2.5.0 Downloading requests-2.28.1-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 189.8 MB/s eta 0:00:00 Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.2/121.2 kB 225.5 MB/s eta 0:00:00 Collecting Jinja2>=2.3 Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.1/133.1 kB 232.2 MB/s eta 0:00:00 Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 157.1 MB/s eta 0:00:00 Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 kB 209.7 MB/s eta 0:00:00 Collecting Pygments>=2.0 Downloading Pygments-2.12.0-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 206.1 MB/s eta 0:00:00 Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 195.2 MB/s eta 0:00:00 Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 256.1 MB/s eta 0:00:00 Collecting pytz>=2015.7 Downloading pytz-2022.1-py2.py3-none-any.whl (503 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 503.5/503.5 kB 246.8 MB/s eta 0:00:00 Collecting zipp>=0.5 Downloading zipp-3.8.1-py3-none-any.whl (5.6 kB) Collecting typing-extensions>=3.6.4 Downloading typing_extensions-4.3.0-py3-none-any.whl (25 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting charset-normalizer<3,>=2 Downloading charset_normalizer-2.1.0-py3-none-any.whl (39 kB) Collecting certifi>=2017.4.17 Downloading certifi-2022.6.15-py3-none-any.whl (160 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 160.2/160.2 kB 215.2 MB/s eta 0:00:00 Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 204.8 MB/s eta 0:00:00 Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.10-py2.py3-none-any.whl (139 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 139.2/139.2 kB 228.0 MB/s eta 0:00:00 Collecting pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 212.2 MB/s eta 0:00:00 Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23773 sha256=a445046371c5a51131c92867e01240a9b43d731a6576cda6be96aa0c171a3f55 Stored in directory: /tmp/pip-ephem-wheel-cache-3elfc1y1/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=0844aa4d361ac8eed7e0f31b5a1e0ac792c375bbddabcc33430ee990746d2fa7 Stored in directory: /tmp/pip-ephem-wheel-cache-3elfc1y1/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: snowballstemmer, pytz, mock, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, requests, packaging, Jinja2, importlib-metadata, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.6.15 charset-normalizer-2.1.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.4.1 importlib-metadata-4.12.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.8 recommonmark-0.5.0 requests-2.28.1 snowballstemmer-2.2.0 sphinx-5.0.2 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.3.0 urllib3-1.26.10 zipp-3.8.1 [rtd-command-info] start-time: 2022-07-14T19:41:57.012874Z, end-time: 2022-07-14T19:42:09.489445Z, duration: 12, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting bluepy Downloading bluepy-1.3.0.tar.gz (217 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 217.9/217.9 kB 14.1 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting sphinx==3.4.3 Downloading Sphinx-3.4.3-py3-none-any.whl (2.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.9/2.9 MB 126.1 MB/s eta 0:00:00 Collecting sphinx_rtd_theme==0.5.2 Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.1/9.1 MB 186.4 MB/s eta 0:00:00 Collecting readthedocs-sphinx-search==0.1.0 Downloading readthedocs_sphinx_search-0.1.0-py3-none-any.whl (26 kB) Collecting sphinx-design Downloading sphinx_design-0.2.0-py3-none-any.whl (1.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 241.9 MB/s eta 0:00:00 Collecting sphinx-copybutton Downloading sphinx_copybutton-0.5.0-py3-none-any.whl (12 kB) Collecting sphinx-toolbox Downloading sphinx_toolbox-3.1.2-py3-none-any.whl (512 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 512.2/512.2 kB 252.7 MB/s eta 0:00:00 Collecting m2r2 Downloading m2r2-0.3.2-py3-none-any.whl (11 kB) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (1.4.1) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (0.17.1) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (3.1.2) Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (1.0.1) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (2.10.3) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (1.1.5) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (0.7.12) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (58.2.0) Requirement already satisfied: sphinxcontrib-htmlhelp in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (2.0.0) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (1.0.3) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (21.3) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (1.0.2) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (2.2.0) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (2.28.1) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (2.12.0) Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (1.0.2) Collecting docutils>=0.12 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 548.2/548.2 kB 261.8 MB/s eta 0:00:00 Collecting sphinx-design Downloading sphinx_design-0.1.0-py3-none-any.whl (1.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 239.6 MB/s eta 0:00:00 Requirement already satisfied: typing-extensions!=3.10.0.1,>=3.7.4.3 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx-toolbox->-r docs/requirements.txt (line 10)) (4.3.0) Collecting apeye>=0.4.0 Downloading apeye-1.2.0-py3-none-any.whl (118 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 118.5/118.5 kB 223.4 MB/s eta 0:00:00 Collecting beautifulsoup4>=4.9.1 Downloading beautifulsoup4-4.11.1-py3-none-any.whl (128 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 128.2/128.2 kB 232.7 MB/s eta 0:00:00 Collecting dict2css>=0.2.3 Downloading dict2css-0.3.0-py3-none-any.whl (25 kB) Collecting domdf-python-tools>=2.9.0 Downloading domdf_python_tools-3.3.0-py3-none-any.whl (126 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 126.4/126.4 kB 231.9 MB/s eta 0:00:00 Collecting sphinx-autodoc-typehints>=1.11.1 Downloading sphinx_autodoc_typehints-1.18.3-py3-none-any.whl (12 kB) Collecting lockfile>=0.12.2 Downloading lockfile-0.12.2-py2.py3-none-any.whl (13 kB) Collecting cachecontrol[filecache]>=0.12.6 Downloading CacheControl-0.12.11-py2.py3-none-any.whl (21 kB) Collecting sphinx-prompt>=1.1.0 Downloading sphinx_prompt-1.5.0-py3-none-any.whl (4.5 kB) Collecting typing-inspect>=0.6.0 Downloading typing_inspect-0.7.1-py3-none-any.whl (8.4 kB) Collecting autodocsumm>=0.2.0 Downloading autodocsumm-0.2.8-py3-none-any.whl (13 kB) Collecting ruamel.yaml>=0.16.12 Downloading ruamel.yaml-0.17.21-py3-none-any.whl (109 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 109.5/109.5 kB 223.6 MB/s eta 0:00:00 Collecting sphinx-tabs<3.5.0,>=1.2.1 Downloading sphinx_tabs-3.4.1-py3-none-any.whl (10.0 kB) Collecting html5lib>=1.1 Downloading html5lib-1.1-py2.py3-none-any.whl (112 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 112.2/112.2 kB 235.1 MB/s eta 0:00:00 Collecting sphinx-jinja2-compat>=0.1.0 Downloading sphinx_jinja2_compat-0.1.2-py3-none-any.whl (12 kB) Collecting tabulate>=0.8.7 Downloading tabulate-0.8.10-py3-none-any.whl (29 kB) Collecting mistune==0.8.4 Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Requirement already satisfied: idna>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from apeye>=0.4.0->sphinx-toolbox->-r docs/requirements.txt (line 10)) (3.3) Collecting platformdirs>=2.3.0 Downloading platformdirs-2.5.2-py3-none-any.whl (14 kB) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from babel>=1.3->sphinx==3.4.3->-r docs/requirements.txt (line 3)) (2022.1) Collecting soupsieve>1.2 Downloading soupsieve-2.3.2.post1-py3-none-any.whl (37 kB) Collecting msgpack>=0.5.2 Downloading msgpack-1.0.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (299 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 299.8/299.8 kB 240.8 MB/s eta 0:00:00 Collecting cssutils>=2.2.0 Downloading cssutils-2.5.0-py3-none-any.whl (399 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 399.7/399.7 kB 248.7 MB/s eta 0:00:00 Collecting natsort>=7.0.1 Downloading natsort-8.1.0-py3-none-any.whl (37 kB) Requirement already satisfied: importlib-metadata>=3.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from domdf-python-tools>=2.9.0->sphinx-toolbox->-r docs/requirements.txt (line 10)) (4.12.0) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting six>=1.9 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx==3.4.3->-r docs/requirements.txt (line 3)) (2.1.1) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from requests>=2.5.0->sphinx==3.4.3->-r docs/requirements.txt (line 3)) (2022.6.15) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from requests>=2.5.0->sphinx==3.4.3->-r docs/requirements.txt (line 3)) (1.26.10) Requirement already satisfied: charset-normalizer<3,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from requests>=2.5.0->sphinx==3.4.3->-r docs/requirements.txt (line 3)) (2.1.0) Collecting ruamel.yaml.clib>=0.2.6 Downloading ruamel.yaml.clib-0.2.6-cp37-cp37m-manylinux1_x86_64.whl (546 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 546.8/546.8 kB 226.1 MB/s eta 0:00:00 Collecting sphinx-autodoc-typehints>=1.11.1 Downloading sphinx_autodoc_typehints-1.18.2-py3-none-any.whl (12 kB) Downloading sphinx_autodoc_typehints-1.18.1-py3-none-any.whl (12 kB) Downloading sphinx_autodoc_typehints-1.18.0-py3-none-any.whl (12 kB) Downloading sphinx_autodoc_typehints-1.17.1-py3-none-any.whl (12 kB) Downloading sphinx_autodoc_typehints-1.17.0-py3-none-any.whl (12 kB) Downloading sphinx_autodoc_typehints-1.16.0-py3-none-any.whl (12 kB) Downloading sphinx_autodoc_typehints-1.15.3-py3-none-any.whl (11 kB) Downloading sphinx_autodoc_typehints-1.15.2-py3-none-any.whl (11 kB) Downloading sphinx_autodoc_typehints-1.15.1-py3-none-any.whl (11 kB) Downloading sphinx_autodoc_typehints-1.15.0-py3-none-any.whl (11 kB) Downloading sphinx_autodoc_typehints-1.14.1-py3-none-any.whl (11 kB) Downloading sphinx_autodoc_typehints-1.14.0-py3-none-any.whl (11 kB) Downloading sphinx_autodoc_typehints-1.13.1-py3-none-any.whl (10 kB) Downloading sphinx_autodoc_typehints-1.13.0-py3-none-any.whl (10 kB) Downloading sphinx_autodoc_typehints-1.12.0-py3-none-any.whl (9.4 kB) Collecting sphinx-tabs<3.5.0,>=1.2.1 Downloading sphinx_tabs-3.4.0-py3-none-any.whl (10.0 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.6/133.6 kB 227.3 MB/s eta 0:00:00 Collecting sphinx-tabs<3.5.0,>=1.2.1 Downloading sphinx_tabs-3.3.1-py3-none-any.whl (10.0 kB) Downloading sphinx_tabs-3.3.0-py3-none-any.whl (10 kB) Downloading sphinx_tabs-3.2.0-py3-none-any.whl (9.8 kB) Collecting mypy-extensions>=0.3.0 Downloading mypy_extensions-0.4.3-py2.py3-none-any.whl (4.5 kB) Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from packaging->sphinx==3.4.3->-r docs/requirements.txt (line 3)) (3.0.9) Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from importlib-metadata>=3.6.0->domdf-python-tools>=2.9.0->sphinx-toolbox->-r docs/requirements.txt (line 10)) (3.8.1) Building wheels for collected packages: bluepy Building wheel for bluepy (setup.py): started Building wheel for bluepy (setup.py): finished with status 'done' Created wheel for bluepy: filename=bluepy-1.3.0-cp37-cp37m-linux_x86_64.whl size=554825 sha256=2cf7c1eed817958054c2c284a356c25ba7af799f29a7ba28453ffe4095f2b349 Stored in directory: /tmp/pip-ephem-wheel-cache-dv516ku5/wheels/29/02/3d/a378a65b6771fb8359bf2c862f0ffe6f4bd6b0af88f4309c1c Successfully built bluepy Installing collected packages: webencodings, mypy-extensions, msgpack, mistune, lockfile, bluepy, typing-inspect, tabulate, soupsieve, six, ruamel.yaml.clib, readthedocs-sphinx-search, platformdirs, natsort, docutils, sphinx-jinja2-compat, sphinx, ruamel.yaml, m2r2, html5lib, domdf-python-tools, cssutils, cachecontrol, beautifulsoup4, sphinx-tabs, sphinx_rtd_theme, sphinx-prompt, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, dict2css, autodocsumm, apeye, sphinx-toolbox Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 5.0.2 Uninstalling Sphinx-5.0.2: Successfully uninstalled Sphinx-5.0.2 Attempting uninstall: sphinx_rtd_theme Found existing installation: sphinx-rtd-theme 1.0.0 Uninstalling sphinx-rtd-theme-1.0.0: Successfully uninstalled sphinx-rtd-theme-1.0.0 Successfully installed apeye-1.2.0 autodocsumm-0.2.8 beautifulsoup4-4.11.1 bluepy-1.3.0 cachecontrol-0.12.11 cssutils-2.5.0 dict2css-0.3.0 docutils-0.16 domdf-python-tools-3.3.0 html5lib-1.1 lockfile-0.12.2 m2r2-0.3.2 mistune-0.8.4 msgpack-1.0.4 mypy-extensions-0.4.3 natsort-8.1.0 platformdirs-2.5.2 readthedocs-sphinx-search-0.1.0 ruamel.yaml-0.17.21 ruamel.yaml.clib-0.2.6 six-1.16.0 soupsieve-2.3.2.post1 sphinx-3.4.3 sphinx-autodoc-typehints-1.12.0 sphinx-copybutton-0.5.0 sphinx-design-0.1.0 sphinx-jinja2-compat-0.1.2 sphinx-prompt-1.5.0 sphinx-tabs-3.2.0 sphinx-toolbox-3.1.2 sphinx_rtd_theme-0.5.2 tabulate-0.8.10 typing-inspect-0.7.1 webencodings-0.5.1 [rtd-command-info] start-time: 2022-07-14T19:42:10.959179Z, end-time: 2022-07-14T19:42:11.022939Z, duration: 0, exit-code: 0 cat docs/source/conf.py # Configuration file for the Sphinx documentation builder. # # This file only contains a selection of the most common options. For a full # list see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import sys #sys.path.insert(0, os.path.abspath('.')) # -- Project information ----------------------------------------------------- project = 'Giotto' copyright = '2021, Ruben Dries, Qian Zhu, Huipeng Li, Rui Dong, Guo-Cheng Yuan' author = 'Developed by Ruben Dries, Qian Zhu, Huipeng Li, Rui Dong, Guo-Cheng Yuan.' # The full version, including alpha/beta/rc tags release = '1.0' # -- General configuration --------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. #import os #import sys # from sphinx.application import Sphinx import sphinx_rtd_theme master_dox = 'index' extensions = [ 'sphinx_rtd_theme', #added to fix bullet-point issue 'sphinx.ext.autosectionlabel', # may cause duplicate label warnings 'sphinx.ext.autodoc', 'sphinx_rtd_theme', 'sphinx_design', 'sphinx_copybutton', 'sphinx_toolbox', 'sphinx_toolbox.shields', 'sphinx_toolbox.github', #'sphinx_last_updated_by_git', #fatal error on readthedocs #'recommonmark', #'m2r2', -- moved to requirements.txt #'sphinxcontrib.images' #'myst_parser' #myst_parser caused a fatal error #'sphinxcontrib.spelling' #spell checker fatal error ] #Added for m2r2 extension source_suffix = ['.rst', '.md'] # Configuration for sphinx_toolbox github_repository = "Giotto" github_username = "RubD" # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. suppress_warnings = [ #'Unknown directive type dropdown', 'autosectionlabel.*', 'epub.duplicated_toc_entry'] #autosectionlabel_prefix_document = True #caused many warnings #autosectionlabel_maxdepth = 1 #caused many warnings # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_theme = "sphinx_rtd_theme" html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] html_static_path = ["_static"] html_logo = "images/GiottoLogo.png" html_theme_options = { 'logo_only': True, 'display_version': True, 'navigation_depth': 4, #Toc Tree Options 'collapse_navigation': True, 'sticky_navigation': True, 'body_max_width': 'none' } html_sidebars = { '**': ['globaltoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html'] } html_css_files = ["css/theme_edits.css"] panels_add_fontawesome_latex = True panels_add_bootstrap_css = True # Toc Tree options navtree_root_links = True navtree_shift = False def setup(app): app.add_css_file("css/theme_edits.css") #Link badges def get_badge_inputs(text, cls: str = ""): return text, cls.split() def get_link_badge_inputs(link, text=None, type="link", cls: str = "", tooltip=None): return link, text or link, type, cls.split(), tooltip #Copy clipboard image #To use a different image for your copy buttons, do the following: #Place the image in the _static/ folder of your site. #Set the copybutton_image_path variable in your conf.py to be the path to your image file, relative to _static/. #copybutton_image_path = "_static/AdditionalImages/copyclipboard.png" # EXCLUDE DOCUMENTS # exclude_patterns = [] ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "suite", 'version_slug': "suite", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("master", "/en/master/"), ("suite", "/en/suite/"), ], 'downloads': [ ("html", "//giottoteam-giotto.readthedocs-hosted.com/_/downloads/en/suite/htmlzip/"), ("epub", "//giottoteam-giotto.readthedocs-hosted.com/_/downloads/en/suite/epub/"), ], 'subprojects': [ ], 'slug': 'giottoteam-giotto', 'name': u'Giotto', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://giottoteam-giotto.readthedocs-hosted.com/en/master/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/source/', 'api_host': 'https://readthedocs.com', 'github_user': 'sistia01', 'proxied_api_host': '/_', 'github_repo': 'Giotto', 'github_version': 'suite', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'suite', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'suite', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'b9d0a818', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/giottoteam-giotto/builds/1014372/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2022-07-14T19:42:11.310784Z, end-time: 2022-07-14T19:43:07.141540Z, duration: 55, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v3.4.3 loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 675 source files that are out of date updating environment: [new config] 675 added, 0 changed, 0 removed reading sources... [ 0%] Workflow reading sources... [ 0%] additionalinformation reading sources... [ 0%] contribute reading sources... [ 0%] datasets reading sources... [ 0%] development reading sources... [ 0%] documentation reading sources... [ 1%] errorsfaqsandtips reading sources... [ 1%] faqs reading sources... [ 1%] gettingstarted reading sources... [ 1%] giottoworkflowanalyses reading sources... [ 1%] github_issues reading sources... [ 1%] index reading sources... [ 1%] subsections/citing_giotto reading sources... [ 2%] subsections/code_of_conduct reading sources... [ 2%] subsections/datasets/STARmap_mouse_cortex reading sources... [ 2%] subsections/datasets/human_CyCIF_PDAC reading sources... [ 2%] subsections/datasets/merFISH_hypot_preopt_region reading sources... [ 2%] subsections/datasets/mini_3D_STARmap reading sources... [ 2%] subsections/datasets/mini_seqFISH reading sources... [ 2%] subsections/datasets/mini_visium reading sources... [ 3%] subsections/datasets/mouse_CODEX_spleen reading sources... [ 3%] subsections/datasets/mouse_visium_brain reading sources... [ 3%] subsections/datasets/mouse_visium_kidney reading sources... [ 3%] subsections/datasets/nanostring_lung_12 reading sources... [ 3%] subsections/datasets/nanostring_overview reading sources... [ 3%] subsections/datasets/osmFISH_mouse_SS_cortex reading sources... [ 4%] subsections/datasets/other_technologies_coming_soon reading sources... [ 4%] subsections/datasets/resolve_bc_210928 reading sources... [ 4%] subsections/datasets/seqFISH_cortex reading sources... [ 4%] subsections/datasets/singlecell_prostate_integration reading sources... [ 4%] subsections/datasets/singlecell_prostate_standard reading sources... [ 4%] subsections/datasets/tcyCIF reading sources... [ 4%] subsections/datasets/visium_prostate_integration reading sources... [ 5%] subsections/datasets/vizgen_mouse_brain reading sources... [ 5%] subsections/detailed_workflow reading sources... [ 5%] subsections/license reading sources... [ 5%] subsections/md_rst/DT_removeNA reading sources... [ 5%] subsections/md_rst/FSV_show reading sources... [ 5%] subsections/md_rst/OR_test_fnc reading sources... [ 5%] subsections/md_rst/PAGEEnrich reading sources... [ 6%] subsections/md_rst/PAGE_DT_method reading sources... [ 6%] subsections/md_rst/adapt_aspect_ratio reading sources... [ 6%] subsections/md_rst/addCellIntMetadata reading sources... [ 6%] subsections/md_rst/addCellMetadata reading sources... [ 6%] subsections/md_rst/addCellStatistics reading sources... [ 6%] subsections/md_rst/addCellsFromPolygon reading sources... [ 6%] subsections/md_rst/addFeatMetadata reading sources... [ 7%] subsections/md_rst/addFeatStatistics reading sources... [ 7%] subsections/md_rst/addFeatsPerc reading sources... [ 7%] subsections/md_rst/addGeneMetadata reading sources... [ 7%] subsections/md_rst/addGeneStatistics reading sources... [ 7%] subsections/md_rst/addGenesPerc reading sources... [ 7%] subsections/md_rst/addGiottoImage reading sources... [ 8%] subsections/md_rst/addGiottoImageMG reading sources... [ 8%] subsections/md_rst/addGiottoImageToSpatPlot reading sources... [ 8%] subsections/md_rst/addGiottoLargeImage reading sources... [ 8%] subsections/md_rst/addGiottoPoints reading sources... [ 8%] subsections/md_rst/addGiottoPolygons reading sources... [ 8%] subsections/md_rst/addHMRF reading sources... [ 8%] subsections/md_rst/addNetworkLayout reading sources... [ 9%] subsections/md_rst/addSpatialCentroidLocations reading sources... [ 9%] subsections/md_rst/addSpatialCentroidLocationsLayer reading sources... [ 9%] subsections/md_rst/addStatistics reading sources... [ 9%] subsections/md_rst/add_img_array_alpha reading sources... [ 9%] subsections/md_rst/adjustGiottoMatrix reading sources... [ 9%] subsections/md_rst/aes_string2 reading sources... [ 9%] subsections/md_rst/all_plots_save_function reading sources... [ 10%] subsections/md_rst/anndataToGiotto reading sources... [ 10%] subsections/md_rst/annotateGiotto reading sources... [ 10%] subsections/md_rst/annotateSpatialGrid reading sources... [ 10%] subsections/md_rst/annotateSpatialNetwork reading sources... [ 10%] subsections/md_rst/annotate_spatlocs_with_spatgrid_2D reading sources... [ 10%] subsections/md_rst/annotate_spatlocs_with_spatgrid_3D reading sources... [ 10%] subsections/md_rst/average_feat_feat_expression_in_groups reading sources... [ 11%] subsections/md_rst/binSpect reading sources... [ 11%] subsections/md_rst/binSpectMulti reading sources... [ 11%] subsections/md_rst/binSpectMultiMatrix reading sources... [ 11%] subsections/md_rst/binSpectSingle reading sources... [ 11%] subsections/md_rst/binSpectSingleMatrix reading sources... [ 11%] subsections/md_rst/calc_cov_group_HVF reading sources... [ 12%] subsections/md_rst/calc_cov_loess_HVF reading sources... [ 12%] subsections/md_rst/calc_spatial_enrichment_DT reading sources... [ 12%] subsections/md_rst/calc_spatial_enrichment_matrix reading sources... [ 12%] subsections/md_rst/calc_spatial_enrichment_minimum reading sources... [ 12%] subsections/md_rst/calc_var_HVF reading sources... [ 12%] subsections/md_rst/calculateHVF reading sources... [ 12%] subsections/md_rst/calculateHVG reading sources... [ 13%] subsections/md_rst/calculateMetaTable reading sources... [ 13%] subsections/md_rst/calculateMetaTableCells reading sources... [ 13%] subsections/md_rst/calculateOverlapParallel reading sources... [ 13%] subsections/md_rst/calculateOverlapRaster reading sources... [ 13%] subsections/md_rst/calculateOverlapSerial reading sources... [ 13%] subsections/md_rst/calculate_centroids_polygons reading sources... [ 13%] subsections/md_rst/calculate_distance_and_weight reading sources... [ 14%] subsections/md_rst/cellProximityBarplot reading sources... [ 14%] subsections/md_rst/cellProximityEnrichment reading sources... [ 14%] subsections/md_rst/cellProximityHeatmap reading sources... [ 14%] subsections/md_rst/cellProximityNetwork reading sources... [ 14%] subsections/md_rst/cellProximitySpatPlot reading sources... [ 14%] subsections/md_rst/cellProximitySpatPlot2D reading sources... [ 14%] subsections/md_rst/cellProximitySpatPlot3D reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot_2D_ggplot reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot_2D_plotly reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot_3D_plotly reading sources... [ 15%] subsections/md_rst/changeGiottoInstructions reading sources... [ 15%] subsections/md_rst/changeImageBg reading sources... [ 16%] subsections/md_rst/checkGiottoEnvironment reading sources... [ 16%] subsections/md_rst/check_spatial_location_data reading sources... [ 16%] subsections/md_rst/clusterCells reading sources... [ 16%] subsections/md_rst/clusterSpatialCorFeats reading sources... [ 16%] subsections/md_rst/clusterSpatialCorGenes reading sources... [ 16%] subsections/md_rst/cluster_enrich_analysis reading sources... [ 16%] subsections/md_rst/colMeans_flex reading sources... [ 17%] subsections/md_rst/colSums_flex reading sources... [ 17%] subsections/md_rst/combCCcom reading sources... [ 17%] subsections/md_rst/combineCPG reading sources... [ 17%] subsections/md_rst/combineCellData reading sources... [ 17%] subsections/md_rst/combineCellProximityGenes reading sources... [ 17%] subsections/md_rst/combineCellProximityGenes_per_interaction reading sources... [ 17%] subsections/md_rst/combineFeatureData reading sources... [ 18%] subsections/md_rst/combineFeatureOverlapData reading sources... [ 18%] subsections/md_rst/combineICG reading sources... [ 18%] subsections/md_rst/combineInteractionChangedGenes reading sources... [ 18%] subsections/md_rst/combineMetadata reading sources... [ 18%] subsections/md_rst/combineSpatialCellFeatureInfo reading sources... [ 18%] subsections/md_rst/combineSpatialCellMetadataInfo reading sources... [ 18%] subsections/md_rst/compatible_spatial_network reading sources... [ 19%] subsections/md_rst/convertEnsemblToGeneSymbol reading sources... [ 19%] subsections/md_rst/convertGiottoLargeImageToMG reading sources... [ 19%] subsections/md_rst/convert_mgImage_to_array_DT reading sources... [ 19%] subsections/md_rst/convert_to_full_spatial_network reading sources... [ 19%] subsections/md_rst/convert_to_reduced_spatial_network reading sources... [ 19%] subsections/md_rst/cor_flex reading sources... [ 20%] subsections/md_rst/createCrossSection reading sources... [ 20%] subsections/md_rst/createGiottoImage reading sources... [ 20%] subsections/md_rst/createGiottoImageOLD reading sources... [ 20%] subsections/md_rst/createGiottoInstructions reading sources... [ 20%] subsections/md_rst/createGiottoLargeImage reading sources... [ 20%] subsections/md_rst/createGiottoLargeImageList reading sources... [ 20%] subsections/md_rst/createGiottoObject reading sources... [ 21%] subsections/md_rst/createGiottoObjectSubcellular reading sources... [ 21%] subsections/md_rst/createGiottoPoints reading sources... [ 21%] subsections/md_rst/createGiottoPolygonsFromDfr reading sources... [ 21%] subsections/md_rst/createGiottoPolygonsFromMask reading sources... [ 21%] subsections/md_rst/createGiottoVisiumObject reading sources... [ 21%] subsections/md_rst/createHeatmap_DT reading sources... [ 21%] subsections/md_rst/createMetafeats reading sources... [ 22%] subsections/md_rst/createMetagenes reading sources... [ 22%] subsections/md_rst/createNearestNetwork reading sources... [ 22%] subsections/md_rst/createSpatialDefaultGrid reading sources... [ 22%] subsections/md_rst/createSpatialDelaunayNetwork reading sources... [ 22%] subsections/md_rst/createSpatialEnrich reading sources... [ 22%] subsections/md_rst/createSpatialFeaturesKNNnetwork reading sources... [ 22%] subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan reading sources... [ 23%] subsections/md_rst/createSpatialGrid reading sources... [ 23%] subsections/md_rst/createSpatialKNNnetwork reading sources... [ 23%] subsections/md_rst/createSpatialNetwork reading sources... [ 23%] subsections/md_rst/create_2d_mesh_grid_line_obj reading sources... [ 23%] subsections/md_rst/create_KNNnetwork_dbscan reading sources... [ 23%] subsections/md_rst/create_average_DT reading sources... [ 24%] subsections/md_rst/create_average_detection_DT reading sources... [ 24%] subsections/md_rst/create_cell_type_random_cell_IDs reading sources... [ 24%] subsections/md_rst/create_cluster_matrix reading sources... [ 24%] subsections/md_rst/create_crossSection_object reading sources... [ 24%] subsections/md_rst/create_delaunayNetwork2D reading sources... [ 24%] subsections/md_rst/create_delaunayNetwork3D reading sources... [ 24%] subsections/md_rst/create_delaunayNetwork_RTriangle reading sources... [ 25%] subsections/md_rst/create_delaunayNetwork_deldir reading sources... [ 25%] subsections/md_rst/create_delaunayNetwork_geometry reading sources... [ 25%] subsections/md_rst/create_delaunayNetwork_geometry_3D reading sources... [ 25%] subsections/md_rst/create_dimObject reading sources... [ 25%] subsections/md_rst/create_featureNetwork_object reading sources... [ 25%] subsections/md_rst/create_genes_to_use_matrix reading sources... [ 25%] subsections/md_rst/create_giotto_points_object reading sources... [ 26%] subsections/md_rst/create_giotto_polygon_object reading sources... [ 26%] subsections/md_rst/create_jackstrawplot reading sources... [ 26%] subsections/md_rst/create_mesh_grid_lines reading sources... [ 26%] subsections/md_rst/create_screeplot reading sources... [ 26%] subsections/md_rst/create_segm_polygons reading sources... [ 26%] subsections/md_rst/create_spatialGridObject reading sources... [ 26%] subsections/md_rst/create_spatialGrid_default_2D reading sources... [ 27%] subsections/md_rst/create_spatialGrid_default_3D reading sources... [ 27%] subsections/md_rst/create_spatialNetworkObject reading sources... [ 27%] subsections/md_rst/create_spatvector_object_from_dfr reading sources... [ 27%] subsections/md_rst/cropGiottoLargeImage reading sources... [ 27%] subsections/md_rst/crossSectionGenePlot reading sources... [ 27%] subsections/md_rst/crossSectionGenePlot3D reading sources... [ 28%] subsections/md_rst/crossSectionPlot reading sources... [ 28%] subsections/md_rst/crossSectionPlot3D reading sources... [ 28%] subsections/md_rst/decide_cluster_order reading sources... [ 28%] subsections/md_rst/density_giottoLargeImage reading sources... [ 28%] subsections/md_rst/depth reading sources... [ 28%] subsections/md_rst/detectSpatialCorFeats reading sources... [ 28%] subsections/md_rst/detectSpatialCorFeatsMatrix reading sources... [ 29%] subsections/md_rst/detectSpatialCorGenes reading sources... [ 29%] subsections/md_rst/detectSpatialPatterns reading sources... [ 29%] subsections/md_rst/determine_cores reading sources... [ 29%] subsections/md_rst/dimCellPlot reading sources... [ 29%] subsections/md_rst/dimCellPlot2D reading sources... [ 29%] subsections/md_rst/dimFeatPlot2D reading sources... [ 29%] subsections/md_rst/dimGenePlot reading sources... [ 30%] subsections/md_rst/dimGenePlot2D reading sources... [ 30%] subsections/md_rst/dimGenePlot3D reading sources... [ 30%] subsections/md_rst/dimPlot reading sources... [ 30%] subsections/md_rst/dimPlot2D reading sources... [ 30%] subsections/md_rst/dimPlot2D_single reading sources... [ 30%] subsections/md_rst/dimPlot3D reading sources... [ 30%] subsections/md_rst/dimPlot_2D_plotly reading sources... [ 31%] subsections/md_rst/dimPlot_3D_plotly reading sources... [ 31%] subsections/md_rst/distGiottoImage reading sources... [ 31%] subsections/md_rst/doCellSegmentation reading sources... [ 31%] subsections/md_rst/doHMRF reading sources... [ 31%] subsections/md_rst/doHclust reading sources... [ 31%] subsections/md_rst/doKmeans reading sources... [ 32%] subsections/md_rst/doLeidenCluster reading sources... [ 32%] subsections/md_rst/doLeidenSubCluster reading sources... [ 32%] subsections/md_rst/doLouvainCluster reading sources... [ 32%] subsections/md_rst/doLouvainCluster_community reading sources... [ 32%] subsections/md_rst/doLouvainCluster_multinet reading sources... [ 32%] subsections/md_rst/doLouvainSubCluster reading sources... [ 32%] subsections/md_rst/doLouvainSubCluster_community reading sources... [ 33%] subsections/md_rst/doLouvainSubCluster_multinet reading sources... [ 33%] subsections/md_rst/doRandomWalkCluster reading sources... [ 33%] subsections/md_rst/doSNNCluster reading sources... [ 33%] subsections/md_rst/doScrubletDetect reading sources... [ 33%] subsections/md_rst/do_cell_proximity_test reading sources... [ 33%] subsections/md_rst/do_limmatest reading sources... [ 33%] subsections/md_rst/do_multi_permuttest_random reading sources... [ 34%] subsections/md_rst/do_page_permutation reading sources... [ 34%] subsections/md_rst/do_permuttest_original reading sources... [ 34%] subsections/md_rst/do_permuttest_random reading sources... [ 34%] subsections/md_rst/do_rank_permutation reading sources... [ 34%] subsections/md_rst/do_spatial_grid_averaging reading sources... [ 34%] subsections/md_rst/do_spatial_knn_smoothing reading sources... [ 34%] subsections/md_rst/do_ttest reading sources... [ 35%] subsections/md_rst/do_wilctest reading sources... [ 35%] subsections/md_rst/dt_to_matrix reading sources... [ 35%] subsections/md_rst/dt_to_spatVector_points reading sources... [ 35%] subsections/md_rst/dt_to_spatVector_polygon reading sources... [ 35%] subsections/md_rst/enrich_analysis reading sources... [ 35%] subsections/md_rst/enrich_deconvolution reading sources... [ 36%] subsections/md_rst/estimateCellCellDistance reading sources... [ 36%] subsections/md_rst/estimateImageBg reading sources... [ 36%] subsections/md_rst/evaluate_expr_matrix reading sources... [ 36%] subsections/md_rst/evaluate_feat_info reading sources... [ 36%] subsections/md_rst/evaluate_provided_spatial_locations reading sources... [ 36%] subsections/md_rst/evaluate_spatial_info reading sources... [ 36%] subsections/md_rst/evaluate_spatial_locations reading sources... [ 37%] subsections/md_rst/evaluate_spatial_locations_OLD reading sources... [ 37%] subsections/md_rst/evaluate_spatial_network reading sources... [ 37%] subsections/md_rst/exportGiottoViewer reading sources... [ 37%] subsections/md_rst/exprCellCellcom reading sources... [ 37%] subsections/md_rst/extend_vector reading sources... [ 37%] subsections/md_rst/extended_gini_fun reading sources... [ 37%] subsections/md_rst/extractNearestNetwork reading sources... [ 38%] subsections/md_rst/extract_points_list reading sources... [ 38%] subsections/md_rst/extract_polygon_list reading sources... [ 38%] subsections/md_rst/fDataDT reading sources... [ 38%] subsections/md_rst/featureNetwork-class reading sources... [ 38%] subsections/md_rst/filterCPG reading sources... [ 38%] subsections/md_rst/filterCellProximityGenes reading sources... [ 38%] subsections/md_rst/filterCombinations reading sources... [ 39%] subsections/md_rst/filterDistributions reading sources... [ 39%] subsections/md_rst/filterGiotto reading sources... [ 39%] subsections/md_rst/filterICF reading sources... [ 39%] subsections/md_rst/filterICG reading sources... [ 39%] subsections/md_rst/filterInteractionChangedFeats reading sources... [ 39%] subsections/md_rst/filterInteractionChangedGenes reading sources... [ 40%] subsections/md_rst/filter_network reading sources... [ 40%] subsections/md_rst/findCPG reading sources... [ 40%] subsections/md_rst/findCellProximityFeats_per_interaction reading sources... [ 40%] subsections/md_rst/findCellProximityGenes reading sources... [ 40%] subsections/md_rst/findGiniMarkers reading sources... [ 40%] subsections/md_rst/findGiniMarkers_one_vs_all reading sources... [ 40%] subsections/md_rst/findICF reading sources... [ 41%] subsections/md_rst/findICG reading sources... [ 41%] subsections/md_rst/findInteractionChangedFeats reading sources... [ 41%] subsections/md_rst/findInteractionChangedGenes reading sources... [ 41%] subsections/md_rst/findMarkers reading sources... [ 41%] subsections/md_rst/findMarkers_one_vs_all reading sources... [ 41%] subsections/md_rst/findMastMarkers reading sources... [ 41%] subsections/md_rst/findMastMarkers_one_vs_all reading sources... [ 42%] subsections/md_rst/findNetworkNeighbors reading sources... [ 42%] subsections/md_rst/findScranMarkers reading sources... [ 42%] subsections/md_rst/findScranMarkers_one_vs_all reading sources... [ 42%] subsections/md_rst/find_dampening_constant reading sources... [ 42%] subsections/md_rst/find_grid_2D reading sources... [ 42%] subsections/md_rst/find_grid_3D reading sources... [ 42%] subsections/md_rst/find_grid_x reading sources... [ 43%] subsections/md_rst/find_grid_y reading sources... [ 43%] subsections/md_rst/find_grid_z reading sources... [ 43%] subsections/md_rst/find_terra_writeRaster_dataType reading sources... [ 43%] subsections/md_rst/find_x_y_ranges reading sources... [ 43%] subsections/md_rst/fix_multipart_geoms reading sources... [ 43%] subsections/md_rst/flex_lapply reading sources... [ 44%] subsections/md_rst/general_save_function reading sources... [ 44%] subsections/md_rst/get10Xmatrix reading sources... [ 44%] subsections/md_rst/get10XmatrixOLD reading sources... [ 44%] subsections/md_rst/get10Xmatrix_h5 reading sources... [ 44%] subsections/md_rst/getCellsFromPolygon reading sources... [ 44%] subsections/md_rst/getClusterSimilarity reading sources... [ 44%] subsections/md_rst/getDendrogramSplits reading sources... [ 45%] subsections/md_rst/getDistinctColors reading sources... [ 45%] subsections/md_rst/getSpatialDataset reading sources... [ 45%] subsections/md_rst/get_NearestNetwork reading sources... [ 45%] subsections/md_rst/get_adj_rescale_img reading sources... [ 45%] subsections/md_rst/get_args reading sources... [ 45%] subsections/md_rst/get_cross_section_coordinates reading sources... [ 45%] subsections/md_rst/get_dimReduction reading sources... [ 46%] subsections/md_rst/get_distance reading sources... [ 46%] subsections/md_rst/get_expression_values reading sources... [ 46%] subsections/md_rst/get_feature_info reading sources... [ 46%] subsections/md_rst/get_giottoImage reading sources... [ 46%] subsections/md_rst/get_giottoImage_MG reading sources... [ 46%] subsections/md_rst/get_giottoLargeImage reading sources... [ 46%] subsections/md_rst/get_img_corners reading sources... [ 47%] subsections/md_rst/get_img_minmax reading sources... [ 47%] subsections/md_rst/get_os reading sources... [ 47%] subsections/md_rst/get_polygon_info reading sources... [ 47%] subsections/md_rst/get_sectionThickness reading sources... [ 47%] subsections/md_rst/get_spatialGrid reading sources... [ 47%] subsections/md_rst/get_spatialNetwork reading sources... [ 48%] subsections/md_rst/get_spatial_enrichment reading sources... [ 48%] subsections/md_rst/get_spatial_locations reading sources... [ 48%] subsections/md_rst/ggplot_save_function reading sources... [ 48%] subsections/md_rst/giotto-class reading sources... [ 48%] subsections/md_rst/giottoImage-class reading sources... [ 48%] subsections/md_rst/giottoLargeImage-class reading sources... [ 48%] subsections/md_rst/giottoPoints-class reading sources... [ 49%] subsections/md_rst/giottoPolygon-class reading sources... [ 49%] subsections/md_rst/giottoToSeurat reading sources... [ 49%] subsections/md_rst/giotto_point reading sources... [ 49%] subsections/md_rst/heatmSpatialCorFeats reading sources... [ 49%] subsections/md_rst/heatmSpatialCorGenes reading sources... [ 49%] subsections/md_rst/hyperGeometricEnrich reading sources... [ 49%] subsections/md_rst/identify_background_range_polygons reading sources... [ 50%] subsections/md_rst/insertCrossSectionGenePlot3D reading sources... [ 50%] subsections/md_rst/insertCrossSectionSpatPlot3D reading sources... [ 50%] subsections/md_rst/installGiottoEnvironment reading sources... [ 50%] subsections/md_rst/install_giotto_environment reading sources... [ 50%] subsections/md_rst/install_giotto_environment_specific reading sources... [ 50%] subsections/md_rst/jackstrawPlot reading sources... [ 50%] subsections/md_rst/joinGiottoObjects reading sources... [ 51%] subsections/md_rst/join_cell_meta reading sources... [ 51%] subsections/md_rst/join_expression_matrices reading sources... [ 51%] subsections/md_rst/join_spatlocs reading sources... [ 51%] subsections/md_rst/kmeans_arma_binarize reading sources... [ 51%] subsections/md_rst/kmeans_arma_subset_binarize reading sources... [ 51%] subsections/md_rst/kmeans_binarize reading sources... [ 52%] subsections/md_rst/kmeans_binarize_wrapper reading sources... [ 52%] subsections/md_rst/lapply_flex reading sources... [ 52%] subsections/md_rst/libNorm_giotto reading sources... [ 52%] subsections/md_rst/list_cell_metadata reading sources... [ 52%] subsections/md_rst/list_dim_reductions reading sources... [ 52%] subsections/md_rst/list_dim_reductions_names reading sources... [ 52%] subsections/md_rst/list_expression reading sources... [ 53%] subsections/md_rst/list_expression_names reading sources... [ 53%] subsections/md_rst/list_feat_metadata reading sources... [ 53%] subsections/md_rst/list_feature_info reading sources... [ 53%] subsections/md_rst/list_feature_info_names reading sources... [ 53%] subsections/md_rst/list_giotto_data reading sources... [ 53%] subsections/md_rst/list_images reading sources... [ 53%] subsections/md_rst/list_images_names reading sources... [ 54%] subsections/md_rst/list_spatial_enrichments reading sources... [ 54%] subsections/md_rst/list_spatial_enrichments_names reading sources... [ 54%] subsections/md_rst/list_spatial_grids reading sources... [ 54%] subsections/md_rst/list_spatial_grids_names reading sources... [ 54%] subsections/md_rst/list_spatial_info reading sources... [ 54%] subsections/md_rst/list_spatial_info_names reading sources... [ 54%] subsections/md_rst/list_spatial_locations reading sources... [ 55%] subsections/md_rst/list_spatial_locations_names reading sources... [ 55%] subsections/md_rst/list_spatial_networks reading sources... [ 55%] subsections/md_rst/list_spatial_networks_names reading sources... [ 55%] subsections/md_rst/loadHMRF reading sources... [ 55%] subsections/md_rst/logNorm_giotto reading sources... [ 55%] subsections/md_rst/makeSignMatrixDWLS reading sources... [ 56%] subsections/md_rst/makeSignMatrixDWLSfromMatrix reading sources... [ 56%] subsections/md_rst/makeSignMatrixPAGE reading sources... [ 56%] subsections/md_rst/makeSignMatrixRank reading sources... [ 56%] subsections/md_rst/make_simulated_network reading sources... [ 56%] subsections/md_rst/mean_expr_det_test reading sources... [ 56%] subsections/md_rst/mean_flex reading sources... [ 56%] subsections/md_rst/mergeClusters reading sources... [ 57%] subsections/md_rst/merge_spatial_locs_feat_info reading sources... [ 57%] subsections/md_rst/mini_giotto_3D reading sources... [ 57%] subsections/md_rst/mini_giotto_multi_cell reading sources... [ 57%] subsections/md_rst/mini_giotto_single_cell reading sources... [ 57%] subsections/md_rst/my_arowMeans reading sources... [ 57%] subsections/md_rst/my_growMeans reading sources... [ 57%] subsections/md_rst/my_rowMeans reading sources... [ 58%] subsections/md_rst/mygini_fun reading sources... [ 58%] subsections/md_rst/nnDT_to_kNN reading sources... [ 58%] subsections/md_rst/node_clusters reading sources... [ 58%] subsections/md_rst/normalizeGiotto reading sources... [ 58%] subsections/md_rst/optimize_deconvolute_dwls reading sources... [ 58%] subsections/md_rst/optimize_solveDampenedWLS reading sources... [ 58%] subsections/md_rst/overlapToMatrix reading sources... [ 59%] subsections/md_rst/overlapToMatrixMultiPoly reading sources... [ 59%] subsections/md_rst/overlap_points_per_polygon reading sources... [ 59%] subsections/md_rst/overlap_points_per_polygon_wrapped reading sources... [ 59%] subsections/md_rst/overlap_points_single_polygon reading sources... [ 59%] subsections/md_rst/pDataDT reading sources... [ 59%] subsections/md_rst/package_check reading sources... [ 60%] subsections/md_rst/pca_giotto reading sources... [ 60%] subsections/md_rst/pipe reading sources... [ 60%] subsections/md_rst/plotCCcomDotplot reading sources... [ 60%] subsections/md_rst/plotCCcomHeatmap reading sources... [ 60%] subsections/md_rst/plotCPG reading sources... [ 60%] subsections/md_rst/plotCellProximityGenes reading sources... [ 60%] subsections/md_rst/plotCombineCCcom reading sources... [ 61%] subsections/md_rst/plotCombineCPG reading sources... [ 61%] subsections/md_rst/plotCombineCellCellCommunication reading sources... [ 61%] subsections/md_rst/plotCombineCellProximityGenes reading sources... [ 61%] subsections/md_rst/plotCombineICG reading sources... [ 61%] subsections/md_rst/plotCombineInteractionChangedGenes reading sources... [ 61%] subsections/md_rst/plotGiottoImage reading sources... [ 61%] subsections/md_rst/plotHeatmap reading sources... [ 62%] subsections/md_rst/plotICF reading sources... [ 62%] subsections/md_rst/plotICG reading sources... [ 62%] subsections/md_rst/plotInteractionChangedFeats reading sources... [ 62%] subsections/md_rst/plotInteractionChangedGenes reading sources... [ 62%] subsections/md_rst/plotInteractivePolygons reading sources... [ 62%] subsections/md_rst/plotMetaDataCellsHeatmap reading sources... [ 62%] subsections/md_rst/plotMetaDataHeatmap reading sources... [ 63%] subsections/md_rst/plotPCA reading sources... [ 63%] subsections/md_rst/plotPCA_2D reading sources... [ 63%] subsections/md_rst/plotPCA_3D reading sources... [ 63%] subsections/md_rst/plotRankSpatvsExpr reading sources... [ 63%] subsections/md_rst/plotRecovery reading sources... [ 63%] subsections/md_rst/plotRecovery_sub reading sources... [ 64%] subsections/md_rst/plotStatDelaunayNetwork reading sources... [ 64%] subsections/md_rst/plotTSNE reading sources... [ 64%] subsections/md_rst/plotTSNE_2D reading sources... [ 64%] subsections/md_rst/plotTSNE_3D reading sources... [ 64%] subsections/md_rst/plotUMAP reading sources... [ 64%] subsections/md_rst/plotUMAP_2D reading sources... [ 64%] subsections/md_rst/plotUMAP_3D reading sources... [ 65%] subsections/md_rst/plot_auto_largeImage_resample reading sources... [ 65%] subsections/md_rst/plot_cell_polygon_layer reading sources... [ 65%] subsections/md_rst/plot_feature_hexbin_layer reading sources... [ 65%] subsections/md_rst/plot_feature_points_layer reading sources... [ 65%] subsections/md_rst/plot_feature_raster_density_layer reading sources... [ 65%] subsections/md_rst/plot_giottoImage_MG reading sources... [ 65%] subsections/md_rst/plot_giottoLargeImage reading sources... [ 66%] subsections/md_rst/plot_network_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_point_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_point_layer_ggplot_noFILL reading sources... [ 66%] subsections/md_rst/plot_spat_image_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_spat_point_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_spat_point_layer_ggplot_noFILL reading sources... [ 66%] subsections/md_rst/plot_spat_scatterpie_layer_ggplot reading sources... [ 67%] subsections/md_rst/plot_spat_voronoi_layer_ggplot reading sources... [ 67%] subsections/md_rst/plotly_axis_scale_2D reading sources... [ 67%] subsections/md_rst/plotly_axis_scale_3D reading sources... [ 67%] subsections/md_rst/plotly_grid reading sources... [ 67%] subsections/md_rst/plotly_network reading sources... [ 67%] subsections/md_rst/polygon_to_raster reading sources... [ 68%] subsections/md_rst/processGiotto reading sources... [ 68%] subsections/md_rst/projection_fun reading sources... [ 68%] subsections/md_rst/rankEnrich reading sources... [ 68%] subsections/md_rst/rankSpatialCorGroups reading sources... [ 68%] subsections/md_rst/rank_binarize reading sources... [ 68%] subsections/md_rst/rank_binarize_wrapper reading sources... [ 68%] subsections/md_rst/readExprMatrix reading sources... [ 69%] subsections/md_rst/readGiottoInstructions reading sources... [ 69%] subsections/md_rst/readPolygonFilesVizgen reading sources... [ 69%] subsections/md_rst/readPolygonFilesVizgenHDF5 reading sources... [ 69%] subsections/md_rst/read_crossSection reading sources... [ 69%] subsections/md_rst/read_dimension_reduction reading sources... [ 69%] subsections/md_rst/read_expression_data reading sources... [ 69%] subsections/md_rst/read_nearest_networks reading sources... [ 70%] subsections/md_rst/read_spatial_enrichment reading sources... [ 70%] subsections/md_rst/read_spatial_location_data reading sources... [ 70%] subsections/md_rst/read_spatial_networks reading sources... [ 70%] subsections/md_rst/reconnectGiottoImage reading sources... [ 70%] subsections/md_rst/reconnect_giottoImage_MG reading sources... [ 70%] subsections/md_rst/reconnect_giottoLargeImage reading sources... [ 70%] subsections/md_rst/reconnect_image_object reading sources... [ 71%] subsections/md_rst/reg_img_minmax_finder reading sources... [ 71%] subsections/md_rst/registerGiottoObjectList reading sources... [ 71%] subsections/md_rst/registerGiottoObjectListFiji reading sources... [ 71%] subsections/md_rst/registerGiottoObjectListRvision reading sources... [ 71%] subsections/md_rst/registerImagesFIJI reading sources... [ 71%] subsections/md_rst/removeCellAnnotation reading sources... [ 72%] subsections/md_rst/removeFeatAnnotation reading sources... [ 72%] subsections/md_rst/removeGiottoEnvironment reading sources... [ 72%] subsections/md_rst/replaceGiottoInstructions reading sources... [ 72%] subsections/md_rst/reshape_to_data_point reading sources... [ 72%] subsections/md_rst/reshape_to_mesh_grid_obj reading sources... [ 72%] subsections/md_rst/return_giotto_environment_path reading sources... [ 72%] subsections/md_rst/return_giotto_environment_path_executable reading sources... [ 73%] subsections/md_rst/rigid_transform_spatial_locations reading sources... [ 73%] subsections/md_rst/rna_osmfish_normalization reading sources... [ 73%] subsections/md_rst/rna_pears_resid_normalization reading sources... [ 73%] subsections/md_rst/rna_standard_normalization reading sources... [ 73%] subsections/md_rst/rotate_spatial_locations reading sources... [ 73%] subsections/md_rst/rowMeans_flex reading sources... [ 73%] subsections/md_rst/rowSums_flex reading sources... [ 74%] subsections/md_rst/runDWLSDeconv reading sources... [ 74%] subsections/md_rst/runFijiMacro reading sources... [ 74%] subsections/md_rst/runGiottoHarmony reading sources... [ 74%] subsections/md_rst/runHyperGeometricEnrich reading sources... [ 74%] subsections/md_rst/runPAGEEnrich reading sources... [ 74%] subsections/md_rst/runPAGEEnrich_OLD reading sources... [ 74%] subsections/md_rst/runPCA reading sources... [ 75%] subsections/md_rst/runPCA_BiocSingular reading sources... [ 75%] subsections/md_rst/runPCA_factominer reading sources... [ 75%] subsections/md_rst/runPCA_prcomp_irlba reading sources... [ 75%] subsections/md_rst/runPatternSimulation reading sources... [ 75%] subsections/md_rst/runRankEnrich reading sources... [ 75%] subsections/md_rst/runSpatialDeconv reading sources... [ 76%] subsections/md_rst/runSpatialEnrich reading sources... [ 76%] subsections/md_rst/runUMAP reading sources... [ 76%] subsections/md_rst/run_spatial_sim_tests_multi reading sources... [ 76%] subsections/md_rst/run_spatial_sim_tests_one_rep reading sources... [ 76%] subsections/md_rst/runtSNE reading sources... [ 76%] subsections/md_rst/scale_spatial_locations reading sources... [ 76%] subsections/md_rst/screePlot reading sources... [ 77%] subsections/md_rst/selectPatternGenes reading sources... [ 77%] subsections/md_rst/select_NearestNetwork reading sources... [ 77%] subsections/md_rst/select_dimReduction reading sources... [ 77%] subsections/md_rst/select_expression_values reading sources... [ 77%] subsections/md_rst/select_feature_info reading sources... [ 77%] subsections/md_rst/select_gimage reading sources... [ 77%] subsections/md_rst/select_polygon_info reading sources... [ 78%] subsections/md_rst/select_spatialGrid reading sources... [ 78%] subsections/md_rst/select_spatialNetwork reading sources... [ 78%] subsections/md_rst/select_spatial_locations reading sources... [ 78%] subsections/md_rst/set_NearestNetwork reading sources... [ 78%] subsections/md_rst/set_cell_and_feat_IDs reading sources... [ 78%] subsections/md_rst/set_cell_metadata reading sources... [ 78%] subsections/md_rst/set_default_feat_type reading sources... [ 79%] subsections/md_rst/set_default_spat_unit reading sources... [ 79%] subsections/md_rst/set_dimReduction reading sources... [ 79%] subsections/md_rst/set_expression_values reading sources... [ 79%] subsections/md_rst/set_feature_info reading sources... [ 79%] subsections/md_rst/set_feature_metadata reading sources... [ 79%] subsections/md_rst/set_giottoImage reading sources... [ 80%] subsections/md_rst/set_giottoImage_MG reading sources... [ 80%] subsections/md_rst/set_giottoLargeImage reading sources... [ 80%] subsections/md_rst/set_giotto_python_path reading sources... [ 80%] subsections/md_rst/set_polygon_info reading sources... [ 80%] subsections/md_rst/set_spatialGrid reading sources... [ 80%] subsections/md_rst/set_spatialNetwork reading sources... [ 80%] subsections/md_rst/set_spatial_enrichment reading sources... [ 81%] subsections/md_rst/set_spatial_locations reading sources... [ 81%] subsections/md_rst/seuratToGiotto reading sources... [ 81%] subsections/md_rst/seuratToGiotto_OLD reading sources... [ 81%] subsections/md_rst/show-methods reading sources... [ 81%] subsections/md_rst/showClusterDendrogram reading sources... [ 81%] subsections/md_rst/showClusterHeatmap reading sources... [ 81%] subsections/md_rst/showGiottoDimRed reading sources... [ 82%] subsections/md_rst/showGiottoExpression reading sources... [ 82%] subsections/md_rst/showGiottoFeatInfo reading sources... [ 82%] subsections/md_rst/showGiottoImageNames reading sources... [ 82%] subsections/md_rst/showGiottoInstructions reading sources... [ 82%] subsections/md_rst/showGiottoSpatEnrichments reading sources... [ 82%] subsections/md_rst/showGiottoSpatGrids reading sources... [ 82%] subsections/md_rst/showGiottoSpatLocs reading sources... [ 83%] subsections/md_rst/showGiottoSpatNetworks reading sources... [ 83%] subsections/md_rst/showGiottoSpatialInfo reading sources... [ 83%] subsections/md_rst/showGrids reading sources... [ 83%] subsections/md_rst/showNetworks reading sources... [ 83%] subsections/md_rst/showPattern reading sources... [ 83%] subsections/md_rst/showPattern2D reading sources... [ 84%] subsections/md_rst/showPattern3D reading sources... [ 84%] subsections/md_rst/showPatternGenes reading sources... [ 84%] subsections/md_rst/showProcessingSteps reading sources... [ 84%] subsections/md_rst/showSaveParameters reading sources... [ 84%] subsections/md_rst/showSpatialCorFeats reading sources... [ 84%] subsections/md_rst/showSpatialCorGenes reading sources... [ 84%] subsections/md_rst/signPCA reading sources... [ 85%] subsections/md_rst/silhouetteRank reading sources... [ 85%] subsections/md_rst/silhouetteRankTest reading sources... [ 85%] subsections/md_rst/simulateOneGenePatternGiottoObject reading sources... [ 85%] subsections/md_rst/smoothGiottoPolygons reading sources... [ 85%] subsections/md_rst/solve_OLS_internal reading sources... [ 85%] subsections/md_rst/solve_dampened_WLSj reading sources... [ 85%] subsections/md_rst/sort_combine_two_DT_columns reading sources... [ 86%] subsections/md_rst/spark reading sources... [ 86%] subsections/md_rst/spatCellCellcom reading sources... [ 86%] subsections/md_rst/spatCellPlot reading sources... [ 86%] subsections/md_rst/spatCellPlot2D reading sources... [ 86%] subsections/md_rst/spatDeconvPlot reading sources... [ 86%] subsections/md_rst/spatDimCellPlot reading sources... [ 86%] subsections/md_rst/spatDimCellPlot2D reading sources... [ 87%] subsections/md_rst/spatDimFeatPlot2D reading sources... [ 87%] subsections/md_rst/spatDimGenePlot reading sources... [ 87%] subsections/md_rst/spatDimGenePlot2D reading sources... [ 87%] subsections/md_rst/spatDimGenePlot3D reading sources... [ 87%] subsections/md_rst/spatDimPlot reading sources... [ 87%] subsections/md_rst/spatDimPlot2D reading sources... [ 88%] subsections/md_rst/spatDimPlot3D reading sources... [ 88%] subsections/md_rst/spatFeatPlot2D reading sources... [ 88%] subsections/md_rst/spatFeatPlot2D_single reading sources... [ 88%] subsections/md_rst/spatGenePlot reading sources... [ 88%] subsections/md_rst/spatGenePlot2D reading sources... [ 88%] subsections/md_rst/spatGenePlot3D reading sources... [ 88%] subsections/md_rst/spatInSituPlotDensity reading sources... [ 89%] subsections/md_rst/spatInSituPlotDensity_single reading sources... [ 89%] subsections/md_rst/spatInSituPlotHex reading sources... [ 89%] subsections/md_rst/spatInSituPlotHex_single reading sources... [ 89%] subsections/md_rst/spatInSituPlotPoints reading sources... [ 89%] subsections/md_rst/spatNetwDistributions reading sources... [ 89%] subsections/md_rst/spatNetwDistributionsDistance reading sources... [ 89%] subsections/md_rst/spatNetwDistributionsKneighbors reading sources... [ 90%] subsections/md_rst/spatPlot reading sources... [ 90%] subsections/md_rst/spatPlot2D reading sources... [ 90%] subsections/md_rst/spatPlot2D_single reading sources... [ 90%] subsections/md_rst/spatPlot3D reading sources... [ 90%] subsections/md_rst/spatPlot_2D_plotly reading sources... [ 90%] subsections/md_rst/spatPlot_3D_plotly reading sources... [ 90%] subsections/md_rst/spatVector_to_dt reading sources... [ 91%] subsections/md_rst/spat_OR_func reading sources... [ 91%] subsections/md_rst/spat_OR_func_DT reading sources... [ 91%] subsections/md_rst/spat_fish_func reading sources... [ 91%] subsections/md_rst/spat_fish_func_DT reading sources... [ 91%] subsections/md_rst/spatialAEH reading sources... [ 91%] subsections/md_rst/spatialDE reading sources... [ 92%] subsections/md_rst/specificCellCellcommunicationScores reading sources... [ 92%] subsections/md_rst/spline_poly reading sources... [ 92%] subsections/md_rst/split_dendrogram_in_two reading sources... [ 92%] subsections/md_rst/spot_deconvolution reading sources... [ 92%] subsections/md_rst/standardise_flex reading sources... [ 92%] subsections/md_rst/stitchFieldCoordinates reading sources... [ 92%] subsections/md_rst/stitchGiottoLargeImage reading sources... [ 93%] subsections/md_rst/stitchTileCoordinates reading sources... [ 93%] subsections/md_rst/subClusterCells reading sources... [ 93%] subsections/md_rst/subsetGiotto reading sources... [ 93%] subsections/md_rst/subsetGiottoLocs reading sources... [ 93%] subsections/md_rst/subsetGiottoLocsMulti reading sources... [ 93%] subsections/md_rst/subset_cell_metadata reading sources... [ 93%] subsections/md_rst/subset_dimension_reduction reading sources... [ 94%] subsections/md_rst/subset_expression_data reading sources... [ 94%] subsections/md_rst/subset_feature_info_data reading sources... [ 94%] subsections/md_rst/subset_feature_metadata reading sources... [ 94%] subsections/md_rst/subset_giotto_points_object reading sources... [ 94%] subsections/md_rst/subset_giotto_polygon_object reading sources... [ 94%] subsections/md_rst/subset_nearest_network reading sources... [ 94%] subsections/md_rst/subset_spatial_enrichment reading sources... [ 95%] subsections/md_rst/subset_spatial_info_data reading sources... [ 95%] subsections/md_rst/subset_spatial_locations reading sources... [ 95%] subsections/md_rst/subset_spatial_network reading sources... [ 95%] subsections/md_rst/t_flex reading sources... [ 95%] subsections/md_rst/trakem2_rigid_transf_extract reading sources... [ 95%] subsections/md_rst/transform_2d_mesh_to_3d_mesh reading sources... [ 96%] subsections/md_rst/trendSceek reading sources... [ 96%] subsections/md_rst/updateGiottoImage reading sources... [ 96%] subsections/md_rst/updateGiottoImageMG reading sources... [ 96%] subsections/md_rst/updateGiottoLargeImage reading sources... [ 96%] subsections/md_rst/update_giotto_params reading sources... [ 96%] subsections/md_rst/viewHMRFresults reading sources... [ 96%] subsections/md_rst/viewHMRFresults2D reading sources... [ 97%] subsections/md_rst/viewHMRFresults3D reading sources... [ 97%] subsections/md_rst/violinPlot reading sources... [ 97%] subsections/md_rst/writeGiottoLargeImage reading sources... [ 97%] subsections/md_rst/writeHMRFresults reading sources... [ 97%] subsections/md_rst/write_giotto_viewer_annotation reading sources... [ 97%] subsections/md_rst/write_giotto_viewer_dim_reduction reading sources... [ 97%] subsections/md_rst/write_giotto_viewer_numeric_annotation reading sources... [ 98%] subsections/md_rst/xy_translate_spatial_locations reading sources... [ 98%] subsections/tipsandtricks/NEWS reading sources... [ 98%] subsections/tipsandtricks/giottoclass reading sources... [ 98%] subsections/tipsandtricks/howtosubsetgiottoobject reading sources... [ 98%] subsections/tipsandtricks/howtovisualizeandsaveplots reading sources... [ 98%] subsections/tipsandtricks/testandstoremultipleanayses reading sources... [ 98%] subsections/tipsandtricks/visualizewithvoronoiplots reading sources... [ 99%] subsections/tipsandtricks/waystovisualizespatialdata reading sources... [ 99%] subsections/tipsandtricks/workingwithimages reading sources... [ 99%] subsections/trygiotto/binder reading sources... [ 99%] subsections/trygiotto/docker reading sources... [ 99%] subsections/trygiotto/terra reading sources... [ 99%] tipsandtricks reading sources... [100%] trygiotto /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/citing_giotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/resolve_bc_210928.rst:159: WARNING: Title overline & underline mismatch. ******************************** Part 7: Process Giotto Object ********************************* /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/DT_removeNA.rst:1: WARNING: malformed hyperlink target. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/DT_removeNA.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addCellsFromPolygon.rst:4: WARNING: duplicate label addcellmetadata, other instance in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addCellMetadata.rst /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addFeatStatistics.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneMetadata.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneStatistics.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGenesPerc.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImageMG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImageToSpatPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPoints.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPolygons.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addHMRF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addNetworkLayout.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocationsLayer.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addStatistics.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/adjustGiottoMatrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/aes_string2.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/all_plots_save_function.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/anndataToGiotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotateGiotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotateSpatialGrid.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotateSpatialNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/average_feat_feat_expression_in_groups.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:10: WARNING: Unexpected section title. Description ----------- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:15: WARNING: Unexpected section title. Usage ----- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:47: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:105: WARNING: Unexpected section title. Value ----- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_group_HVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_loess_HVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_minimum.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_var_HVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateHVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateHVG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateMetaTableCells.rst:4: WARNING: duplicate label calculatemetatable, other instance in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateMetaTable.rst /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapParallel.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapRaster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapSerial.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_centroids_polygons.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_distance_and_weight.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityEnrichment.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityHeatmap.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximitySpatPlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_2D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_3D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/changeGiottoInstructions.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/changeImageBg.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/checkGiottoEnvironment.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/check_spatial_location_data.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterCells.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterSpatialCorFeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterSpatialCorGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cluster_enrich_analysis.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colMeans_flex.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colSums_flex.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combCCcom.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCPG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellData.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes_per_interaction.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureData.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureOverlapData.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineICG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineInteractionChangedGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineMetadata.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellFeatureInfo.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellMetadataInfo.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/compatible_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertEnsemblToGeneSymbol.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertGiottoLargeImageToMG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_mgImage_to_array_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_full_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_reduced_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cor_flex.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createCrossSection.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoInstructions.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImageList.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoObjectSubcellular.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPoints.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromDfr.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromMask.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoVisiumObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createHeatmap_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createMetafeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createMetagenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialDefaultGrid.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialDelaunayNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialEnrich.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialGrid.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialKNNnetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_2d_mesh_grid_line_obj.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_KNNnetwork_dbscan.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_detection_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cell_type_random_cell_IDs.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cluster_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_crossSection_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_RTriangle.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_deldir.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_dimObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_featureNetwork_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_genes_to_use_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_points_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_polygon_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_jackstrawplot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_mesh_grid_lines.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_screeplot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGridObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialNetworkObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatvector_object_from_dfr.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cropGiottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionGenePlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionGenePlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionPlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/decide_cluster_order.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/density_giottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/depth.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialPatterns.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/determine_cores.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimCellPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimCellPlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimFeatPlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D_single.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_2D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_3D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/distGiottoImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doCellSegmentation.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doHMRF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doHclust.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doKmeans.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLeidenCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLeidenSubCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_community.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_multinet.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_community.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_multinet.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doRandomWalkCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doSNNCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doScrubletDetect.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_cell_proximity_test.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_limmatest.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_multi_permuttest_random.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_page_permutation.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_original.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_random.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_rank_permutation.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_grid_averaging.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_knn_smoothing.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_ttest.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_wilctest.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_points.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_polygon.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_analysis.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_deconvolution.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/estimateCellCellDistance.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_expr_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_feat_info.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_provided_spatial_locations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_info.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations_OLD.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/exportGiottoViewer.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/exprCellCellcom.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extend_vector.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extended_gini_fun.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extractNearestNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_points_list.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_polygon_list.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/fDataDT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/featureNetwork-class.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCPG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCellProximityGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCombinations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterDistributions.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterGiotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterICF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterICG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterInteractionChangedFeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterInteractionChangedGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filter_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCPG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityFeats_per_interaction.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findGiniMarkers.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findGiniMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findICF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findICG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findInteractionChangedFeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findInteractionChangedGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMarkers.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMastMarkers.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMastMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findNetworkNeighbors.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findScranMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_dampening_constant.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_x.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_y.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_z.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_terra_writeRaster_dataType.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_x_y_ranges.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runRankEnrich.rst:82: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/stitchGiottoLargeImage.rst:82: WARNING: Block quote ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/Workflow.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/development.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/citing_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/STARmap_mouse_cortex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/human_CyCIF_PDAC.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/merFISH_hypot_preopt_region.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mini_3D_STARmap.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mini_seqFISH.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mini_visium.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mouse_CODEX_spleen.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mouse_visium_brain.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mouse_visium_kidney.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/osmFISH_mouse_SS_cortex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/resolve_bc_210928.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/seqFISH_cortex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/tcyCIF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/vizgen_mouse_brain.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/detailed_workflow.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/license.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/DT_removeNA.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/FSV_show.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/OR_test_fnc.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/PAGEEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/PAGE_DT_method.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/adapt_aspect_ratio.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addCellsFromPolygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneMetadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneStatistics.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGenesPerc.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImageMG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPoints.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPolygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocationsLayer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/add_img_array_alpha.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/aes_string2.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/all_plots_save_function.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/anndataToGiotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/average_feat_feat_expression_in_groups.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_group_HVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_loess_HVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_minimum.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_var_HVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateHVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapParallel.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapRaster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapSerial.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_centroids_polygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_distance_and_weight.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximitySpatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_2D_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_2D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_3D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/check_spatial_location_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cluster_enrich_analysis.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colMeans_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colSums_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combCCcom.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellData.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes_per_interaction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureData.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureOverlapData.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellFeatureInfo.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellMetadataInfo.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/compatible_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertEnsemblToGeneSymbol.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertGiottoLargeImageToMG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_mgImage_to_array_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_full_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_reduced_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cor_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoImageOLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImageList.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPoints.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromDfr.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromMask.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createHeatmap_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createMetafeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialDefaultGrid.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_2d_mesh_grid_line_obj.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_KNNnetwork_dbscan.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_detection_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cell_type_random_cell_IDs.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cluster_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_crossSection_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_RTriangle.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_deldir.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_dimObject.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_featureNetwork_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_genes_to_use_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_points_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_polygon_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_jackstrawplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_mesh_grid_lines.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_screeplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_segm_polygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGridObject.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialNetworkObject.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatvector_object_from_dfr.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cropGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/decide_cluster_order.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/density_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/depth.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialCorFeatsMatrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialPatterns.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/determine_cores.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimCellPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimFeatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_2D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_3D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/distGiottoImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doCellSegmentation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_community.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_multinet.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_community.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_multinet.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doRandomWalkCluster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doSNNCluster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doScrubletDetect.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_cell_proximity_test.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_limmatest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_multi_permuttest_random.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_page_permutation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_original.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_random.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_rank_permutation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_grid_averaging.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_knn_smoothing.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_ttest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_wilctest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_points.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_polygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_analysis.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_deconvolution.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/estimateCellCellDistance.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_expr_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_feat_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_provided_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations_OLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/exportGiottoViewer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extend_vector.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extended_gini_fun.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extractNearestNetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_points_list.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_polygon_list.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/featureNetwork-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCombinations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterDistributions.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filter_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityFeats_per_interaction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_dampening_constant.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_x.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_y.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_z.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_terra_writeRaster_dataType.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_x_y_ranges.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/fix_multipart_geoms.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/flex_lapply.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/general_save_function.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get10XmatrixOLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/getCellsFromPolygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/getDistinctColors.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_adj_rescale_img.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_args.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_cross_section_coordinates.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_distance.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_img_corners.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_img_minmax.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_os.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_sectionThickness.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/ggplot_save_function.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giotto-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoImage-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoLargeImage-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoPoints-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoPolygon-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoToSeurat.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giotto_point.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/heatmSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/hyperGeometricEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/identify_background_range_polygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/install_giotto_environment.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/install_giotto_environment_specific.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/join_cell_meta.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/join_expression_matrices.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/join_spatlocs.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_arma_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_arma_subset_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_binarize_wrapper.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/lapply_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/libNorm_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_cell_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_dim_reductions.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_dim_reductions_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_expression.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_expression_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_feat_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_feature_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_feature_info_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_giotto_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_images.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_images_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_enrichments.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_enrichments_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_grids.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_grids_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_info_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_locations_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_networks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_networks_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/logNorm_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/make_simulated_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mean_expr_det_test.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mean_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/merge_spatial_locs_feat_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mini_giotto_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mini_giotto_multi_cell.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mini_giotto_single_cell.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/my_arowMeans.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/my_growMeans.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/my_rowMeans.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mygini_fun.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/nnDT_to_kNN.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/node_clusters.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/optimize_deconvolute_dwls.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/optimize_solveDampenedWLS.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlapToMatrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlapToMatrixMultiPoly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlap_points_per_polygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlap_points_per_polygon_wrapped.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlap_points_single_polygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/package_check.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/pca_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/pipe.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCCcomHeatmap.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCCcom.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCellCellCommunication.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotICF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotInteractionChangedFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotInteractivePolygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotPCA_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotRecovery_sub.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotTSNE_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotUMAP_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_auto_largeImage_resample.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_cell_polygon_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_feature_hexbin_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_feature_points_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_feature_raster_density_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_network_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_point_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_point_layer_ggplot_noFILL.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_image_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_point_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_point_layer_ggplot_noFILL.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_scatterpie_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_voronoi_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_axis_scale_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_axis_scale_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_grid.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/polygon_to_raster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/processGiotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/projection_fun.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rankEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rank_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rank_binarize_wrapper.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/readPolygonFilesVizgen.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/readPolygonFilesVizgenHDF5.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_crossSection.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_dimension_reduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_expression_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_nearest_networks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_spatial_enrichment.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_spatial_location_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_spatial_networks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnectGiottoImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnect_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnect_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnect_image_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reg_img_minmax_finder.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerGiottoObjectList.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerGiottoObjectListFiji.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerGiottoObjectListRvision.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerImagesFIJI.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reshape_to_data_point.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reshape_to_mesh_grid_obj.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/return_giotto_environment_path.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/return_giotto_environment_path_executable.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rigid_transform_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rna_osmfish_normalization.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rna_pears_resid_normalization.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rna_standard_normalization.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rotate_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rowMeans_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rowSums_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runFijiMacro.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runGiottoHarmony.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPAGEEnrich_OLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPCA_BiocSingular.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPCA_factominer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPCA_prcomp_irlba.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/run_spatial_sim_tests_multi.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/run_spatial_sim_tests_one_rep.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/scale_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/selectPatternGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_NearestNetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_dimReduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_expression_values.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_feature_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_gimage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_polygon_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_spatialGrid.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_spatialNetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_cell_and_feat_IDs.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_cell_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_default_feat_type.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_default_spat_unit.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_feature_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giottoImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giotto_python_path.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/seuratToGiotto_OLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/show-methods.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showGrids.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showNetworks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPattern.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPattern2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPattern3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPatternGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showSaveParameters.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/silhouetteRank.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/silhouetteRankTest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/smoothGiottoPolygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/solve_OLS_internal.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/solve_dampened_WLSj.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/sort_combine_two_DT_columns.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatCellPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDeconvPlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimCellPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimFeatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimGenePlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimGenePlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimGenePlot3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatFeatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatFeatPlot2D_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatGenePlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatGenePlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatGenePlot3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotDensity.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotDensity_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotHex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotHex_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotPoints.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot2D_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot_2D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot_3D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatVector_to_dt.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_OR_func.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_OR_func_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_fish_func.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_fish_func_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/specificCellCellcommunicationScores.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spline_poly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/split_dendrogram_in_two.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spot_deconvolution.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/standardise_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/stitchGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subsetGiottoLocsMulti.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_cell_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_dimension_reduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_expression_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_feature_info_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_feature_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_giotto_points_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_giotto_polygon_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_nearest_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_enrichment.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_info_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/t_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/trakem2_rigid_transf_extract.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/transform_2d_mesh_to_3d_mesh.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/updateGiottoImageMG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/updateGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/update_giotto_params.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/writeGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/write_giotto_viewer_annotation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/write_giotto_viewer_dim_reduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/write_giotto_viewer_numeric_annotation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/xy_translate_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/tipsandtricks/NEWS.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/tipsandtricks.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] Workflow writing output... [ 0%] additionalinformation writing output... [ 0%] contribute writing output... [ 0%] datasets writing output... [ 0%] development writing output... [ 0%] documentation writing output... [ 1%] errorsfaqsandtips writing output... [ 1%] faqs writing output... [ 1%] gettingstarted writing output... [ 1%] giottoworkflowanalyses writing output... [ 1%] github_issues writing output... [ 1%] index writing output... [ 1%] subsections/citing_giotto writing output... [ 2%] subsections/code_of_conduct writing output... [ 2%] subsections/datasets/STARmap_mouse_cortex writing output... [ 2%] subsections/datasets/human_CyCIF_PDAC writing output... [ 2%] subsections/datasets/merFISH_hypot_preopt_region writing output... [ 2%] subsections/datasets/mini_3D_STARmap writing output... [ 2%] subsections/datasets/mini_seqFISH writing output... [ 2%] subsections/datasets/mini_visium writing output... [ 3%] subsections/datasets/mouse_CODEX_spleen writing output... [ 3%] subsections/datasets/mouse_visium_brain writing output... [ 3%] subsections/datasets/mouse_visium_kidney writing output... [ 3%] subsections/datasets/nanostring_lung_12 writing output... [ 3%] subsections/datasets/nanostring_overview writing output... [ 3%] subsections/datasets/osmFISH_mouse_SS_cortex writing output... [ 4%] subsections/datasets/other_technologies_coming_soon writing output... [ 4%] subsections/datasets/resolve_bc_210928 writing output... [ 4%] subsections/datasets/seqFISH_cortex writing output... [ 4%] subsections/datasets/singlecell_prostate_integration writing output... [ 4%] subsections/datasets/singlecell_prostate_standard writing output... [ 4%] subsections/datasets/tcyCIF writing output... [ 4%] subsections/datasets/visium_prostate_integration writing output... [ 5%] subsections/datasets/vizgen_mouse_brain writing output... [ 5%] subsections/detailed_workflow writing output... [ 5%] subsections/license writing output... [ 5%] subsections/md_rst/DT_removeNA writing output... [ 5%] subsections/md_rst/FSV_show writing output... [ 5%] subsections/md_rst/OR_test_fnc writing output... [ 5%] subsections/md_rst/PAGEEnrich writing output... [ 6%] subsections/md_rst/PAGE_DT_method writing output... [ 6%] subsections/md_rst/adapt_aspect_ratio writing output... [ 6%] subsections/md_rst/addCellIntMetadata writing output... [ 6%] subsections/md_rst/addCellMetadata writing output... [ 6%] subsections/md_rst/addCellStatistics writing output... [ 6%] subsections/md_rst/addCellsFromPolygon writing output... [ 6%] subsections/md_rst/addFeatMetadata writing output... [ 7%] subsections/md_rst/addFeatStatistics writing output... [ 7%] subsections/md_rst/addFeatsPerc writing output... [ 7%] subsections/md_rst/addGeneMetadata writing output... [ 7%] subsections/md_rst/addGeneStatistics writing output... [ 7%] subsections/md_rst/addGenesPerc writing output... [ 7%] subsections/md_rst/addGiottoImage writing output... [ 8%] subsections/md_rst/addGiottoImageMG writing output... [ 8%] subsections/md_rst/addGiottoImageToSpatPlot writing output... [ 8%] subsections/md_rst/addGiottoLargeImage writing output... [ 8%] subsections/md_rst/addGiottoPoints writing output... [ 8%] subsections/md_rst/addGiottoPolygons writing output... [ 8%] subsections/md_rst/addHMRF writing output... [ 8%] subsections/md_rst/addNetworkLayout writing output... [ 9%] subsections/md_rst/addSpatialCentroidLocations writing output... [ 9%] subsections/md_rst/addSpatialCentroidLocationsLayer writing output... [ 9%] subsections/md_rst/addStatistics writing output... [ 9%] subsections/md_rst/add_img_array_alpha writing output... [ 9%] subsections/md_rst/adjustGiottoMatrix writing output... [ 9%] subsections/md_rst/aes_string2 writing output... [ 9%] subsections/md_rst/all_plots_save_function writing output... [ 10%] subsections/md_rst/anndataToGiotto writing output... [ 10%] subsections/md_rst/annotateGiotto writing output... [ 10%] subsections/md_rst/annotateSpatialGrid writing output... [ 10%] subsections/md_rst/annotateSpatialNetwork writing output... [ 10%] subsections/md_rst/annotate_spatlocs_with_spatgrid_2D writing output... [ 10%] subsections/md_rst/annotate_spatlocs_with_spatgrid_3D writing output... [ 10%] subsections/md_rst/average_feat_feat_expression_in_groups writing output... [ 11%] subsections/md_rst/binSpect writing output... [ 11%] subsections/md_rst/binSpectMulti writing output... [ 11%] subsections/md_rst/binSpectMultiMatrix writing output... [ 11%] subsections/md_rst/binSpectSingle writing output... [ 11%] subsections/md_rst/binSpectSingleMatrix writing output... [ 11%] subsections/md_rst/calc_cov_group_HVF writing output... [ 12%] subsections/md_rst/calc_cov_loess_HVF writing output... [ 12%] subsections/md_rst/calc_spatial_enrichment_DT writing output... [ 12%] subsections/md_rst/calc_spatial_enrichment_matrix writing output... [ 12%] subsections/md_rst/calc_spatial_enrichment_minimum writing output... [ 12%] subsections/md_rst/calc_var_HVF writing output... [ 12%] subsections/md_rst/calculateHVF writing output... [ 12%] subsections/md_rst/calculateHVG writing output... [ 13%] subsections/md_rst/calculateMetaTable writing output... [ 13%] subsections/md_rst/calculateMetaTableCells writing output... [ 13%] subsections/md_rst/calculateOverlapParallel writing output... [ 13%] subsections/md_rst/calculateOverlapRaster writing output... [ 13%] subsections/md_rst/calculateOverlapSerial writing output... [ 13%] subsections/md_rst/calculate_centroids_polygons writing output... [ 13%] subsections/md_rst/calculate_distance_and_weight writing output... [ 14%] subsections/md_rst/cellProximityBarplot writing output... [ 14%] subsections/md_rst/cellProximityEnrichment writing output... [ 14%] subsections/md_rst/cellProximityHeatmap writing output... [ 14%] subsections/md_rst/cellProximityNetwork writing output... [ 14%] subsections/md_rst/cellProximitySpatPlot writing output... [ 14%] subsections/md_rst/cellProximitySpatPlot2D writing output... [ 14%] subsections/md_rst/cellProximitySpatPlot3D writing output... [ 15%] subsections/md_rst/cellProximityVisPlot writing output... [ 15%] subsections/md_rst/cellProximityVisPlot_2D_ggplot writing output... [ 15%] subsections/md_rst/cellProximityVisPlot_2D_plotly writing output... [ 15%] subsections/md_rst/cellProximityVisPlot_3D_plotly writing output... [ 15%] subsections/md_rst/changeGiottoInstructions writing output... [ 15%] subsections/md_rst/changeImageBg writing output... [ 16%] subsections/md_rst/checkGiottoEnvironment writing output... [ 16%] subsections/md_rst/check_spatial_location_data writing output... [ 16%] subsections/md_rst/clusterCells writing output... [ 16%] subsections/md_rst/clusterSpatialCorFeats writing output... [ 16%] subsections/md_rst/clusterSpatialCorGenes writing output... [ 16%] subsections/md_rst/cluster_enrich_analysis writing output... [ 16%] subsections/md_rst/colMeans_flex writing output... [ 17%] subsections/md_rst/colSums_flex writing output... [ 17%] subsections/md_rst/combCCcom writing output... [ 17%] subsections/md_rst/combineCPG writing output... [ 17%] subsections/md_rst/combineCellData writing output... [ 17%] subsections/md_rst/combineCellProximityGenes writing output... [ 17%] subsections/md_rst/combineCellProximityGenes_per_interaction writing output... [ 17%] subsections/md_rst/combineFeatureData writing output... [ 18%] subsections/md_rst/combineFeatureOverlapData writing output... [ 18%] subsections/md_rst/combineICG writing output... [ 18%] subsections/md_rst/combineInteractionChangedGenes writing output... [ 18%] subsections/md_rst/combineMetadata writing output... [ 18%] subsections/md_rst/combineSpatialCellFeatureInfo writing output... [ 18%] subsections/md_rst/combineSpatialCellMetadataInfo writing output... [ 18%] subsections/md_rst/compatible_spatial_network writing output... [ 19%] subsections/md_rst/convertEnsemblToGeneSymbol writing output... [ 19%] subsections/md_rst/convertGiottoLargeImageToMG writing output... [ 19%] subsections/md_rst/convert_mgImage_to_array_DT writing output... [ 19%] subsections/md_rst/convert_to_full_spatial_network writing output... [ 19%] subsections/md_rst/convert_to_reduced_spatial_network writing output... [ 19%] subsections/md_rst/cor_flex writing output... [ 20%] subsections/md_rst/createCrossSection writing output... [ 20%] subsections/md_rst/createGiottoImage writing output... [ 20%] subsections/md_rst/createGiottoImageOLD writing output... [ 20%] subsections/md_rst/createGiottoInstructions writing output... [ 20%] subsections/md_rst/createGiottoLargeImage writing output... [ 20%] subsections/md_rst/createGiottoLargeImageList writing output... [ 20%] subsections/md_rst/createGiottoObject writing output... [ 21%] subsections/md_rst/createGiottoObjectSubcellular writing output... [ 21%] subsections/md_rst/createGiottoPoints writing output... [ 21%] subsections/md_rst/createGiottoPolygonsFromDfr writing output... [ 21%] subsections/md_rst/createGiottoPolygonsFromMask writing output... [ 21%] subsections/md_rst/createGiottoVisiumObject writing output... [ 21%] subsections/md_rst/createHeatmap_DT writing output... [ 21%] subsections/md_rst/createMetafeats writing output... [ 22%] subsections/md_rst/createMetagenes writing output... [ 22%] subsections/md_rst/createNearestNetwork writing output... [ 22%] subsections/md_rst/createSpatialDefaultGrid writing output... [ 22%] subsections/md_rst/createSpatialDelaunayNetwork writing output... [ 22%] subsections/md_rst/createSpatialEnrich writing output... [ 22%] subsections/md_rst/createSpatialFeaturesKNNnetwork writing output... [ 22%] subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan writing output... [ 23%] subsections/md_rst/createSpatialGrid writing output... [ 23%] subsections/md_rst/createSpatialKNNnetwork writing output... [ 23%] subsections/md_rst/createSpatialNetwork writing output... [ 23%] subsections/md_rst/create_2d_mesh_grid_line_obj writing output... [ 23%] subsections/md_rst/create_KNNnetwork_dbscan writing output... [ 23%] subsections/md_rst/create_average_DT writing output... [ 24%] subsections/md_rst/create_average_detection_DT writing output... [ 24%] subsections/md_rst/create_cell_type_random_cell_IDs writing output... [ 24%] subsections/md_rst/create_cluster_matrix writing output... [ 24%] subsections/md_rst/create_crossSection_object writing output... [ 24%] subsections/md_rst/create_delaunayNetwork2D writing output... [ 24%] subsections/md_rst/create_delaunayNetwork3D writing output... [ 24%] subsections/md_rst/create_delaunayNetwork_RTriangle writing output... [ 25%] subsections/md_rst/create_delaunayNetwork_deldir writing output... [ 25%] subsections/md_rst/create_delaunayNetwork_geometry writing output... [ 25%] subsections/md_rst/create_delaunayNetwork_geometry_3D writing output... [ 25%] subsections/md_rst/create_dimObject writing output... [ 25%] subsections/md_rst/create_featureNetwork_object writing output... [ 25%] subsections/md_rst/create_genes_to_use_matrix writing output... [ 25%] subsections/md_rst/create_giotto_points_object writing output... [ 26%] subsections/md_rst/create_giotto_polygon_object writing output... [ 26%] subsections/md_rst/create_jackstrawplot writing output... [ 26%] subsections/md_rst/create_mesh_grid_lines writing output... [ 26%] subsections/md_rst/create_screeplot writing output... [ 26%] subsections/md_rst/create_segm_polygons writing output... [ 26%] subsections/md_rst/create_spatialGridObject writing output... [ 26%] subsections/md_rst/create_spatialGrid_default_2D writing output... [ 27%] subsections/md_rst/create_spatialGrid_default_3D writing output... [ 27%] subsections/md_rst/create_spatialNetworkObject writing output... [ 27%] subsections/md_rst/create_spatvector_object_from_dfr writing output... [ 27%] subsections/md_rst/cropGiottoLargeImage writing output... [ 27%] subsections/md_rst/crossSectionGenePlot writing output... [ 27%] subsections/md_rst/crossSectionGenePlot3D writing output... [ 28%] subsections/md_rst/crossSectionPlot writing output... [ 28%] subsections/md_rst/crossSectionPlot3D writing output... [ 28%] subsections/md_rst/decide_cluster_order writing output... [ 28%] subsections/md_rst/density_giottoLargeImage writing output... [ 28%] subsections/md_rst/depth writing output... [ 28%] subsections/md_rst/detectSpatialCorFeats writing output... [ 28%] subsections/md_rst/detectSpatialCorFeatsMatrix writing output... [ 29%] subsections/md_rst/detectSpatialCorGenes writing output... [ 29%] subsections/md_rst/detectSpatialPatterns writing output... [ 29%] subsections/md_rst/determine_cores writing output... [ 29%] subsections/md_rst/dimCellPlot writing output... [ 29%] subsections/md_rst/dimCellPlot2D writing output... [ 29%] subsections/md_rst/dimFeatPlot2D writing output... [ 29%] subsections/md_rst/dimGenePlot writing output... [ 30%] subsections/md_rst/dimGenePlot2D writing output... [ 30%] subsections/md_rst/dimGenePlot3D writing output... [ 30%] subsections/md_rst/dimPlot writing output... [ 30%] subsections/md_rst/dimPlot2D writing output... [ 30%] subsections/md_rst/dimPlot2D_single writing output... [ 30%] subsections/md_rst/dimPlot3D writing output... [ 30%] subsections/md_rst/dimPlot_2D_plotly writing output... [ 31%] subsections/md_rst/dimPlot_3D_plotly writing output... [ 31%] subsections/md_rst/distGiottoImage writing output... [ 31%] subsections/md_rst/doCellSegmentation writing output... [ 31%] subsections/md_rst/doHMRF writing output... [ 31%] subsections/md_rst/doHclust writing output... [ 31%] subsections/md_rst/doKmeans writing output... [ 32%] subsections/md_rst/doLeidenCluster writing output... [ 32%] subsections/md_rst/doLeidenSubCluster writing output... [ 32%] subsections/md_rst/doLouvainCluster writing output... [ 32%] subsections/md_rst/doLouvainCluster_community writing output... [ 32%] subsections/md_rst/doLouvainCluster_multinet writing output... [ 32%] subsections/md_rst/doLouvainSubCluster writing output... [ 32%] subsections/md_rst/doLouvainSubCluster_community writing output... [ 33%] subsections/md_rst/doLouvainSubCluster_multinet writing output... [ 33%] subsections/md_rst/doRandomWalkCluster writing output... [ 33%] subsections/md_rst/doSNNCluster writing output... [ 33%] subsections/md_rst/doScrubletDetect writing output... [ 33%] subsections/md_rst/do_cell_proximity_test writing output... [ 33%] subsections/md_rst/do_limmatest writing output... [ 33%] subsections/md_rst/do_multi_permuttest_random writing output... [ 34%] subsections/md_rst/do_page_permutation writing output... [ 34%] subsections/md_rst/do_permuttest_original writing output... [ 34%] subsections/md_rst/do_permuttest_random writing output... [ 34%] subsections/md_rst/do_rank_permutation writing output... [ 34%] subsections/md_rst/do_spatial_grid_averaging writing output... [ 34%] subsections/md_rst/do_spatial_knn_smoothing writing output... [ 34%] subsections/md_rst/do_ttest writing output... [ 35%] subsections/md_rst/do_wilctest writing output... [ 35%] subsections/md_rst/dt_to_matrix writing output... [ 35%] subsections/md_rst/dt_to_spatVector_points writing output... [ 35%] subsections/md_rst/dt_to_spatVector_polygon writing output... [ 35%] subsections/md_rst/enrich_analysis writing output... [ 35%] subsections/md_rst/enrich_deconvolution writing output... [ 36%] subsections/md_rst/estimateCellCellDistance writing output... [ 36%] subsections/md_rst/estimateImageBg writing output... [ 36%] subsections/md_rst/evaluate_expr_matrix writing output... [ 36%] subsections/md_rst/evaluate_feat_info writing output... [ 36%] subsections/md_rst/evaluate_provided_spatial_locations writing output... [ 36%] subsections/md_rst/evaluate_spatial_info writing output... [ 36%] subsections/md_rst/evaluate_spatial_locations writing output... [ 37%] subsections/md_rst/evaluate_spatial_locations_OLD writing output... [ 37%] subsections/md_rst/evaluate_spatial_network writing output... [ 37%] subsections/md_rst/exportGiottoViewer writing output... [ 37%] subsections/md_rst/exprCellCellcom writing output... [ 37%] subsections/md_rst/extend_vector writing output... [ 37%] subsections/md_rst/extended_gini_fun writing output... [ 37%] subsections/md_rst/extractNearestNetwork writing output... [ 38%] subsections/md_rst/extract_points_list writing output... [ 38%] subsections/md_rst/extract_polygon_list writing output... [ 38%] subsections/md_rst/fDataDT writing output... [ 38%] subsections/md_rst/featureNetwork-class writing output... [ 38%] subsections/md_rst/filterCPG writing output... [ 38%] subsections/md_rst/filterCellProximityGenes writing output... [ 38%] subsections/md_rst/filterCombinations writing output... [ 39%] subsections/md_rst/filterDistributions writing output... [ 39%] subsections/md_rst/filterGiotto writing output... [ 39%] subsections/md_rst/filterICF writing output... [ 39%] subsections/md_rst/filterICG writing output... [ 39%] subsections/md_rst/filterInteractionChangedFeats writing output... [ 39%] subsections/md_rst/filterInteractionChangedGenes writing output... [ 40%] subsections/md_rst/filter_network writing output... [ 40%] subsections/md_rst/findCPG writing output... [ 40%] subsections/md_rst/findCellProximityFeats_per_interaction writing output... [ 40%] subsections/md_rst/findCellProximityGenes writing output... [ 40%] subsections/md_rst/findGiniMarkers writing output... [ 40%] subsections/md_rst/findGiniMarkers_one_vs_all writing output... [ 40%] subsections/md_rst/findICF writing output... [ 41%] subsections/md_rst/findICG writing output... [ 41%] subsections/md_rst/findInteractionChangedFeats writing output... [ 41%] subsections/md_rst/findInteractionChangedGenes writing output... [ 41%] subsections/md_rst/findMarkers writing output... [ 41%] subsections/md_rst/findMarkers_one_vs_all writing output... [ 41%] subsections/md_rst/findMastMarkers writing output... [ 41%] subsections/md_rst/findMastMarkers_one_vs_all writing output... [ 42%] subsections/md_rst/findNetworkNeighbors writing output... [ 42%] subsections/md_rst/findScranMarkers writing output... [ 42%] subsections/md_rst/findScranMarkers_one_vs_all writing output... [ 42%] subsections/md_rst/find_dampening_constant writing output... [ 42%] subsections/md_rst/find_grid_2D writing output... [ 42%] subsections/md_rst/find_grid_3D writing output... [ 42%] subsections/md_rst/find_grid_x writing output... [ 43%] subsections/md_rst/find_grid_y writing output... [ 43%] subsections/md_rst/find_grid_z writing output... [ 43%] subsections/md_rst/find_terra_writeRaster_dataType writing output... [ 43%] subsections/md_rst/find_x_y_ranges writing output... [ 43%] subsections/md_rst/fix_multipart_geoms writing output... [ 43%] subsections/md_rst/flex_lapply writing output... [ 44%] subsections/md_rst/general_save_function writing output... [ 44%] subsections/md_rst/get10Xmatrix writing output... [ 44%] subsections/md_rst/get10XmatrixOLD writing output... [ 44%] subsections/md_rst/get10Xmatrix_h5 writing output... [ 44%] subsections/md_rst/getCellsFromPolygon writing output... [ 44%] subsections/md_rst/getClusterSimilarity writing output... [ 44%] subsections/md_rst/getDendrogramSplits writing output... [ 45%] subsections/md_rst/getDistinctColors writing output... [ 45%] subsections/md_rst/getSpatialDataset writing output... [ 45%] subsections/md_rst/get_NearestNetwork writing output... [ 45%] subsections/md_rst/get_adj_rescale_img writing output... [ 45%] subsections/md_rst/get_args writing output... [ 45%] subsections/md_rst/get_cross_section_coordinates writing output... [ 45%] subsections/md_rst/get_dimReduction writing output... [ 46%] subsections/md_rst/get_distance writing output... [ 46%] subsections/md_rst/get_expression_values writing output... [ 46%] subsections/md_rst/get_feature_info writing output... [ 46%] subsections/md_rst/get_giottoImage writing output... [ 46%] subsections/md_rst/get_giottoImage_MG writing output... [ 46%] subsections/md_rst/get_giottoLargeImage writing output... [ 46%] subsections/md_rst/get_img_corners writing output... [ 47%] subsections/md_rst/get_img_minmax writing output... [ 47%] subsections/md_rst/get_os writing output... [ 47%] subsections/md_rst/get_polygon_info writing output... [ 47%] subsections/md_rst/get_sectionThickness writing output... [ 47%] subsections/md_rst/get_spatialGrid writing output... [ 47%] subsections/md_rst/get_spatialNetwork writing output... [ 48%] subsections/md_rst/get_spatial_enrichment writing output... [ 48%] subsections/md_rst/get_spatial_locations writing output... [ 48%] subsections/md_rst/ggplot_save_function writing output... [ 48%] subsections/md_rst/giotto-class writing output... [ 48%] subsections/md_rst/giottoImage-class writing output... [ 48%] subsections/md_rst/giottoLargeImage-class writing output... [ 48%] subsections/md_rst/giottoPoints-class writing output... [ 49%] subsections/md_rst/giottoPolygon-class writing output... [ 49%] subsections/md_rst/giottoToSeurat writing output... [ 49%] subsections/md_rst/giotto_point writing output... [ 49%] subsections/md_rst/heatmSpatialCorFeats writing output... [ 49%] subsections/md_rst/heatmSpatialCorGenes writing output... [ 49%] subsections/md_rst/hyperGeometricEnrich writing output... [ 49%] subsections/md_rst/identify_background_range_polygons writing output... [ 50%] subsections/md_rst/insertCrossSectionGenePlot3D writing output... [ 50%] subsections/md_rst/insertCrossSectionSpatPlot3D writing output... [ 50%] subsections/md_rst/installGiottoEnvironment writing output... [ 50%] subsections/md_rst/install_giotto_environment writing output... [ 50%] subsections/md_rst/install_giotto_environment_specific writing output... [ 50%] subsections/md_rst/jackstrawPlot writing output... [ 50%] subsections/md_rst/joinGiottoObjects writing output... [ 51%] subsections/md_rst/join_cell_meta writing output... [ 51%] subsections/md_rst/join_expression_matrices writing output... [ 51%] subsections/md_rst/join_spatlocs writing output... [ 51%] subsections/md_rst/kmeans_arma_binarize writing output... [ 51%] subsections/md_rst/kmeans_arma_subset_binarize writing output... [ 51%] subsections/md_rst/kmeans_binarize writing output... [ 52%] subsections/md_rst/kmeans_binarize_wrapper writing output... [ 52%] subsections/md_rst/lapply_flex writing output... [ 52%] subsections/md_rst/libNorm_giotto writing output... [ 52%] subsections/md_rst/list_cell_metadata writing output... [ 52%] subsections/md_rst/list_dim_reductions writing output... [ 52%] subsections/md_rst/list_dim_reductions_names writing output... [ 52%] subsections/md_rst/list_expression writing output... [ 53%] subsections/md_rst/list_expression_names writing output... [ 53%] subsections/md_rst/list_feat_metadata writing output... [ 53%] subsections/md_rst/list_feature_info writing output... [ 53%] subsections/md_rst/list_feature_info_names writing output... [ 53%] subsections/md_rst/list_giotto_data writing output... [ 53%] subsections/md_rst/list_images writing output... [ 53%] subsections/md_rst/list_images_names writing output... [ 54%] subsections/md_rst/list_spatial_enrichments writing output... [ 54%] subsections/md_rst/list_spatial_enrichments_names writing output... [ 54%] subsections/md_rst/list_spatial_grids writing output... [ 54%] subsections/md_rst/list_spatial_grids_names writing output... [ 54%] subsections/md_rst/list_spatial_info writing output... [ 54%] subsections/md_rst/list_spatial_info_names writing output... [ 54%] subsections/md_rst/list_spatial_locations writing output... [ 55%] subsections/md_rst/list_spatial_locations_names writing output... [ 55%] subsections/md_rst/list_spatial_networks writing output... [ 55%] subsections/md_rst/list_spatial_networks_names writing output... [ 55%] subsections/md_rst/loadHMRF writing output... [ 55%] subsections/md_rst/logNorm_giotto writing output... [ 55%] subsections/md_rst/makeSignMatrixDWLS writing output... [ 56%] subsections/md_rst/makeSignMatrixDWLSfromMatrix writing output... [ 56%] subsections/md_rst/makeSignMatrixPAGE writing output... [ 56%] subsections/md_rst/makeSignMatrixRank writing output... [ 56%] subsections/md_rst/make_simulated_network writing output... [ 56%] subsections/md_rst/mean_expr_det_test writing output... [ 56%] subsections/md_rst/mean_flex writing output... [ 56%] subsections/md_rst/mergeClusters writing output... [ 57%] subsections/md_rst/merge_spatial_locs_feat_info writing output... [ 57%] subsections/md_rst/mini_giotto_3D writing output... [ 57%] subsections/md_rst/mini_giotto_multi_cell writing output... [ 57%] subsections/md_rst/mini_giotto_single_cell writing output... [ 57%] subsections/md_rst/my_arowMeans writing output... [ 57%] subsections/md_rst/my_growMeans writing output... [ 57%] subsections/md_rst/my_rowMeans writing output... [ 58%] subsections/md_rst/mygini_fun writing output... [ 58%] subsections/md_rst/nnDT_to_kNN writing output... [ 58%] subsections/md_rst/node_clusters writing output... [ 58%] subsections/md_rst/normalizeGiotto writing output... [ 58%] subsections/md_rst/optimize_deconvolute_dwls writing output... [ 58%] subsections/md_rst/optimize_solveDampenedWLS writing output... [ 58%] subsections/md_rst/overlapToMatrix writing output... [ 59%] subsections/md_rst/overlapToMatrixMultiPoly writing output... [ 59%] subsections/md_rst/overlap_points_per_polygon writing output... [ 59%] subsections/md_rst/overlap_points_per_polygon_wrapped writing output... [ 59%] subsections/md_rst/overlap_points_single_polygon writing output... [ 59%] subsections/md_rst/pDataDT writing output... [ 59%] subsections/md_rst/package_check writing output... [ 60%] subsections/md_rst/pca_giotto writing output... [ 60%] subsections/md_rst/pipe writing output... [ 60%] subsections/md_rst/plotCCcomDotplot writing output... [ 60%] subsections/md_rst/plotCCcomHeatmap writing output... [ 60%] subsections/md_rst/plotCPG writing output... [ 60%] subsections/md_rst/plotCellProximityGenes writing output... [ 60%] subsections/md_rst/plotCombineCCcom writing output... [ 61%] subsections/md_rst/plotCombineCPG writing output... [ 61%] subsections/md_rst/plotCombineCellCellCommunication writing output... [ 61%] subsections/md_rst/plotCombineCellProximityGenes writing output... [ 61%] subsections/md_rst/plotCombineICG writing output... [ 61%] subsections/md_rst/plotCombineInteractionChangedGenes writing output... [ 61%] subsections/md_rst/plotGiottoImage writing output... [ 61%] subsections/md_rst/plotHeatmap writing output... [ 62%] subsections/md_rst/plotICF writing output... [ 62%] subsections/md_rst/plotICG writing output... [ 62%] subsections/md_rst/plotInteractionChangedFeats writing output... [ 62%] subsections/md_rst/plotInteractionChangedGenes writing output... [ 62%] subsections/md_rst/plotInteractivePolygons writing output... [ 62%] subsections/md_rst/plotMetaDataCellsHeatmap writing output... [ 62%] subsections/md_rst/plotMetaDataHeatmap writing output... [ 63%] subsections/md_rst/plotPCA writing output... [ 63%] subsections/md_rst/plotPCA_2D writing output... [ 63%] subsections/md_rst/plotPCA_3D writing output... [ 63%] subsections/md_rst/plotRankSpatvsExpr writing output... [ 63%] subsections/md_rst/plotRecovery writing output... [ 63%] subsections/md_rst/plotRecovery_sub writing output... [ 64%] subsections/md_rst/plotStatDelaunayNetwork writing output... [ 64%] subsections/md_rst/plotTSNE writing output... [ 64%] subsections/md_rst/plotTSNE_2D writing output... [ 64%] subsections/md_rst/plotTSNE_3D writing output... [ 64%] subsections/md_rst/plotUMAP writing output... [ 64%] subsections/md_rst/plotUMAP_2D writing output... [ 64%] subsections/md_rst/plotUMAP_3D writing output... [ 65%] subsections/md_rst/plot_auto_largeImage_resample writing output... [ 65%] subsections/md_rst/plot_cell_polygon_layer writing output... [ 65%] subsections/md_rst/plot_feature_hexbin_layer writing output... [ 65%] subsections/md_rst/plot_feature_points_layer writing output... [ 65%] subsections/md_rst/plot_feature_raster_density_layer writing output... [ 65%] subsections/md_rst/plot_giottoImage_MG writing output... [ 65%] subsections/md_rst/plot_giottoLargeImage writing output... [ 66%] subsections/md_rst/plot_network_layer_ggplot writing output... [ 66%] subsections/md_rst/plot_point_layer_ggplot writing output... [ 66%] subsections/md_rst/plot_point_layer_ggplot_noFILL writing output... [ 66%] subsections/md_rst/plot_spat_image_layer_ggplot writing output... [ 66%] subsections/md_rst/plot_spat_point_layer_ggplot writing output... [ 66%] subsections/md_rst/plot_spat_point_layer_ggplot_noFILL writing output... [ 66%] subsections/md_rst/plot_spat_scatterpie_layer_ggplot writing output... [ 67%] subsections/md_rst/plot_spat_voronoi_layer_ggplot writing output... [ 67%] subsections/md_rst/plotly_axis_scale_2D writing output... [ 67%] subsections/md_rst/plotly_axis_scale_3D writing output... [ 67%] subsections/md_rst/plotly_grid writing output... [ 67%] subsections/md_rst/plotly_network writing output... [ 67%] subsections/md_rst/polygon_to_raster writing output... [ 68%] subsections/md_rst/processGiotto writing output... [ 68%] subsections/md_rst/projection_fun writing output... [ 68%] subsections/md_rst/rankEnrich writing output... [ 68%] subsections/md_rst/rankSpatialCorGroups writing output... [ 68%] subsections/md_rst/rank_binarize writing output... [ 68%] subsections/md_rst/rank_binarize_wrapper writing output... [ 68%] subsections/md_rst/readExprMatrix writing output... [ 69%] subsections/md_rst/readGiottoInstructions writing output... [ 69%] subsections/md_rst/readPolygonFilesVizgen writing output... [ 69%] subsections/md_rst/readPolygonFilesVizgenHDF5 writing output... [ 69%] subsections/md_rst/read_crossSection writing output... [ 69%] subsections/md_rst/read_dimension_reduction writing output... [ 69%] subsections/md_rst/read_expression_data writing output... [ 69%] subsections/md_rst/read_nearest_networks writing output... [ 70%] subsections/md_rst/read_spatial_enrichment writing output... [ 70%] subsections/md_rst/read_spatial_location_data writing output... [ 70%] subsections/md_rst/read_spatial_networks writing output... [ 70%] subsections/md_rst/reconnectGiottoImage writing output... [ 70%] subsections/md_rst/reconnect_giottoImage_MG writing output... [ 70%] subsections/md_rst/reconnect_giottoLargeImage writing output... [ 70%] subsections/md_rst/reconnect_image_object writing output... [ 71%] subsections/md_rst/reg_img_minmax_finder writing output... [ 71%] subsections/md_rst/registerGiottoObjectList writing output... [ 71%] subsections/md_rst/registerGiottoObjectListFiji writing output... [ 71%] subsections/md_rst/registerGiottoObjectListRvision writing output... [ 71%] subsections/md_rst/registerImagesFIJI writing output... [ 71%] subsections/md_rst/removeCellAnnotation writing output... [ 72%] subsections/md_rst/removeFeatAnnotation writing output... [ 72%] subsections/md_rst/removeGiottoEnvironment writing output... [ 72%] subsections/md_rst/replaceGiottoInstructions writing output... [ 72%] subsections/md_rst/reshape_to_data_point writing output... [ 72%] subsections/md_rst/reshape_to_mesh_grid_obj writing output... [ 72%] subsections/md_rst/return_giotto_environment_path writing output... [ 72%] subsections/md_rst/return_giotto_environment_path_executable writing output... [ 73%] subsections/md_rst/rigid_transform_spatial_locations writing output... [ 73%] subsections/md_rst/rna_osmfish_normalization writing output... [ 73%] subsections/md_rst/rna_pears_resid_normalization writing output... [ 73%] subsections/md_rst/rna_standard_normalization writing output... [ 73%] subsections/md_rst/rotate_spatial_locations writing output... [ 73%] subsections/md_rst/rowMeans_flex writing output... [ 73%] subsections/md_rst/rowSums_flex writing output... [ 74%] subsections/md_rst/runDWLSDeconv writing output... [ 74%] subsections/md_rst/runFijiMacro writing output... [ 74%] subsections/md_rst/runGiottoHarmony writing output... [ 74%] subsections/md_rst/runHyperGeometricEnrich writing output... [ 74%] subsections/md_rst/runPAGEEnrich writing output... [ 74%] subsections/md_rst/runPAGEEnrich_OLD writing output... [ 74%] subsections/md_rst/runPCA writing output... [ 75%] subsections/md_rst/runPCA_BiocSingular writing output... [ 75%] subsections/md_rst/runPCA_factominer writing output... [ 75%] subsections/md_rst/runPCA_prcomp_irlba writing output... [ 75%] subsections/md_rst/runPatternSimulation writing output... [ 75%] subsections/md_rst/runRankEnrich writing output... [ 75%] subsections/md_rst/runSpatialDeconv writing output... [ 76%] subsections/md_rst/runSpatialEnrich writing output... [ 76%] subsections/md_rst/runUMAP writing output... [ 76%] subsections/md_rst/run_spatial_sim_tests_multi writing output... [ 76%] subsections/md_rst/run_spatial_sim_tests_one_rep writing output... [ 76%] subsections/md_rst/runtSNE writing output... [ 76%] subsections/md_rst/scale_spatial_locations writing output... [ 76%] subsections/md_rst/screePlot writing output... [ 77%] subsections/md_rst/selectPatternGenes writing output... [ 77%] subsections/md_rst/select_NearestNetwork writing output... [ 77%] subsections/md_rst/select_dimReduction writing output... [ 77%] subsections/md_rst/select_expression_values writing output... [ 77%] subsections/md_rst/select_feature_info writing output... [ 77%] subsections/md_rst/select_gimage writing output... [ 77%] subsections/md_rst/select_polygon_info writing output... [ 78%] subsections/md_rst/select_spatialGrid writing output... [ 78%] subsections/md_rst/select_spatialNetwork writing output... [ 78%] subsections/md_rst/select_spatial_locations writing output... [ 78%] subsections/md_rst/set_NearestNetwork writing output... [ 78%] subsections/md_rst/set_cell_and_feat_IDs writing output... [ 78%] subsections/md_rst/set_cell_metadata writing output... [ 78%] subsections/md_rst/set_default_feat_type writing output... [ 79%] subsections/md_rst/set_default_spat_unit writing output... [ 79%] subsections/md_rst/set_dimReduction writing output... [ 79%] subsections/md_rst/set_expression_values writing output... [ 79%] subsections/md_rst/set_feature_info writing output... [ 79%] subsections/md_rst/set_feature_metadata writing output... [ 79%] subsections/md_rst/set_giottoImage writing output... [ 80%] subsections/md_rst/set_giottoImage_MG writing output... [ 80%] subsections/md_rst/set_giottoLargeImage writing output... [ 80%] subsections/md_rst/set_giotto_python_path writing output... [ 80%] subsections/md_rst/set_polygon_info writing output... [ 80%] subsections/md_rst/set_spatialGrid writing output... [ 80%] subsections/md_rst/set_spatialNetwork writing output... [ 80%] subsections/md_rst/set_spatial_enrichment writing output... [ 81%] subsections/md_rst/set_spatial_locations writing output... [ 81%] subsections/md_rst/seuratToGiotto writing output... [ 81%] subsections/md_rst/seuratToGiotto_OLD writing output... [ 81%] subsections/md_rst/show-methods writing output... [ 81%] subsections/md_rst/showClusterDendrogram writing output... [ 81%] subsections/md_rst/showClusterHeatmap writing output... [ 81%] subsections/md_rst/showGiottoDimRed writing output... [ 82%] subsections/md_rst/showGiottoExpression writing output... [ 82%] subsections/md_rst/showGiottoFeatInfo writing output... [ 82%] subsections/md_rst/showGiottoImageNames writing output... [ 82%] subsections/md_rst/showGiottoInstructions writing output... [ 82%] subsections/md_rst/showGiottoSpatEnrichments writing output... [ 82%] subsections/md_rst/showGiottoSpatGrids writing output... [ 82%] subsections/md_rst/showGiottoSpatLocs writing output... [ 83%] subsections/md_rst/showGiottoSpatNetworks writing output... [ 83%] subsections/md_rst/showGiottoSpatialInfo writing output... [ 83%] subsections/md_rst/showGrids writing output... [ 83%] subsections/md_rst/showNetworks writing output... [ 83%] subsections/md_rst/showPattern writing output... [ 83%] subsections/md_rst/showPattern2D writing output... [ 84%] subsections/md_rst/showPattern3D writing output... [ 84%] subsections/md_rst/showPatternGenes writing output... [ 84%] subsections/md_rst/showProcessingSteps writing output... [ 84%] subsections/md_rst/showSaveParameters writing output... [ 84%] subsections/md_rst/showSpatialCorFeats writing output... [ 84%] subsections/md_rst/showSpatialCorGenes writing output... [ 84%] subsections/md_rst/signPCA writing output... [ 85%] subsections/md_rst/silhouetteRank writing output... [ 85%] subsections/md_rst/silhouetteRankTest writing output... [ 85%] subsections/md_rst/simulateOneGenePatternGiottoObject writing output... [ 85%] subsections/md_rst/smoothGiottoPolygons writing output... [ 85%] subsections/md_rst/solve_OLS_internal writing output... [ 85%] subsections/md_rst/solve_dampened_WLSj writing output... [ 85%] subsections/md_rst/sort_combine_two_DT_columns writing output... [ 86%] subsections/md_rst/spark writing output... [ 86%] subsections/md_rst/spatCellCellcom writing output... [ 86%] subsections/md_rst/spatCellPlot writing output... [ 86%] subsections/md_rst/spatCellPlot2D writing output... [ 86%] subsections/md_rst/spatDeconvPlot writing output... [ 86%] subsections/md_rst/spatDimCellPlot writing output... [ 86%] subsections/md_rst/spatDimCellPlot2D writing output... [ 87%] subsections/md_rst/spatDimFeatPlot2D writing output... [ 87%] subsections/md_rst/spatDimGenePlot writing output... [ 87%] subsections/md_rst/spatDimGenePlot2D writing output... [ 87%] subsections/md_rst/spatDimGenePlot3D writing output... [ 87%] subsections/md_rst/spatDimPlot writing output... [ 87%] subsections/md_rst/spatDimPlot2D writing output... [ 88%] subsections/md_rst/spatDimPlot3D writing output... [ 88%] subsections/md_rst/spatFeatPlot2D writing output... [ 88%] subsections/md_rst/spatFeatPlot2D_single writing output... [ 88%] subsections/md_rst/spatGenePlot writing output... [ 88%] subsections/md_rst/spatGenePlot2D writing output... [ 88%] subsections/md_rst/spatGenePlot3D writing output... [ 88%] subsections/md_rst/spatInSituPlotDensity writing output... [ 89%] subsections/md_rst/spatInSituPlotDensity_single writing output... [ 89%] subsections/md_rst/spatInSituPlotHex writing output... [ 89%] subsections/md_rst/spatInSituPlotHex_single writing output... [ 89%] subsections/md_rst/spatInSituPlotPoints writing output... [ 89%] subsections/md_rst/spatNetwDistributions writing output... [ 89%] subsections/md_rst/spatNetwDistributionsDistance writing output... [ 89%] subsections/md_rst/spatNetwDistributionsKneighbors writing output... [ 90%] subsections/md_rst/spatPlot writing output... [ 90%] subsections/md_rst/spatPlot2D writing output... [ 90%] subsections/md_rst/spatPlot2D_single writing output... [ 90%] subsections/md_rst/spatPlot3D writing output... [ 90%] subsections/md_rst/spatPlot_2D_plotly writing output... [ 90%] subsections/md_rst/spatPlot_3D_plotly writing output... [ 90%] subsections/md_rst/spatVector_to_dt writing output... [ 91%] subsections/md_rst/spat_OR_func writing output... [ 91%] subsections/md_rst/spat_OR_func_DT writing output... [ 91%] subsections/md_rst/spat_fish_func writing output... [ 91%] subsections/md_rst/spat_fish_func_DT writing output... [ 91%] subsections/md_rst/spatialAEH writing output... [ 91%] subsections/md_rst/spatialDE writing output... [ 92%] subsections/md_rst/specificCellCellcommunicationScores writing output... [ 92%] subsections/md_rst/spline_poly writing output... [ 92%] subsections/md_rst/split_dendrogram_in_two writing output... [ 92%] subsections/md_rst/spot_deconvolution writing output... [ 92%] subsections/md_rst/standardise_flex writing output... [ 92%] subsections/md_rst/stitchFieldCoordinates writing output... [ 92%] subsections/md_rst/stitchGiottoLargeImage writing output... [ 93%] subsections/md_rst/stitchTileCoordinates writing output... [ 93%] subsections/md_rst/subClusterCells writing output... [ 93%] subsections/md_rst/subsetGiotto writing output... [ 93%] subsections/md_rst/subsetGiottoLocs writing output... [ 93%] subsections/md_rst/subsetGiottoLocsMulti writing output... [ 93%] subsections/md_rst/subset_cell_metadata writing output... [ 93%] subsections/md_rst/subset_dimension_reduction writing output... [ 94%] subsections/md_rst/subset_expression_data writing output... [ 94%] subsections/md_rst/subset_feature_info_data writing output... [ 94%] subsections/md_rst/subset_feature_metadata writing output... [ 94%] subsections/md_rst/subset_giotto_points_object writing output... [ 94%] subsections/md_rst/subset_giotto_polygon_object writing output... [ 94%] subsections/md_rst/subset_nearest_network writing output... [ 94%] subsections/md_rst/subset_spatial_enrichment writing output... [ 95%] subsections/md_rst/subset_spatial_info_data writing output... [ 95%] subsections/md_rst/subset_spatial_locations writing output... [ 95%] subsections/md_rst/subset_spatial_network writing output... [ 95%] subsections/md_rst/t_flex writing output... [ 95%] subsections/md_rst/trakem2_rigid_transf_extract writing output... [ 95%] subsections/md_rst/transform_2d_mesh_to_3d_mesh writing output... [ 96%] subsections/md_rst/trendSceek writing output... [ 96%] subsections/md_rst/updateGiottoImage writing output... [ 96%] subsections/md_rst/updateGiottoImageMG writing output... [ 96%] subsections/md_rst/updateGiottoLargeImage writing output... [ 96%] subsections/md_rst/update_giotto_params writing output... [ 96%] subsections/md_rst/viewHMRFresults writing output... [ 96%] subsections/md_rst/viewHMRFresults2D writing output... [ 97%] subsections/md_rst/viewHMRFresults3D writing output... [ 97%] subsections/md_rst/violinPlot writing output... [ 97%] subsections/md_rst/writeGiottoLargeImage writing output... [ 97%] subsections/md_rst/writeHMRFresults writing output... [ 97%] subsections/md_rst/write_giotto_viewer_annotation writing output... [ 97%] subsections/md_rst/write_giotto_viewer_dim_reduction writing output... [ 97%] subsections/md_rst/write_giotto_viewer_numeric_annotation writing output... [ 98%] subsections/md_rst/xy_translate_spatial_locations writing output... [ 98%] subsections/tipsandtricks/NEWS writing output... [ 98%] subsections/tipsandtricks/giottoclass writing output... [ 98%] subsections/tipsandtricks/howtosubsetgiottoobject writing output... [ 98%] subsections/tipsandtricks/howtovisualizeandsaveplots writing output... [ 98%] subsections/tipsandtricks/testandstoremultipleanayses writing output... [ 98%] subsections/tipsandtricks/visualizewithvoronoiplots writing output... [ 99%] subsections/tipsandtricks/waystovisualizespatialdata writing output... [ 99%] subsections/tipsandtricks/workingwithimages writing output... [ 99%] subsections/trygiotto/binder writing output... [ 99%] subsections/trygiotto/docker writing output... [ 99%] subsections/trygiotto/terra writing output... [ 99%] tipsandtricks writing output... [100%] trygiotto /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/nanostring_overview.rst:10: WARNING: unknown document: subsections/datasets/nanostring_lung_12 generating indices... genindex done writing additional pages... search done copying images... [ 0%] images/dataset_page/visium_kidney_image_summary.png copying images... [ 0%] images/dataset_page/visium_prostate_summary.png copying images... [ 0%] images/dataset_page/coming_soon_summary.png copying images... [ 0%] images/dataset_page/cortex_image_summary.png copying images... [ 0%] images/dataset_page/osmFISH_SS_cortex_image_summary.png copying images... [ 1%] images/dataset_page/merFISH_hypoth_image_summary.png copying images... [ 1%] images/dataset_page/starmap_cortex_image_summary.png copying images... [ 1%] images/dataset_page/vizgen_brain_summary.png copying images... [ 1%] images/dataset_page/resolve_bioscience_cancer_summary.png copying images... [ 1%] images/dataset_page/nanostring_overview_icon.png copying images... [ 2%] images/dataset_page/CODEX_spleen_image_summary.png copying images... [ 2%] images/dataset_page/cyCIF_PDAC_image_summary.png copying images... [ 2%] images/dataset_page/SC_RNAseq_standard.png copying images... [ 2%] images/dataset_page/SC_RNAseq_integration.png copying images... [ 2%] images/GiottoInstallationWorkflow.png copying images... [ 3%] images/getting_started/icons_configuration.png copying images... [ 3%] images/getting_started/icons_giotto.png copying images... [ 3%] images/getting_started/icons_processing.png copying images... [ 3%] images/getting_started/icons_clustering.png copying images... [ 3%] images/getting_started/icons_images.png copying images... [ 4%] images/getting_started/icons_visualizations.png copying images... [ 4%] images/getting_started/icons_saving.png copying images... [ 4%] images/getting_started/icons_distribution.png copying images... [ 4%] images/getting_started/icons_cell_type.png copying images... [ 4%] images/getting_started/icons_deconvolution.png copying images... [ 4%] images/getting_started/icons_interaction.png copying images... [ 5%] images/getting_started/icons_patterns.png copying images... [ 5%] images/getting_started/icons_subcellular.png copying images... [ 5%] images/diagram_giotto_workflow.png copying images... [ 5%] images/index/giotto_suite.png copying images... [ 5%] images/index/input_Compatibility.png copying images... [ 6%] images/index/data_structure_Data_Structure.png copying images... [ 6%] images/index/analysis.png copying images... [ 6%] images/other/mouse_starmap_cortex/vignette_200917/2_a_distribution_genes.png copying images... [ 6%] images/other/mouse_starmap_cortex/vignette_200917/2_b_distribution_cells.png copying images... [ 6%] images/other/mouse_starmap_cortex/vignette_200917/2_c_distribution_filters.png copying images... [ 7%] images/other/mouse_starmap_cortex/vignette_200917/2_d_spatial_locations.png copying images... [ 7%] images/other/mouse_starmap_cortex/vignette_200917/3_a_hvg.png copying images... [ 7%] images/other/mouse_starmap_cortex/vignette_200917/3_b_signPCs.png copying images... [ 7%] images/other/mouse_starmap_cortex/vignette_200917/3_c_umap.png copying images... [ 7%] images/other/mouse_starmap_cortex/vignette_200917/4_leiden_0.2.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/5_a_covisualize_leiden_0.2.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/6_a_violinplot.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/6_b_heatmap_leiden_0.2.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/7_a_general_cell_type.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/7_b_dim_plot_detailed_cell_type.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/7_c_cluster_annotation_heatmap.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/8_cell_type_co_vis.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/9_a_Rorb_dim_plot.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/9_b_Pcp4_dim_plot.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/9_c_Pcp4_spat_plot.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/9_d_Cux2_dim_plot.png copying images... [ 10%] images/other/mouse_starmap_cortex/vignette_200917/9_e_detailed_cell_types.png copying images... [ 10%] images/other/mouse_starmap_cortex/vignette_200917/9_f_Cux2_spat_plot.png copying images... [ 10%] images/other/mouse_starmap_cortex/vignette_200917/9_g_Ctgf_dim_plot.png copying images... [ 10%] images/other/mouse_starmap_cortex/vignette_200917/9_h_Ctgf_spat_plot.png copying images... [ 10%] images/other/mouse_starmap_cortex/vignette_200917/10_a_insert_cross_section_cell_types.png copying images... [ 11%] images/other/mouse_starmap_cortex/vignette_200917/10_b_insert_cross_section_Slc17a7.png copying images... [ 11%] images/other/mouse_starmap_cortex/vignette_200917/10_c_cross_section_spat.png copying images... [ 11%] images/other/mouse_starmap_cortex/vignette_200917/10_d_cross_section_spat3d.png copying images... [ 11%] images/other/mouse_starmap_cortex/vignette_200917/10_e_Slc17a7_cross_section_gene3d.png copying images... [ 11%] images/other/human_cycif_PDAC/vignette_200916/2_a_spatPlot.png copying images... [ 12%] images/other/human_cycif_PDAC/vignette_200916/2_b_spatPlot_column.png copying images... [ 12%] images/other/human_cycif_PDAC/vignette_200916/2_c_spatPlot_row.png copying images... [ 12%] images/other/human_cycif_PDAC/vignette_200916/2_d_spatPlot_hist.png copying images... [ 12%] images/other/human_cycif_PDAC/vignette_200916/2_e_spatPlot_hist2.png copying images... [ 12%] images/other/human_cycif_PDAC/vignette_200916/3_a_signPCA.png copying images... [ 12%] images/other/human_cycif_PDAC/vignette_200916/3_b_PCAplot.png copying images... [ 13%] images/other/human_cycif_PDAC/vignette_200916/3_c_UMAP.png copying images... [ 13%] images/other/human_cycif_PDAC/vignette_200916/4_a_UMAP.png copying images... [ 13%] images/other/human_cycif_PDAC/vignette_200916/4_b_UMAP.png copying images... [ 13%] images/other/human_cycif_PDAC/vignette_200916/4_c_spatplot.png copying images... [ 13%] images/other/human_cycif_PDAC/vignette_200916/4_d_spatPlot.png copying images... [ 14%] images/other/human_cycif_PDAC/vignette_200916/5_a_spatdimplot.png copying images... [ 14%] images/other/human_cycif_PDAC/vignette_200916/5_b_spatdimplot.png copying images... [ 14%] images/other/human_cycif_PDAC/vignette_200916/5_c_spatdimplot.png copying images... [ 14%] images/other/human_cycif_PDAC/vignette_200916/6_a_metaheatmap.png copying images... [ 14%] images/other/human_cycif_PDAC/vignette_200916/6_b_violinplot_gini.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/7_a_metaheatmap.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/7_b_metaheatmap.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/7_c_spatplot.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/7_d_spatplot.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/7_e_spatplot.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_f_spatplot.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_g_spatplot_1.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_g_spatplot_2.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_h_spatdimplot.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_i_spatplot.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_j_umap.png copying images... [ 17%] images/other/human_cycif_PDAC/vignette_200916/8_a_spatplot.png copying images... [ 17%] images/other/human_cycif_PDAC/vignette_200916/12_a_barplot.png copying images... [ 17%] images/other/human_cycif_PDAC/vignette_200916/12_b_network.png copying images... [ 17%] images/other/human_cycif_PDAC/vignette_200916/12_c_proxspatplot.png copying images... [ 17%] images/other/human_cycif_PDAC/vignette_200916/xx_a_metaheatmap.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/xx_b_spatplot.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/xx_c_spatgeneplot.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/xx_d_umap.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/xx_e_dimGeneplot.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/xx_f_spatplot.png copying images... [ 19%] images/other/human_cycif_PDAC/vignette_200916/xx_g_spatGeneplot.png copying images... [ 19%] images/other/human_cycif_PDAC/vignette_200916/xx_h_umap.png copying images... [ 19%] images/other/human_cycif_PDAC/vignette_200916/xx_i_dimGeneplot.png copying images... [ 19%] images/other/mouse_merFISH_hypoth/vignette_200909/2_a_distribution_genes.png copying images... [ 19%] images/other/mouse_merFISH_hypoth/vignette_200909/2_b_distribution_cells.png copying images... [ 20%] images/other/mouse_merFISH_hypoth/vignette_200909/2_c_filter_combos.png copying images... [ 20%] images/other/mouse_merFISH_hypoth/vignette_200909/2_d_spatial_locations2D.png copying images... [ 20%] images/other/mouse_merFISH_hypoth/vignette_200909/2_e_spatial_locations3D.png copying images... [ 20%] images/other/mouse_merFISH_hypoth/vignette_200909/3_a_screeplot.png copying images... [ 20%] images/other/mouse_merFISH_hypoth/vignette_200909/3_b_UMAP_reduction.png copying images... [ 20%] images/other/mouse_merFISH_hypoth/vignette_200909/4_a_UMAP_leiden.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/5_b_leiden_2D.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/6_a_violinplot.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/6_b_clusterheatmap_markers.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/7_a_clusterheatmap_markers.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/7_b_clusterheatmap_markers_celltypes.png copying images... [ 22%] images/other/mouse_merFISH_hypoth/vignette_200909/7_c_umap_cell_types.png copying images... [ 22%] images/other/mouse_merFISH_hypoth/vignette_200909/7_d_spatPlot_cell_types_all.png copying images... [ 22%] images/other/mouse_merFISH_hypoth/vignette_200909/7_e_spatPlot2D_cell_types_all.png copying images... [ 22%] images/other/mouse_merFISH_hypoth/vignette_200909/7_f_spatPlot_cell_types_excit.png copying images... [ 22%] images/other/mouse_merFISH_hypoth/vignette_200909/7_g_spatPlot2D_cell_types_excit.png copying images... [ 23%] images/other/mouse_merFISH_hypoth/vignette_200909/7_h_spatPlot_cell_types_inhib.png copying images... [ 23%] images/other/mouse_merFISH_hypoth/vignette_200909/7_i_spatPlot2D_cell_types_inhib.png copying images... [ 23%] images/other/mouse_merFISH_hypoth/vignette_200909/7_j_spatPlot_cell_types_ODandAstro.png copying images... [ 23%] images/other/mouse_merFISH_hypoth/vignette_200909/7_k_spatPlot2D_cell_types_ODandAstro.png copying images... [ 23%] images/other/mouse_merFISH_hypoth/vignette_200909/7_l_spatPlot_cell_types_other.png copying images... [ 24%] images/other/mouse_merFISH_hypoth/vignette_200909/7_m_spatPlot2D_cell_types_other.png copying images... [ 24%] images/other/mini_datasets/mini_starmap/vignette_200922/2_a_filtergenes.png copying images... [ 24%] images/other/mini_datasets/mini_starmap/vignette_200922/2_b_filtercells.png copying images... [ 24%] images/other/mini_datasets/mini_starmap/vignette_200922/2_c_filtercombos.png copying images... [ 24%] images/other/mini_datasets/mini_starmap/vignette_200922/3_a_screeplot.png copying images... [ 24%] images/other/mini_datasets/mini_starmap/vignette_200922/3_b_PCA.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/3_d_UMAP_3D.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/3_e_TSNE.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/4_a_UMAP.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/4_b_UMAP_3D.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/4_c_spatdimplot.png copying images... [ 26%] images/other/mini_datasets/mini_starmap/vignette_200922/4_e_clusterheatmap.png copying images... [ 26%] images/other/mini_datasets/mini_starmap/vignette_200922/4_f_clusterdendrogram.png copying images... [ 26%] images/other/mini_datasets/mini_starmap/vignette_200922/5_a_violinplot.png copying images... [ 26%] images/other/mini_datasets/mini_starmap/vignette_200922/5_b_metaheatmap.png copying images... [ 26%] images/other/mini_datasets/mini_starmap/vignette_200922/6_a_spatdimplot.png copying images... [ 27%] images/other/mini_datasets/mini_starmap/vignette_200922/6_b_dimgeneplot.png copying images... [ 27%] images/other/mini_datasets/mini_starmap/vignette_200922/6_c_spatgeneplot.png copying images... [ 27%] images/other/mini_datasets/mini_starmap/vignette_200922/7_a_spatplot.png copying images... [ 27%] images/other/mini_datasets/mini_starmap/vignette_200922/8_a_plotStatDelaunayNetwork.png copying images... [ 27%] images/other/mini_datasets/mini_starmap/vignette_200922/8_b_spatplot.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/8_c_spatplot.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/9_a_spatgeneplot.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/9_b_spatgeneplot.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/10_a_heatmspatcor.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/10_b_rankcorgroup.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/10_c_spatcellplot.png copying images... [ 29%] images/other/mini_datasets/mini_starmap/vignette_200922/12_a_barplot.png copying images... [ 29%] images/other/mini_datasets/mini_starmap/vignette_200922/12_b_heatmap.png copying images... [ 29%] images/other/mini_datasets/mini_starmap/vignette_200922/12_c_network.png copying images... [ 29%] images/other/mini_datasets/mini_starmap/vignette_200922/12_d_network.png copying images... [ 29%] images/other/mini_datasets/mini_starmap/vignette_200922/12_e_spatplot.png copying images... [ 30%] images/other/mini_datasets/mini_starmap/vignette_200922/12_e_cellproximity.png copying images... [ 30%] images/other/mini_datasets/mini_starmap/vignette_200922/13_a_insert.png copying images... [ 30%] images/other/mini_datasets/mini_starmap/vignette_200922/13_b_crossplot.png copying images... [ 30%] images/other/mini_datasets/mini_starmap/vignette_200922/13_c_cross.png copying images... [ 30%] images/other/mini_datasets/mini_starmap/vignette_200922/13_d_crossgeneplot.png copying images... [ 31%] images/other/mini_datasets/mini_starmap/vignette_200922/13_e_crossgene.png copying images... [ 31%] images/other/mini_datasets/mini_seqfish/vignette_200921/3.1_HVGplot.png copying images... [ 31%] images/other/mini_datasets/mini_seqfish/vignette_200921/3.2_screePlot.png copying images... [ 31%] images/other/mini_datasets/mini_seqfish/vignette_200921/3.3_jackstrawPlot.png copying images... [ 31%] images/other/mini_datasets/mini_seqfish/vignette_200921/3.4_PCA.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/3.5_tSNE.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/4.1_UMAP.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/4.2_showClusterHeatmap.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/4.3_showClusterDendrogram.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/5.1_violinPlot.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/5.2_plotMetaDataHeatmap.png copying images... [ 33%] images/other/mini_datasets/mini_seqfish/vignette_200921/6.1_spatDimPlot2D.png copying images... [ 33%] images/other/mini_datasets/mini_seqfish/vignette_200921/9.1_spatGenePlot2D.png copying images... [ 33%] images/other/mini_datasets/mini_seqfish/vignette_200921/10.1_heatmSpatialCorGenes.png copying images... [ 33%] images/other/mini_datasets/mini_seqfish/vignette_200921/10.2_spatCellPlot2D.png copying images... [ 33%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.1_cellProximityBarplot.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.2_spatCellPlot2D.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.3_cellProximityHeatmap.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.4_cellProximityNetwork.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.5_cellProximitySpatPlot2D.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.6_spatPlot2D.png copying images... [ 35%] images/other/mini_datasets/mini_seqfish/vignette_200921/13.1_plotCellProximityGenes.png copying images... [ 35%] images/other/mini_datasets/mini_seqfish/vignette_200921/13.2_plotICG.png copying images... [ 35%] images/other/mini_datasets/mini_seqfish/vignette_200921/14.1_plotCCcomHeatmap.png copying images... [ 35%] images/other/mini_datasets/mini_seqfish/vignette_200921/14.2_plotCCcomDotplot.png copying images... [ 35%] images/other/mini_datasets/mini_seqfish/vignette_200921/14.3_plotRankSpatvsExpr.png copying images... [ 36%] images/other/mini_datasets/mini_seqfish/vignette_200921/14.4_plotRecovery.png copying images... [ 36%] images/other/mouse_codex_spleen/vignette_200921/2_a_spatPlot.png copying images... [ 36%] images/other/mouse_codex_spleen/vignette_200921/2_b_spatPlot.png copying images... [ 36%] images/other/mouse_codex_spleen/vignette_200921/3_a_spatPlot.png copying images... [ 36%] images/other/mouse_codex_spleen/vignette_200921/3_b_PCA.png copying images... [ 36%] images/other/mouse_codex_spleen/vignette_200921/3_c_UMAP.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/4_a_UMAP.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/4_b_spatplot.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/5_a_spatdimplot.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/6_a_metaheatmap.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/6_b_violinplot.png copying images... [ 38%] images/other/mouse_codex_spleen/vignette_200921/6_c_metaheatmap.png copying images... [ 38%] images/other/mouse_codex_spleen/vignette_200921/6_d_violinplot.png copying images... [ 38%] images/other/mouse_codex_spleen/vignette_200921/7_a_metaheatmap.png copying images... [ 38%] images/other/mouse_codex_spleen/vignette_200921/7_b_umap.png copying images... [ 38%] images/other/mouse_codex_spleen/vignette_200921/7_c_spatplot.png copying images... [ 39%] images/other/mouse_codex_spleen/vignette_200921/8_a_umap.png copying images... [ 39%] images/other/mouse_codex_spleen/vignette_200921/8_b_spatplot.png copying images... [ 39%] images/other/mouse_codex_spleen/vignette_200921/8_c_spatdimplot.png copying images... [ 39%] images/other/mouse_codex_spleen/vignette_200921/8_d_umap.png copying images... [ 39%] images/other/mouse_codex_spleen/vignette_200921/8_e_spatPlot.png copying images... [ 40%] images/other/mouse_codex_spleen/vignette_200921/8_f_spatdimgeneplot.png copying images... [ 40%] images/other/general_figs/visium_technology.png copying images... [ 40%] images/other/general_figs/visium_brain_image_summary.png copying images... [ 40%] images/other/mouse_Visium_brain/vignette_201226/2_a_spatplot_image.png copying images... [ 40%] images/other/mouse_Visium_brain/vignette_201226/2_b_spatplot_image_adjusted.png copying images... [ 40%] images/other/mouse_Visium_brain/vignette_201226/2_c_in_tissue.png copying images... [ 41%] images/other/mouse_Visium_brain/vignette_201226/2_d_spatial_locations.png copying images... [ 41%] images/other/mouse_Visium_brain/vignette_201226/2_e_nr_genes.png copying images... [ 41%] images/other/mouse_Visium_brain/vignette_201226/3_a_HVGplot.png copying images... [ 41%] images/other/mouse_Visium_brain/vignette_201226/3_b_screeplot.png copying images... [ 41%] images/other/mouse_Visium_brain/vignette_201226/3_c_PCA_reduction.png copying images... [ 42%] images/other/mouse_Visium_brain/vignette_201226/3_d_UMAP_reduction.png copying images... [ 42%] images/other/mouse_Visium_brain/vignette_201226/3_e_tSNE_reduction.png copying images... [ 42%] images/other/mouse_Visium_brain/vignette_201226/4_a_UMAP_leiden.png copying images... [ 42%] images/other/mouse_Visium_brain/vignette_201226/5_a_covis_leiden.png copying images... [ 42%] images/other/mouse_Visium_brain/vignette_201226/5_b_nr_genes.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/5_c_DEG_subset.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/6_a_violinplot_gini.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/6_b_metaheatmap_gini.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/6_c_gini_umap.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/6_d_violinplot_scran.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/6_e_metaheatmap_scran.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/6_f_scran_umap.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/7_a_metaheatmap.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/7_b_spatcellplot.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/7_c_spatcellplot.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/7_d_spatDimCellPlot.png copying images... [ 45%] images/other/mouse_Visium_brain/vignette_201226/8_grid.png copying images... [ 45%] images/other/mouse_Visium_brain/vignette_201226/9_a_knn_network.png copying images... [ 45%] images/other/mouse_Visium_brain/vignette_201226/10_a_spatial_genes_km.png copying images... [ 45%] images/other/mouse_Visium_brain/vignette_201226/10_b_spatial_genes_rank.png copying images... [ 45%] images/other/mouse_Visium_brain/vignette_201226/10_c_heatmap.png copying images... [ 46%] images/other/mouse_Visium_brain/vignette_201226/10_d_spatPlot2D_HMRF.png copying images... [ 46%] images/other/mouse_Visium_kidney/mouse_kidney_highres.png copying images... [ 46%] images/other/mouse_Visium_kidney/vignette_200916/2_a_spatplot_image.png copying images... [ 46%] images/other/mouse_Visium_kidney/vignette_200916/2_b_spatplot_image_adjusted.png copying images... [ 46%] images/other/mouse_Visium_kidney/vignette_200916/2_c_in_tissue.png copying images... [ 47%] images/other/mouse_Visium_kidney/vignette_200916/2_d_spatial_locations.png copying images... [ 47%] images/other/mouse_Visium_kidney/vignette_200916/2_e_nr_genes.png copying images... [ 47%] images/other/mouse_Visium_kidney/vignette_200916/3_a_HVGplot.png copying images... [ 47%] images/other/mouse_Visium_kidney/vignette_200916/3_b_screeplot.png copying images... [ 47%] images/other/mouse_Visium_kidney/vignette_200916/3_c_PCA_reduction.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/3_d_UMAP_reduction.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/3_e_tSNE_reduction.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/4_a_UMAP_leiden.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/5_a_covis_leiden.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/5_b_nr_genes.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/6_a_violinplot_gini.png copying images... [ 49%] images/other/mouse_Visium_kidney/vignette_200916/6_b_metaheatmap_gini.png copying images... [ 49%] images/other/mouse_Visium_kidney/vignette_200916/6_c_gini_umap.png copying images... [ 49%] images/other/mouse_Visium_kidney/vignette_200916/6_d_violinplot_scran.png copying images... [ 49%] images/other/mouse_Visium_kidney/vignette_200916/6_e_metaheatmap_scran.png copying images... [ 49%] images/other/mouse_Visium_kidney/vignette_200916/6_f_scran_umap.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/8_grid.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/9_a_delaunay_network.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/9_b_delaunay_network.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/10_a_spatial_genes_km.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/10_b_spatial_genes_rank.png copying images... [ 51%] images/other/mouse_Visium_kidney/vignette_200916/10_d_Napsa_correlated_genes.png copying images... [ 51%] images/other/mouse_Visium_kidney/vignette_200916/10_e_heatmap_correlated_genes.png copying images... [ 51%] images/other/mouse_Visium_kidney/vignette_200916/10_f_rank_correlated_groups.png copying images... [ 51%] images/other/mouse_Visium_kidney/vignette_200916/10_g_spat_enrichment_score_plots.png copying images... [ 51%] images/other/mouse_Visium_kidney/vignette_200916/10_h_spat_enrichment_score_plots_genes.png copying images... [ 52%] images/other/nanostring_cosmx_subcellular_lung_cancer/Rplot1.png copying images... [ 52%] images/other/nanostring_cosmx_subcellular_lung_cancer/Rplot2.png copying images... [ 52%] images/other/nanostring_cosmx_subcellular_lung_cancer/Rplothist.png copying images... [ 52%] images/other/nanostring_cosmx_subcellular_lung_cancer/Rplot3.png copying images... [ 52%] images/other/nanostring_cosmx_subcellular_lung_cancer/Rplot5.png copying images... [ 52%] images/other/nanostring_cosmx_subcellular_lung_cancer/4-HVFplot.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/5-HVFplot.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/6-screePlot.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/7-PCA.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/8-UMAP.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/9-UMAP.png copying images... [ 54%] images/other/nanostring_cosmx_subcellular_lung_cancer/10-spatDimPlot2D.png copying images... [ 54%] images/other/nanostring_cosmx_subcellular_lung_cancer/spatinsituclustered.png copying images... [ 54%] images/other/nanostring_cosmx_subcellular_lung_cancer/12-spatInSituPlotPoints.png copying images... [ 54%] images/other/nanostring_cosmx_subcellular_lung_cancer/13-spatFeatPlot2D.png copying images... [ 54%] images/other/nanostring_cosmx_subcellular_lung_cancer/14-violinPlot.png copying images... [ 55%] images/other/nanostring_cosmx_subcellular_lung_cancer/6-plotMetaDataHeatmap.png copying images... [ 55%] images/other/nanostring_cosmx_subcellular_lung_cancer/15-UMAP.png copying images... [ 55%] images/other/nanostring_cosmx_subcellular_lung_cancer/16-spatDimPlot2D.png copying images... [ 55%] images/other/nanostring_cosmx_subcellular_lung_cancer/17-spatInSituPlotPoints.png copying images... [ 55%] images/other/nanostring_cosmx_subcellular_lung_cancer/18-spatInSituPlotPoints.png copying images... [ 56%] images/other/general_figs/osmfish_image_demo.png copying images... [ 56%] images/other//mouse_osmfish_ss_cortex/vignette_200915/2_a_original_clusters.png copying images... [ 56%] images/other/mouse_osmfish_ss_cortex/vignette_200915/2_b_original_regions.png copying images... [ 56%] images/other/mouse_osmfish_ss_cortex/vignette_200915/2_c_clusterID.png copying images... [ 56%] images/other/mouse_osmfish_ss_cortex/vignette_200915/2_d_total_expr_limits.png copying images... [ 56%] images/other/mouse_osmfish_ss_cortex/vignette_200915/3_a_screeplot.png copying images... [ 57%] images/other/mouse_osmfish_ss_cortex/vignette_200915/3_b_PCA_reduction.png copying images... [ 57%] images/other/mouse_osmfish_ss_cortex/vignette_200915/3_c_UMAP_reduction.png copying images... [ 57%] images/other/mouse_osmfish_ss_cortex/vignette_200915/3_d_UMAP_reduction_expression.png copying images... [ 57%] images/other/mouse_osmfish_ss_cortex/vignette_200915/3_e_tSNE_reduction.png copying images... [ 57%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_a_UMAP_hclust.png copying images... [ 58%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_b_UMAP_kmeans.png copying images... [ 58%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_c_UMAP_leiden.png copying images... [ 58%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_d_UMAP_leiden_merged.png copying images... [ 58%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_e_heatmap.png copying images... [ 58%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_f_dendro.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915//5_a_covis_leiden.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915/5_b_covis_leiden_m.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915/5_c_covis_leiden_merged_selected.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915/5_d_total_expr.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915/6_a_violinplot.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/6_b_metaheatmap.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/6_e_metaheatmap_all_genes.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/6_f_metaheatmap_all_genes_names.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/7_a_annotation_leiden_merged_detailed.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/7_b_annotation_leiden_merged_coarse.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/7_c_clusterHeatmap_det_cell_types.png copying images... [ 61%] images/other/mouse_osmfish_ss_cortex/vignette_200915/7_d_heatamp_det_cell_types.png copying images... [ 61%] images/other/mouse_osmfish_ss_cortex/vignette_200915/7_e_metaheatmap.png copying images... [ 61%] images/other/mouse_osmfish_ss_cortex/vignette_200915/8_grid_det_cell_types.png copying images... [ 61%] images/other/mouse_osmfish_ss_cortex/vignette_200915/9_spatial_network_k10.png copying images... [ 61%] images/other/mouse_osmfish_ss_cortex/vignette_200915/10_a_spatial_genes_km.png copying images... [ 62%] images/other/mouse_osmfish_ss_cortex/vignette_200915/11_a_barplot_cell_cell_enrichment.png copying images... [ 62%] images/other/mouse_osmfish_ss_cortex/vignette_200915/11_b_heatmap_cell_cell_enrichment.png copying images... [ 62%] images/other/mouse_osmfish_ss_cortex/vignette_200915/11_c_network_cell_cell_enrichment.png copying images... [ 62%] images/other/mouse_osmfish_ss_cortex/vignette_200915/11_d_cell_cell_enrichment_selected.png copying images... [ 62%] images/other/general_figs/construction-boy.png copying images... [ 63%] images/other/resolve_bc_subcellular/0-spatPlot2D.png copying images... [ 63%] images/other/resolve_bc_subcellular/1-spatPlot2D.png copying images... [ 63%] images/other/resolve_bc_subcellular/69-spatPlot2D.png copying images... [ 63%] images/other/resolve_bc_subcellular/4-HVFplot.png copying images... [ 63%] images/other/resolve_bc_subcellular/5-HVFplot.png copying images... [ 64%] images/other/resolve_bc_subcellular/6-screePlot.png copying images... [ 64%] images/other/resolve_bc_subcellular/7-PCA.png copying images... [ 64%] images/other/resolve_bc_subcellular/8-UMAP.png copying images... [ 64%] images/other/resolve_bc_subcellular/39-UMAP.png copying images... [ 64%] images/other/resolve_bc_subcellular/51-spatDimPlot2D.png copying images... [ 64%] images/other/resolve_bc_subcellular/72-Heatmap.png copying images... [ 65%] images/other/resolve_bc_subcellular/12-showClusterDendrogram.png copying images... [ 65%] images/other/resolve_bc_subcellular/13-spatPlot2D.png copying images... [ 65%] images/other/resolve_bc_subcellular/54-spatInSituPlotPoints.png copying images... [ 65%] images/other/resolve_bc_subcellular/16-spatInSituPlotPoints.png copying images... [ 65%] images/other/resolve_bc_subcellular/17-spatInSituPlotPoints.png copying images... [ 66%] images/other/resolve_bc_subcellular/18-spatInSituPlotPoints.png copying images... [ 66%] images/other/resolve_bc_subcellular/19-spatInSituPlotPoints.png copying images... [ 66%] images/other/resolve_bc_subcellular/21-spatInSituPlotPoints.png copying images... [ 66%] images/other/resolve_bc_subcellular/61-spatInSituPlotPoints.png copying images... [ 66%] images/other/resolve_bc_subcellular/22-spatInSituPlotPoints.png copying images... [ 67%] images/other/resolve_bc_subcellular/66-spatInSituPlotPoints.png copying images... [ 67%] images/other/resolve_bc_subcellular/43-spatInSituPlotPoints.png copying images... [ 67%] images/other/general_figs/cortex_svz_location_fields.png copying images... [ 67%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/2_a_spatplot.png copying images... [ 67%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/3_a_HVGplot.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/3_b_screeplot.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/3_c_PCA_reduction.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/3_d_UMAP_reduction.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/3_e_tSNE_reduction.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/4_a_UMAP_leiden.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/4_b_UMAP_leiden_subcluster.png copying images... [ 69%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/4_c_heatmap.png copying images... [ 69%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/4_d_dendro.png copying images... [ 69%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/5_a_covis_leiden.png copying images... [ 69%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/5_b_covis_leiden_selected.png copying images... [ 69%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/6_a_violinplot_gini.png copying images... [ 70%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/6_b_metaheatmap_gini.png copying images... [ 70%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/7_a_violinplot.png copying images... [ 70%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/7_b_covisualization.png copying images... [ 70%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/7_c_heatmap.png copying images... [ 70%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/7_d_heatmap_selected.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/8_a_grid.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/9_a_spatial_network_delaunay.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/9_b_spatial_network_k3.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/9_c_spatial_network_k10.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/9_d_spatial_network_dist.png copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/10_a_spatialgenes_km.png copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/10_b_spatialcoexpression_heatmap.png copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/10_c_spatialcoexpression_rank.png copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/10_d_spatialcoexpression_metagenes.png copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/11_HMRF_2_k9_b.28.pdf copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_a_barplot_cell_cell_enrichment.png copying images... [ 73%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_b_heatmap_cell_cell_enrichment.png copying images... [ 73%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_c_network_cell_cell_enrichment.png copying images... [ 73%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_d_network_cell_cell_enrichment_self.pdf copying images... [ 73%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_e_cell_cell_enrichment_selected.png copying images... [ 73%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_f_cell_cell_enrichment_sel_vs_not.png copying images... [ 74%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/13_a_CPG_dotplot.png copying images... [ 74%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/13_b_ICG_barplot.png copying images... [ 74%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/14_a_communication_dotplot.png copying images... [ 74%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/14_b_expr_vs_spatial_expression_rank.png copying images... [ 74%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/14_c_spatial_recovery_expression_rank.png copying images... [ 75%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/14_d_expr_vs_spatial_activity.png copying images... [ 75%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/14_e_spatial_recovery_activity.png copying images... [ 75%] images/other/singlecell_rna_seq_integration/4_cluster_without_integration.png copying images... [ 75%] images/other/singlecell_rna_seq_integration/4_list_without_integration.png copying images... [ 75%] images/other/singlecell_rna_seq_integration/4_cluster_with_integration.png copying images... [ 76%] images/other/singlecell_rna_seq_integration/4_list_with_integration.png copying images... [ 76%] images/other/singlecell_rna_seq/3_scree_plot.png copying images... [ 76%] images/other/singlecell_rna_seq/4_Cluster.png copying images... [ 76%] images/other/singlecell_rna_seq/5_a_metaheatmap.png copying images... [ 76%] images/other/singlecell_rna_seq/5_b_violinplot_scran.png copying images... [ 76%] images/other/singlecell_rna_seq/6_featureplot.png copying images... [ 77%] images/other/singlecell_rna_seq/7_Annotation.png copying images... [ 77%] images/other/singlecell_rna_seq/8a_scree_plot.png copying images... [ 77%] images/other/singlecell_rna_seq/8b_Cluster.png copying images... [ 77%] images/other/singlecell_rna_seq/8_c_metaheatmap.png copying images... [ 77%] images/other/singlecell_rna_seq/8d_Annotation.png copying images... [ 78%] images/other/visium_prostate_integration/Visium_FFPE_Human_Normal_Prostate_image.png copying images... [ 78%] images/other/visium_prostate_integration/Visium_FFPE_Human_Prostate_Cancer_image.png copying images... [ 78%] images/other/visium_prostate_integration/1a_plot.png copying images... [ 78%] images/other/visium_prostate_integration/1b_plot.png copying images... [ 78%] images/other/visium_prostate_integration/1c_plot.png copying images... [ 79%] images/other/visium_prostate_integration/2a_plot.png copying images... [ 79%] images/other/visium_prostate_integration/2b_plot.png copying images... [ 79%] images/other/visium_prostate_integration/2c_plot.png copying images... [ 79%] images/other/visium_prostate_integration/3a_screeplot.png copying images... [ 79%] images/other/visium_prostate_integration/4.1a_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4.1b_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4.1c_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4.2a_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4.2b_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4.2c_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4_w_o_integration_plot.png copying images... [ 81%] images/other/visium_prostate_integration/5a_PAGE_plot.png copying images... [ 81%] images/other/visium_prostate_integration/5b_HyperGeometric_plot.png copying images... [ 81%] images/other/visium_prostate_integration/5c_Rank_plot.png copying images... [ 81%] images/other/visium_prostate_integration/5d_DWLS_plot.png copying images... [ 81%] images/other/vizgen_mouse_brain/0-spatPlot2D.png copying images... [ 82%] images/other/vizgen_mouse_brain/1-spatPlot2D.png copying images... [ 82%] images/other/vizgen_mouse_brain/2-spatPlot2D.png copying images... [ 82%] images/other/vizgen_mouse_brain/3-screePlot.png copying images... [ 82%] images/other/vizgen_mouse_brain/4-PCA.png copying images... [ 82%] images/other/vizgen_mouse_brain/5-UMAP.png copying images... [ 83%] images/other/vizgen_mouse_brain/6-UMAP.png copying images... [ 83%] images/other/vizgen_mouse_brain/7-spatPlot2D.png copying images... [ 83%] images/other/vizgen_mouse_brain/8-spatPlot2D.png copying images... [ 83%] images/other/vizgen_mouse_brain/9-spatFeatPlot2D.png copying images... [ 83%] images/other/vizgen_mouse_brain/10-spatPlot2D.png copying images... [ 84%] images/other/vizgen_mouse_brain/11-spatInSituPlotPoints.png copying images... [ 84%] images/other/vizgen_mouse_brain/12-spatInSituPlotPoints.png copying images... [ 84%] subsections/../images/detailed_workflow/giotto_ip.png copying images... [ 84%] subsections/../images/detailed_workflow/giotto_ds.png copying images... [ 84%] subsections/../images/detailed_workflow/giotto_analysis.png copying images... [ 84%] subsections/../images/detailed_workflow/giotto_viz.png copying images... [ 85%] images/howtos/subset_giotto/vignette_1/1_whole_brain.png copying images... [ 85%] images/howtos/subset_giotto/vignette_1/2_whole_brain_clus4.png copying images... [ 85%] images/howtos/subset_giotto/vignette_1/3_whole_brain_clus4_noOther.png copying images... [ 85%] images/howtos/subset_giotto/vignette_1/4_whole_brain_by_group_leiden_1.png copying images... [ 85%] images/howtos/subset_giotto/vignette_1/4_whole_brain_by_group_leiden_2.png copying images... [ 86%] images/howtos/subset_giotto/vignette_1/5_whole_brain_HMRF.png copying images... [ 86%] images/howtos/subset_giotto/vignette_1/5_whole_brain_by_group_HMRF_1.png copying images... [ 86%] images/howtos/subset_giotto/vignette_1/5_whole_brain_by_group_HMRF_2.png copying images... [ 86%] images/howtos/subset_giotto/vignette_1/6_subset_brain.png copying images... [ 86%] images/howtos/subset_giotto/vignette_1/6_subset_brain_nr_genes.png copying images... [ 87%] images/howtos/subset_giotto/vignette_1/7_DG_loc_subset.png copying images... [ 87%] images/howtos/instructions_and_plotting/vignette_1/original_clusters_black.png copying images... [ 87%] images/howtos/work_with_multiple_analyses/ppt_store_multiple_analyses2.png copying images... [ 87%] images/howtos/work_with_multiple_analyses/vignette_1/1_loess_hvg.png copying images... [ 87%] images/howtos/work_with_multiple_analyses/vignette_1/1_group_hvg.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/1_hvg_table.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/2_loess_pca.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/2_group_pca.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/3_loess_umap.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/3_group_umap.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/4_spatial_network.png copying images... [ 89%] images/howtos/work_with_multiple_analyses/vignette_1/4_large_network.png copying images... [ 89%] images/howtos/work_with_multiple_analyses/vignette_1/4_distance_network.png copying images... [ 89%] images/howtos/work_with_multiple_analyses/vignette_1/5_large_network_genes.png copying images... [ 89%] images/howtos/work_with_multiple_analyses/vignette_1/5_large_distance_network_genes.png copying images... [ 89%] images/howtos/voronoi_plots/vignette_1/1_voronoi.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/2_voronoi_no_others.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/3_voronoi_no_others_black_border.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/4_voronoi_spat_dim.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/5_voronoi_neighbors.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/6_original_points.png copying images... [ 91%] images/howtos/voronoi_plots/vignette_1/7_voronoi_genes.png copying images... [ 91%] images/howtos/voronoi_plots/vignette_1/8_voronoi_gene_black_bg.png copying images... [ 91%] images/howtos/giotto_images/vignette_1/2_a_spatplot.png copying images... [ 91%] images/howtos/giotto_images/vignette_1/2_b_spatplot_image.png copying images... [ 91%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_1.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_2.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_3.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_4.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_5.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_6.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_7.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_8.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_9.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_10.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_11.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/2_d_original_plot.png copying images... [ 94%] images/howtos/giotto_images/vignette_1/3_a_background_colors.png copying images... [ 94%] images/howtos/giotto_images/vignette_1/3_b_black_background.png copying images... [ 94%] images/howtos/giotto_images/vignette_1/3_c_white_background.png copying images... [ 94%] images/howtos/giotto_images/vignette_1/4_a_external_image_negated.png copying images... [ 94%] images/howtos/giotto_images/vignette_1/4_b_external_image_charcoal.png copying images... [ 95%] images/howtos/giotto_images/vignette_1/5_1_a_spatial_locations.png copying images... [ 95%] images/howtos/giotto_images/vignette_1/5_1_b_nr_genes.png copying images... [ 95%] images/howtos/giotto_images/vignette_1/5_1_c_nr_genes_black_bg.png copying images... [ 95%] images/howtos/giotto_images/vignette_1/5_1_d_nr_genes_charc_bg.png copying images... [ 95%] images/howtos/giotto_images/vignette_1/5_2_a_UMAP_reduction.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_3_a_UMAP_leiden.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_4_a_covis_leiden_black.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_4_b_covis_leiden_negated.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_4_c_covis_leiden_charc.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_5_a_spatgene_charc_vor.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_5_b_spatgene_charc_vor.png copying images... [ 97%] images/howtos/giotto_images/vignette_1/5_6_a_subset_spatgene_charc.png copying images... [ 97%] images/howtos/giotto_images/vignette_1/5_6_b_subset_spatgene_charc_vor.png copying images... [ 97%] images/GitHub_Logo.png copying images... [ 97%] images/img_terra/01_environments.png copying images... [ 97%] images/img_terra/01_vm.png copying images... [ 98%] images/img_terra/02_docker.png copying images... [ 98%] images/img_terra/03_upload.png copying images... [ 98%] images/img_terra/03_view.png copying images... [ 98%] images/img_terra/03_googlecloud.png copying images... [ 98%] images/img_terra/03_url.png copying images... [ 99%] images/img_terra/03_cloud.png copying images... [ 99%] images/img_terra/04_share.png copying images... [ 99%] images/trygiotto/Binder_1.png copying images... [ 99%] images/trygiotto/Binder_2.png copying images... [ 99%] images/trygiotto/Binder_3.png copying images... [100%] images/trygiotto/Binder_4.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 694 warnings. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2022-07-14T19:43:08.164342Z, end-time: 2022-07-14T19:43:32.800971Z, duration: 24, exit-code: 0 python -m sphinx -T -E -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v3.4.3 loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 675 added, 0 changed, 0 removed reading sources... [ 0%] Workflow reading sources... [ 0%] additionalinformation reading sources... [ 0%] contribute reading sources... [ 0%] datasets reading sources... [ 0%] development reading sources... [ 0%] documentation reading sources... [ 1%] errorsfaqsandtips reading sources... [ 1%] faqs reading sources... [ 1%] gettingstarted reading sources... [ 1%] giottoworkflowanalyses reading sources... [ 1%] github_issues reading sources... [ 1%] index reading sources... [ 1%] subsections/citing_giotto reading sources... [ 2%] subsections/code_of_conduct reading sources... [ 2%] subsections/datasets/STARmap_mouse_cortex reading sources... [ 2%] subsections/datasets/human_CyCIF_PDAC reading sources... [ 2%] subsections/datasets/merFISH_hypot_preopt_region reading sources... [ 2%] subsections/datasets/mini_3D_STARmap reading sources... [ 2%] subsections/datasets/mini_seqFISH reading sources... [ 2%] subsections/datasets/mini_visium reading sources... [ 3%] subsections/datasets/mouse_CODEX_spleen reading sources... [ 3%] subsections/datasets/mouse_visium_brain reading sources... [ 3%] subsections/datasets/mouse_visium_kidney reading sources... [ 3%] subsections/datasets/nanostring_lung_12 reading sources... [ 3%] subsections/datasets/nanostring_overview reading sources... [ 3%] subsections/datasets/osmFISH_mouse_SS_cortex reading sources... [ 4%] subsections/datasets/other_technologies_coming_soon reading sources... [ 4%] subsections/datasets/resolve_bc_210928 reading sources... [ 4%] subsections/datasets/seqFISH_cortex reading sources... [ 4%] subsections/datasets/singlecell_prostate_integration reading sources... [ 4%] subsections/datasets/singlecell_prostate_standard reading sources... [ 4%] subsections/datasets/tcyCIF reading sources... [ 4%] subsections/datasets/visium_prostate_integration reading sources... [ 5%] subsections/datasets/vizgen_mouse_brain reading sources... [ 5%] subsections/detailed_workflow reading sources... [ 5%] subsections/license reading sources... [ 5%] subsections/md_rst/DT_removeNA reading sources... [ 5%] subsections/md_rst/FSV_show reading sources... [ 5%] subsections/md_rst/OR_test_fnc reading sources... [ 5%] subsections/md_rst/PAGEEnrich reading sources... [ 6%] subsections/md_rst/PAGE_DT_method reading sources... [ 6%] subsections/md_rst/adapt_aspect_ratio reading sources... [ 6%] subsections/md_rst/addCellIntMetadata reading sources... [ 6%] subsections/md_rst/addCellMetadata reading sources... [ 6%] subsections/md_rst/addCellStatistics reading sources... [ 6%] subsections/md_rst/addCellsFromPolygon reading sources... [ 6%] subsections/md_rst/addFeatMetadata reading sources... [ 7%] subsections/md_rst/addFeatStatistics reading sources... [ 7%] subsections/md_rst/addFeatsPerc reading sources... [ 7%] subsections/md_rst/addGeneMetadata reading sources... [ 7%] subsections/md_rst/addGeneStatistics reading sources... [ 7%] subsections/md_rst/addGenesPerc reading sources... [ 7%] subsections/md_rst/addGiottoImage reading sources... [ 8%] subsections/md_rst/addGiottoImageMG reading sources... [ 8%] subsections/md_rst/addGiottoImageToSpatPlot reading sources... [ 8%] subsections/md_rst/addGiottoLargeImage reading sources... [ 8%] subsections/md_rst/addGiottoPoints reading sources... [ 8%] subsections/md_rst/addGiottoPolygons reading sources... [ 8%] subsections/md_rst/addHMRF reading sources... [ 8%] subsections/md_rst/addNetworkLayout reading sources... [ 9%] subsections/md_rst/addSpatialCentroidLocations reading sources... [ 9%] subsections/md_rst/addSpatialCentroidLocationsLayer reading sources... [ 9%] subsections/md_rst/addStatistics reading sources... [ 9%] subsections/md_rst/add_img_array_alpha reading sources... [ 9%] subsections/md_rst/adjustGiottoMatrix reading sources... [ 9%] subsections/md_rst/aes_string2 reading sources... [ 9%] subsections/md_rst/all_plots_save_function reading sources... [ 10%] subsections/md_rst/anndataToGiotto reading sources... [ 10%] subsections/md_rst/annotateGiotto reading sources... [ 10%] subsections/md_rst/annotateSpatialGrid reading sources... [ 10%] subsections/md_rst/annotateSpatialNetwork reading sources... [ 10%] subsections/md_rst/annotate_spatlocs_with_spatgrid_2D reading sources... [ 10%] subsections/md_rst/annotate_spatlocs_with_spatgrid_3D reading sources... [ 10%] subsections/md_rst/average_feat_feat_expression_in_groups reading sources... [ 11%] subsections/md_rst/binSpect reading sources... [ 11%] subsections/md_rst/binSpectMulti reading sources... [ 11%] subsections/md_rst/binSpectMultiMatrix reading sources... [ 11%] subsections/md_rst/binSpectSingle reading sources... [ 11%] subsections/md_rst/binSpectSingleMatrix reading sources... [ 11%] subsections/md_rst/calc_cov_group_HVF reading sources... [ 12%] subsections/md_rst/calc_cov_loess_HVF reading sources... [ 12%] subsections/md_rst/calc_spatial_enrichment_DT reading sources... [ 12%] subsections/md_rst/calc_spatial_enrichment_matrix reading sources... [ 12%] subsections/md_rst/calc_spatial_enrichment_minimum reading sources... [ 12%] subsections/md_rst/calc_var_HVF reading sources... [ 12%] subsections/md_rst/calculateHVF reading sources... [ 12%] subsections/md_rst/calculateHVG reading sources... [ 13%] subsections/md_rst/calculateMetaTable reading sources... [ 13%] subsections/md_rst/calculateMetaTableCells reading sources... [ 13%] subsections/md_rst/calculateOverlapParallel reading sources... [ 13%] subsections/md_rst/calculateOverlapRaster reading sources... [ 13%] subsections/md_rst/calculateOverlapSerial reading sources... [ 13%] subsections/md_rst/calculate_centroids_polygons reading sources... [ 13%] subsections/md_rst/calculate_distance_and_weight reading sources... [ 14%] subsections/md_rst/cellProximityBarplot reading sources... [ 14%] subsections/md_rst/cellProximityEnrichment reading sources... [ 14%] subsections/md_rst/cellProximityHeatmap reading sources... [ 14%] subsections/md_rst/cellProximityNetwork reading sources... [ 14%] subsections/md_rst/cellProximitySpatPlot reading sources... [ 14%] subsections/md_rst/cellProximitySpatPlot2D reading sources... [ 14%] subsections/md_rst/cellProximitySpatPlot3D reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot_2D_ggplot reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot_2D_plotly reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot_3D_plotly reading sources... [ 15%] subsections/md_rst/changeGiottoInstructions reading sources... [ 15%] subsections/md_rst/changeImageBg reading sources... [ 16%] subsections/md_rst/checkGiottoEnvironment reading sources... [ 16%] subsections/md_rst/check_spatial_location_data reading sources... [ 16%] subsections/md_rst/clusterCells reading sources... [ 16%] subsections/md_rst/clusterSpatialCorFeats reading sources... [ 16%] subsections/md_rst/clusterSpatialCorGenes reading sources... [ 16%] subsections/md_rst/cluster_enrich_analysis reading sources... [ 16%] subsections/md_rst/colMeans_flex reading sources... [ 17%] subsections/md_rst/colSums_flex reading sources... [ 17%] subsections/md_rst/combCCcom reading sources... [ 17%] subsections/md_rst/combineCPG reading sources... [ 17%] subsections/md_rst/combineCellData reading sources... [ 17%] subsections/md_rst/combineCellProximityGenes reading sources... [ 17%] subsections/md_rst/combineCellProximityGenes_per_interaction reading sources... [ 17%] subsections/md_rst/combineFeatureData reading sources... [ 18%] subsections/md_rst/combineFeatureOverlapData reading sources... [ 18%] subsections/md_rst/combineICG reading sources... [ 18%] subsections/md_rst/combineInteractionChangedGenes reading sources... [ 18%] subsections/md_rst/combineMetadata reading sources... [ 18%] subsections/md_rst/combineSpatialCellFeatureInfo reading sources... [ 18%] subsections/md_rst/combineSpatialCellMetadataInfo reading sources... [ 18%] subsections/md_rst/compatible_spatial_network reading sources... [ 19%] subsections/md_rst/convertEnsemblToGeneSymbol reading sources... [ 19%] subsections/md_rst/convertGiottoLargeImageToMG reading sources... [ 19%] subsections/md_rst/convert_mgImage_to_array_DT reading sources... [ 19%] subsections/md_rst/convert_to_full_spatial_network reading sources... [ 19%] subsections/md_rst/convert_to_reduced_spatial_network reading sources... [ 19%] subsections/md_rst/cor_flex reading sources... [ 20%] subsections/md_rst/createCrossSection reading sources... [ 20%] subsections/md_rst/createGiottoImage reading sources... [ 20%] subsections/md_rst/createGiottoImageOLD reading sources... [ 20%] subsections/md_rst/createGiottoInstructions reading sources... [ 20%] subsections/md_rst/createGiottoLargeImage reading sources... [ 20%] subsections/md_rst/createGiottoLargeImageList reading sources... [ 20%] subsections/md_rst/createGiottoObject reading sources... [ 21%] subsections/md_rst/createGiottoObjectSubcellular reading sources... [ 21%] subsections/md_rst/createGiottoPoints reading sources... [ 21%] subsections/md_rst/createGiottoPolygonsFromDfr reading sources... [ 21%] subsections/md_rst/createGiottoPolygonsFromMask reading sources... [ 21%] subsections/md_rst/createGiottoVisiumObject reading sources... [ 21%] subsections/md_rst/createHeatmap_DT reading sources... [ 21%] subsections/md_rst/createMetafeats reading sources... [ 22%] subsections/md_rst/createMetagenes reading sources... [ 22%] subsections/md_rst/createNearestNetwork reading sources... [ 22%] subsections/md_rst/createSpatialDefaultGrid reading sources... [ 22%] subsections/md_rst/createSpatialDelaunayNetwork reading sources... [ 22%] subsections/md_rst/createSpatialEnrich reading sources... [ 22%] subsections/md_rst/createSpatialFeaturesKNNnetwork reading sources... [ 22%] subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan reading sources... [ 23%] subsections/md_rst/createSpatialGrid reading sources... [ 23%] subsections/md_rst/createSpatialKNNnetwork reading sources... [ 23%] subsections/md_rst/createSpatialNetwork reading sources... [ 23%] subsections/md_rst/create_2d_mesh_grid_line_obj reading sources... [ 23%] subsections/md_rst/create_KNNnetwork_dbscan reading sources... [ 23%] subsections/md_rst/create_average_DT reading sources... [ 24%] subsections/md_rst/create_average_detection_DT reading sources... [ 24%] subsections/md_rst/create_cell_type_random_cell_IDs reading sources... [ 24%] subsections/md_rst/create_cluster_matrix reading sources... [ 24%] subsections/md_rst/create_crossSection_object reading sources... [ 24%] subsections/md_rst/create_delaunayNetwork2D reading sources... [ 24%] subsections/md_rst/create_delaunayNetwork3D reading sources... [ 24%] subsections/md_rst/create_delaunayNetwork_RTriangle reading sources... [ 25%] subsections/md_rst/create_delaunayNetwork_deldir reading sources... [ 25%] subsections/md_rst/create_delaunayNetwork_geometry reading sources... [ 25%] subsections/md_rst/create_delaunayNetwork_geometry_3D reading sources... [ 25%] subsections/md_rst/create_dimObject reading sources... [ 25%] subsections/md_rst/create_featureNetwork_object reading sources... [ 25%] subsections/md_rst/create_genes_to_use_matrix reading sources... [ 25%] subsections/md_rst/create_giotto_points_object reading sources... [ 26%] subsections/md_rst/create_giotto_polygon_object reading sources... [ 26%] subsections/md_rst/create_jackstrawplot reading sources... [ 26%] subsections/md_rst/create_mesh_grid_lines reading sources... [ 26%] subsections/md_rst/create_screeplot reading sources... [ 26%] subsections/md_rst/create_segm_polygons reading sources... [ 26%] subsections/md_rst/create_spatialGridObject reading sources... [ 26%] subsections/md_rst/create_spatialGrid_default_2D reading sources... [ 27%] subsections/md_rst/create_spatialGrid_default_3D reading sources... [ 27%] subsections/md_rst/create_spatialNetworkObject reading sources... [ 27%] subsections/md_rst/create_spatvector_object_from_dfr reading sources... [ 27%] subsections/md_rst/cropGiottoLargeImage reading sources... [ 27%] subsections/md_rst/crossSectionGenePlot reading sources... [ 27%] subsections/md_rst/crossSectionGenePlot3D reading sources... [ 28%] subsections/md_rst/crossSectionPlot reading sources... [ 28%] subsections/md_rst/crossSectionPlot3D reading sources... [ 28%] subsections/md_rst/decide_cluster_order reading sources... [ 28%] subsections/md_rst/density_giottoLargeImage reading sources... [ 28%] subsections/md_rst/depth reading sources... [ 28%] subsections/md_rst/detectSpatialCorFeats reading sources... [ 28%] subsections/md_rst/detectSpatialCorFeatsMatrix reading sources... [ 29%] subsections/md_rst/detectSpatialCorGenes reading sources... [ 29%] subsections/md_rst/detectSpatialPatterns reading sources... [ 29%] subsections/md_rst/determine_cores reading sources... [ 29%] subsections/md_rst/dimCellPlot reading sources... [ 29%] subsections/md_rst/dimCellPlot2D reading sources... [ 29%] subsections/md_rst/dimFeatPlot2D reading sources... [ 29%] subsections/md_rst/dimGenePlot reading sources... [ 30%] subsections/md_rst/dimGenePlot2D reading sources... [ 30%] subsections/md_rst/dimGenePlot3D reading sources... [ 30%] subsections/md_rst/dimPlot reading sources... [ 30%] subsections/md_rst/dimPlot2D reading sources... [ 30%] subsections/md_rst/dimPlot2D_single reading sources... [ 30%] subsections/md_rst/dimPlot3D reading sources... [ 30%] subsections/md_rst/dimPlot_2D_plotly reading sources... [ 31%] subsections/md_rst/dimPlot_3D_plotly reading sources... [ 31%] subsections/md_rst/distGiottoImage reading sources... [ 31%] subsections/md_rst/doCellSegmentation reading sources... [ 31%] subsections/md_rst/doHMRF reading sources... [ 31%] subsections/md_rst/doHclust reading sources... [ 31%] subsections/md_rst/doKmeans reading sources... [ 32%] subsections/md_rst/doLeidenCluster reading sources... [ 32%] subsections/md_rst/doLeidenSubCluster reading sources... [ 32%] subsections/md_rst/doLouvainCluster reading sources... [ 32%] subsections/md_rst/doLouvainCluster_community reading sources... [ 32%] subsections/md_rst/doLouvainCluster_multinet reading sources... [ 32%] subsections/md_rst/doLouvainSubCluster reading sources... [ 32%] subsections/md_rst/doLouvainSubCluster_community reading sources... [ 33%] subsections/md_rst/doLouvainSubCluster_multinet reading sources... [ 33%] subsections/md_rst/doRandomWalkCluster reading sources... [ 33%] subsections/md_rst/doSNNCluster reading sources... [ 33%] subsections/md_rst/doScrubletDetect reading sources... [ 33%] subsections/md_rst/do_cell_proximity_test reading sources... [ 33%] subsections/md_rst/do_limmatest reading sources... [ 33%] subsections/md_rst/do_multi_permuttest_random reading sources... [ 34%] subsections/md_rst/do_page_permutation reading sources... [ 34%] subsections/md_rst/do_permuttest_original reading sources... [ 34%] subsections/md_rst/do_permuttest_random reading sources... [ 34%] subsections/md_rst/do_rank_permutation reading sources... [ 34%] subsections/md_rst/do_spatial_grid_averaging reading sources... [ 34%] subsections/md_rst/do_spatial_knn_smoothing reading sources... [ 34%] subsections/md_rst/do_ttest reading sources... [ 35%] subsections/md_rst/do_wilctest reading sources... [ 35%] subsections/md_rst/dt_to_matrix reading sources... [ 35%] subsections/md_rst/dt_to_spatVector_points reading sources... [ 35%] subsections/md_rst/dt_to_spatVector_polygon reading sources... [ 35%] subsections/md_rst/enrich_analysis reading sources... [ 35%] subsections/md_rst/enrich_deconvolution reading sources... [ 36%] subsections/md_rst/estimateCellCellDistance reading sources... [ 36%] subsections/md_rst/estimateImageBg reading sources... [ 36%] subsections/md_rst/evaluate_expr_matrix reading sources... [ 36%] subsections/md_rst/evaluate_feat_info reading sources... [ 36%] subsections/md_rst/evaluate_provided_spatial_locations reading sources... [ 36%] subsections/md_rst/evaluate_spatial_info reading sources... [ 36%] subsections/md_rst/evaluate_spatial_locations reading sources... [ 37%] subsections/md_rst/evaluate_spatial_locations_OLD reading sources... [ 37%] subsections/md_rst/evaluate_spatial_network reading sources... [ 37%] subsections/md_rst/exportGiottoViewer reading sources... [ 37%] subsections/md_rst/exprCellCellcom reading sources... [ 37%] subsections/md_rst/extend_vector reading sources... [ 37%] subsections/md_rst/extended_gini_fun reading sources... [ 37%] subsections/md_rst/extractNearestNetwork reading sources... [ 38%] subsections/md_rst/extract_points_list reading sources... [ 38%] subsections/md_rst/extract_polygon_list reading sources... [ 38%] subsections/md_rst/fDataDT reading sources... [ 38%] subsections/md_rst/featureNetwork-class reading sources... [ 38%] subsections/md_rst/filterCPG reading sources... [ 38%] subsections/md_rst/filterCellProximityGenes reading sources... [ 38%] subsections/md_rst/filterCombinations reading sources... [ 39%] subsections/md_rst/filterDistributions reading sources... [ 39%] subsections/md_rst/filterGiotto reading sources... [ 39%] subsections/md_rst/filterICF reading sources... [ 39%] subsections/md_rst/filterICG reading sources... [ 39%] subsections/md_rst/filterInteractionChangedFeats reading sources... [ 39%] subsections/md_rst/filterInteractionChangedGenes reading sources... [ 40%] subsections/md_rst/filter_network reading sources... [ 40%] subsections/md_rst/findCPG reading sources... [ 40%] subsections/md_rst/findCellProximityFeats_per_interaction reading sources... [ 40%] subsections/md_rst/findCellProximityGenes reading sources... [ 40%] subsections/md_rst/findGiniMarkers reading sources... [ 40%] subsections/md_rst/findGiniMarkers_one_vs_all reading sources... [ 40%] subsections/md_rst/findICF reading sources... [ 41%] subsections/md_rst/findICG reading sources... [ 41%] subsections/md_rst/findInteractionChangedFeats reading sources... [ 41%] subsections/md_rst/findInteractionChangedGenes reading sources... [ 41%] subsections/md_rst/findMarkers reading sources... [ 41%] subsections/md_rst/findMarkers_one_vs_all reading sources... [ 41%] subsections/md_rst/findMastMarkers reading sources... [ 41%] subsections/md_rst/findMastMarkers_one_vs_all reading sources... [ 42%] subsections/md_rst/findNetworkNeighbors reading sources... [ 42%] subsections/md_rst/findScranMarkers reading sources... [ 42%] subsections/md_rst/findScranMarkers_one_vs_all reading sources... [ 42%] subsections/md_rst/find_dampening_constant reading sources... [ 42%] subsections/md_rst/find_grid_2D reading sources... [ 42%] subsections/md_rst/find_grid_3D reading sources... [ 42%] subsections/md_rst/find_grid_x reading sources... [ 43%] subsections/md_rst/find_grid_y reading sources... [ 43%] subsections/md_rst/find_grid_z reading sources... [ 43%] subsections/md_rst/find_terra_writeRaster_dataType reading sources... [ 43%] subsections/md_rst/find_x_y_ranges reading sources... [ 43%] subsections/md_rst/fix_multipart_geoms reading sources... [ 43%] subsections/md_rst/flex_lapply reading sources... [ 44%] subsections/md_rst/general_save_function reading sources... [ 44%] subsections/md_rst/get10Xmatrix reading sources... [ 44%] subsections/md_rst/get10XmatrixOLD reading sources... [ 44%] subsections/md_rst/get10Xmatrix_h5 reading sources... [ 44%] subsections/md_rst/getCellsFromPolygon reading sources... [ 44%] subsections/md_rst/getClusterSimilarity reading sources... [ 44%] subsections/md_rst/getDendrogramSplits reading sources... [ 45%] subsections/md_rst/getDistinctColors reading sources... [ 45%] subsections/md_rst/getSpatialDataset reading sources... [ 45%] subsections/md_rst/get_NearestNetwork reading sources... [ 45%] subsections/md_rst/get_adj_rescale_img reading sources... [ 45%] subsections/md_rst/get_args reading sources... [ 45%] subsections/md_rst/get_cross_section_coordinates reading sources... [ 45%] subsections/md_rst/get_dimReduction reading sources... [ 46%] subsections/md_rst/get_distance reading sources... [ 46%] subsections/md_rst/get_expression_values reading sources... [ 46%] subsections/md_rst/get_feature_info reading sources... [ 46%] subsections/md_rst/get_giottoImage reading sources... [ 46%] subsections/md_rst/get_giottoImage_MG reading sources... [ 46%] subsections/md_rst/get_giottoLargeImage reading sources... [ 46%] subsections/md_rst/get_img_corners reading sources... [ 47%] subsections/md_rst/get_img_minmax reading sources... [ 47%] subsections/md_rst/get_os reading sources... [ 47%] subsections/md_rst/get_polygon_info reading sources... [ 47%] subsections/md_rst/get_sectionThickness reading sources... [ 47%] subsections/md_rst/get_spatialGrid reading sources... [ 47%] subsections/md_rst/get_spatialNetwork reading sources... [ 48%] subsections/md_rst/get_spatial_enrichment reading sources... [ 48%] subsections/md_rst/get_spatial_locations reading sources... [ 48%] subsections/md_rst/ggplot_save_function reading sources... [ 48%] subsections/md_rst/giotto-class reading sources... [ 48%] subsections/md_rst/giottoImage-class reading sources... [ 48%] subsections/md_rst/giottoLargeImage-class reading sources... [ 48%] subsections/md_rst/giottoPoints-class reading sources... [ 49%] subsections/md_rst/giottoPolygon-class reading sources... [ 49%] subsections/md_rst/giottoToSeurat reading sources... [ 49%] subsections/md_rst/giotto_point reading sources... [ 49%] subsections/md_rst/heatmSpatialCorFeats reading sources... [ 49%] subsections/md_rst/heatmSpatialCorGenes reading sources... [ 49%] subsections/md_rst/hyperGeometricEnrich reading sources... [ 49%] subsections/md_rst/identify_background_range_polygons reading sources... [ 50%] subsections/md_rst/insertCrossSectionGenePlot3D reading sources... [ 50%] subsections/md_rst/insertCrossSectionSpatPlot3D reading sources... [ 50%] subsections/md_rst/installGiottoEnvironment reading sources... [ 50%] subsections/md_rst/install_giotto_environment reading sources... [ 50%] subsections/md_rst/install_giotto_environment_specific reading sources... [ 50%] subsections/md_rst/jackstrawPlot reading sources... [ 50%] subsections/md_rst/joinGiottoObjects reading sources... [ 51%] subsections/md_rst/join_cell_meta reading sources... [ 51%] subsections/md_rst/join_expression_matrices reading sources... [ 51%] subsections/md_rst/join_spatlocs reading sources... [ 51%] subsections/md_rst/kmeans_arma_binarize reading sources... [ 51%] subsections/md_rst/kmeans_arma_subset_binarize reading sources... [ 51%] subsections/md_rst/kmeans_binarize reading sources... [ 52%] subsections/md_rst/kmeans_binarize_wrapper reading sources... [ 52%] subsections/md_rst/lapply_flex reading sources... [ 52%] subsections/md_rst/libNorm_giotto reading sources... [ 52%] subsections/md_rst/list_cell_metadata reading sources... [ 52%] subsections/md_rst/list_dim_reductions reading sources... [ 52%] subsections/md_rst/list_dim_reductions_names reading sources... [ 52%] subsections/md_rst/list_expression reading sources... [ 53%] subsections/md_rst/list_expression_names reading sources... [ 53%] subsections/md_rst/list_feat_metadata reading sources... [ 53%] subsections/md_rst/list_feature_info reading sources... [ 53%] subsections/md_rst/list_feature_info_names reading sources... [ 53%] subsections/md_rst/list_giotto_data reading sources... [ 53%] subsections/md_rst/list_images reading sources... [ 53%] subsections/md_rst/list_images_names reading sources... [ 54%] subsections/md_rst/list_spatial_enrichments reading sources... [ 54%] subsections/md_rst/list_spatial_enrichments_names reading sources... [ 54%] subsections/md_rst/list_spatial_grids reading sources... [ 54%] subsections/md_rst/list_spatial_grids_names reading sources... [ 54%] subsections/md_rst/list_spatial_info reading sources... [ 54%] subsections/md_rst/list_spatial_info_names reading sources... [ 54%] subsections/md_rst/list_spatial_locations reading sources... [ 55%] subsections/md_rst/list_spatial_locations_names reading sources... [ 55%] subsections/md_rst/list_spatial_networks reading sources... [ 55%] subsections/md_rst/list_spatial_networks_names reading sources... [ 55%] subsections/md_rst/loadHMRF reading sources... [ 55%] subsections/md_rst/logNorm_giotto reading sources... [ 55%] subsections/md_rst/makeSignMatrixDWLS reading sources... [ 56%] subsections/md_rst/makeSignMatrixDWLSfromMatrix reading sources... [ 56%] subsections/md_rst/makeSignMatrixPAGE reading sources... [ 56%] subsections/md_rst/makeSignMatrixRank reading sources... [ 56%] subsections/md_rst/make_simulated_network reading sources... [ 56%] subsections/md_rst/mean_expr_det_test reading sources... [ 56%] subsections/md_rst/mean_flex reading sources... [ 56%] subsections/md_rst/mergeClusters reading sources... [ 57%] subsections/md_rst/merge_spatial_locs_feat_info reading sources... [ 57%] subsections/md_rst/mini_giotto_3D reading sources... [ 57%] subsections/md_rst/mini_giotto_multi_cell reading sources... [ 57%] subsections/md_rst/mini_giotto_single_cell reading sources... [ 57%] subsections/md_rst/my_arowMeans reading sources... [ 57%] subsections/md_rst/my_growMeans reading sources... [ 57%] subsections/md_rst/my_rowMeans reading sources... [ 58%] subsections/md_rst/mygini_fun reading sources... [ 58%] subsections/md_rst/nnDT_to_kNN reading sources... [ 58%] subsections/md_rst/node_clusters reading sources... [ 58%] subsections/md_rst/normalizeGiotto reading sources... [ 58%] subsections/md_rst/optimize_deconvolute_dwls reading sources... [ 58%] subsections/md_rst/optimize_solveDampenedWLS reading sources... [ 58%] subsections/md_rst/overlapToMatrix reading sources... [ 59%] subsections/md_rst/overlapToMatrixMultiPoly reading sources... [ 59%] subsections/md_rst/overlap_points_per_polygon reading sources... [ 59%] subsections/md_rst/overlap_points_per_polygon_wrapped reading sources... [ 59%] subsections/md_rst/overlap_points_single_polygon reading sources... [ 59%] subsections/md_rst/pDataDT reading sources... [ 59%] subsections/md_rst/package_check reading sources... [ 60%] subsections/md_rst/pca_giotto reading sources... [ 60%] subsections/md_rst/pipe reading sources... [ 60%] subsections/md_rst/plotCCcomDotplot reading sources... [ 60%] subsections/md_rst/plotCCcomHeatmap reading sources... [ 60%] subsections/md_rst/plotCPG reading sources... [ 60%] subsections/md_rst/plotCellProximityGenes reading sources... [ 60%] subsections/md_rst/plotCombineCCcom reading sources... [ 61%] subsections/md_rst/plotCombineCPG reading sources... [ 61%] subsections/md_rst/plotCombineCellCellCommunication reading sources... [ 61%] subsections/md_rst/plotCombineCellProximityGenes reading sources... [ 61%] subsections/md_rst/plotCombineICG reading sources... [ 61%] subsections/md_rst/plotCombineInteractionChangedGenes reading sources... [ 61%] subsections/md_rst/plotGiottoImage reading sources... [ 61%] subsections/md_rst/plotHeatmap reading sources... [ 62%] subsections/md_rst/plotICF reading sources... [ 62%] subsections/md_rst/plotICG reading sources... [ 62%] subsections/md_rst/plotInteractionChangedFeats reading sources... [ 62%] subsections/md_rst/plotInteractionChangedGenes reading sources... [ 62%] subsections/md_rst/plotInteractivePolygons reading sources... [ 62%] subsections/md_rst/plotMetaDataCellsHeatmap reading sources... [ 62%] subsections/md_rst/plotMetaDataHeatmap reading sources... [ 63%] subsections/md_rst/plotPCA reading sources... [ 63%] subsections/md_rst/plotPCA_2D reading sources... [ 63%] subsections/md_rst/plotPCA_3D reading sources... [ 63%] subsections/md_rst/plotRankSpatvsExpr reading sources... [ 63%] subsections/md_rst/plotRecovery reading sources... [ 63%] subsections/md_rst/plotRecovery_sub reading sources... [ 64%] subsections/md_rst/plotStatDelaunayNetwork reading sources... [ 64%] subsections/md_rst/plotTSNE reading sources... [ 64%] subsections/md_rst/plotTSNE_2D reading sources... [ 64%] subsections/md_rst/plotTSNE_3D reading sources... [ 64%] subsections/md_rst/plotUMAP reading sources... [ 64%] subsections/md_rst/plotUMAP_2D reading sources... [ 64%] subsections/md_rst/plotUMAP_3D reading sources... [ 65%] subsections/md_rst/plot_auto_largeImage_resample reading sources... [ 65%] subsections/md_rst/plot_cell_polygon_layer reading sources... [ 65%] subsections/md_rst/plot_feature_hexbin_layer reading sources... [ 65%] subsections/md_rst/plot_feature_points_layer reading sources... [ 65%] subsections/md_rst/plot_feature_raster_density_layer reading sources... [ 65%] subsections/md_rst/plot_giottoImage_MG reading sources... [ 65%] subsections/md_rst/plot_giottoLargeImage reading sources... [ 66%] subsections/md_rst/plot_network_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_point_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_point_layer_ggplot_noFILL reading sources... [ 66%] subsections/md_rst/plot_spat_image_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_spat_point_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_spat_point_layer_ggplot_noFILL reading sources... [ 66%] subsections/md_rst/plot_spat_scatterpie_layer_ggplot reading sources... [ 67%] subsections/md_rst/plot_spat_voronoi_layer_ggplot reading sources... [ 67%] subsections/md_rst/plotly_axis_scale_2D reading sources... [ 67%] subsections/md_rst/plotly_axis_scale_3D reading sources... [ 67%] subsections/md_rst/plotly_grid reading sources... [ 67%] subsections/md_rst/plotly_network reading sources... [ 67%] subsections/md_rst/polygon_to_raster reading sources... [ 68%] subsections/md_rst/processGiotto reading sources... [ 68%] subsections/md_rst/projection_fun reading sources... [ 68%] subsections/md_rst/rankEnrich reading sources... [ 68%] subsections/md_rst/rankSpatialCorGroups reading sources... [ 68%] subsections/md_rst/rank_binarize reading sources... [ 68%] subsections/md_rst/rank_binarize_wrapper reading sources... [ 68%] subsections/md_rst/readExprMatrix reading sources... [ 69%] subsections/md_rst/readGiottoInstructions reading sources... [ 69%] subsections/md_rst/readPolygonFilesVizgen reading sources... [ 69%] subsections/md_rst/readPolygonFilesVizgenHDF5 reading sources... [ 69%] subsections/md_rst/read_crossSection reading sources... [ 69%] subsections/md_rst/read_dimension_reduction reading sources... [ 69%] subsections/md_rst/read_expression_data reading sources... [ 69%] subsections/md_rst/read_nearest_networks reading sources... [ 70%] subsections/md_rst/read_spatial_enrichment reading sources... [ 70%] subsections/md_rst/read_spatial_location_data reading sources... [ 70%] subsections/md_rst/read_spatial_networks reading sources... [ 70%] subsections/md_rst/reconnectGiottoImage reading sources... [ 70%] subsections/md_rst/reconnect_giottoImage_MG reading sources... [ 70%] subsections/md_rst/reconnect_giottoLargeImage reading sources... [ 70%] subsections/md_rst/reconnect_image_object reading sources... [ 71%] subsections/md_rst/reg_img_minmax_finder reading sources... [ 71%] subsections/md_rst/registerGiottoObjectList reading sources... [ 71%] subsections/md_rst/registerGiottoObjectListFiji reading sources... [ 71%] subsections/md_rst/registerGiottoObjectListRvision reading sources... [ 71%] subsections/md_rst/registerImagesFIJI reading sources... [ 71%] subsections/md_rst/removeCellAnnotation reading sources... [ 72%] subsections/md_rst/removeFeatAnnotation reading sources... [ 72%] subsections/md_rst/removeGiottoEnvironment reading sources... [ 72%] subsections/md_rst/replaceGiottoInstructions reading sources... [ 72%] subsections/md_rst/reshape_to_data_point reading sources... [ 72%] subsections/md_rst/reshape_to_mesh_grid_obj reading sources... [ 72%] subsections/md_rst/return_giotto_environment_path reading sources... [ 72%] subsections/md_rst/return_giotto_environment_path_executable reading sources... [ 73%] subsections/md_rst/rigid_transform_spatial_locations reading sources... [ 73%] subsections/md_rst/rna_osmfish_normalization reading sources... [ 73%] subsections/md_rst/rna_pears_resid_normalization reading sources... [ 73%] subsections/md_rst/rna_standard_normalization reading sources... [ 73%] subsections/md_rst/rotate_spatial_locations reading sources... [ 73%] subsections/md_rst/rowMeans_flex reading sources... [ 73%] subsections/md_rst/rowSums_flex reading sources... [ 74%] subsections/md_rst/runDWLSDeconv reading sources... [ 74%] subsections/md_rst/runFijiMacro reading sources... [ 74%] subsections/md_rst/runGiottoHarmony reading sources... [ 74%] subsections/md_rst/runHyperGeometricEnrich reading sources... [ 74%] subsections/md_rst/runPAGEEnrich reading sources... [ 74%] subsections/md_rst/runPAGEEnrich_OLD reading sources... [ 74%] subsections/md_rst/runPCA reading sources... [ 75%] subsections/md_rst/runPCA_BiocSingular reading sources... [ 75%] subsections/md_rst/runPCA_factominer reading sources... [ 75%] subsections/md_rst/runPCA_prcomp_irlba reading sources... [ 75%] subsections/md_rst/runPatternSimulation reading sources... [ 75%] subsections/md_rst/runRankEnrich reading sources... [ 75%] subsections/md_rst/runSpatialDeconv reading sources... [ 76%] subsections/md_rst/runSpatialEnrich reading sources... [ 76%] subsections/md_rst/runUMAP reading sources... [ 76%] subsections/md_rst/run_spatial_sim_tests_multi reading sources... [ 76%] subsections/md_rst/run_spatial_sim_tests_one_rep reading sources... [ 76%] subsections/md_rst/runtSNE reading sources... [ 76%] subsections/md_rst/scale_spatial_locations reading sources... [ 76%] subsections/md_rst/screePlot reading sources... [ 77%] subsections/md_rst/selectPatternGenes reading sources... [ 77%] subsections/md_rst/select_NearestNetwork reading sources... [ 77%] subsections/md_rst/select_dimReduction reading sources... [ 77%] subsections/md_rst/select_expression_values reading sources... [ 77%] subsections/md_rst/select_feature_info reading sources... [ 77%] subsections/md_rst/select_gimage reading sources... [ 77%] subsections/md_rst/select_polygon_info reading sources... [ 78%] subsections/md_rst/select_spatialGrid reading sources... [ 78%] subsections/md_rst/select_spatialNetwork reading sources... [ 78%] subsections/md_rst/select_spatial_locations reading sources... [ 78%] subsections/md_rst/set_NearestNetwork reading sources... [ 78%] subsections/md_rst/set_cell_and_feat_IDs reading sources... [ 78%] subsections/md_rst/set_cell_metadata reading sources... [ 78%] subsections/md_rst/set_default_feat_type reading sources... [ 79%] subsections/md_rst/set_default_spat_unit reading sources... [ 79%] subsections/md_rst/set_dimReduction reading sources... [ 79%] subsections/md_rst/set_expression_values reading sources... [ 79%] subsections/md_rst/set_feature_info reading sources... [ 79%] subsections/md_rst/set_feature_metadata reading sources... [ 79%] subsections/md_rst/set_giottoImage reading sources... [ 80%] subsections/md_rst/set_giottoImage_MG reading sources... [ 80%] subsections/md_rst/set_giottoLargeImage reading sources... [ 80%] subsections/md_rst/set_giotto_python_path reading sources... [ 80%] subsections/md_rst/set_polygon_info reading sources... [ 80%] subsections/md_rst/set_spatialGrid reading sources... [ 80%] subsections/md_rst/set_spatialNetwork reading sources... [ 80%] subsections/md_rst/set_spatial_enrichment reading sources... [ 81%] subsections/md_rst/set_spatial_locations reading sources... [ 81%] subsections/md_rst/seuratToGiotto reading sources... [ 81%] subsections/md_rst/seuratToGiotto_OLD reading sources... [ 81%] subsections/md_rst/show-methods reading sources... [ 81%] subsections/md_rst/showClusterDendrogram reading sources... [ 81%] subsections/md_rst/showClusterHeatmap reading sources... [ 81%] subsections/md_rst/showGiottoDimRed reading sources... [ 82%] subsections/md_rst/showGiottoExpression reading sources... [ 82%] subsections/md_rst/showGiottoFeatInfo reading sources... [ 82%] subsections/md_rst/showGiottoImageNames reading sources... [ 82%] subsections/md_rst/showGiottoInstructions reading sources... [ 82%] subsections/md_rst/showGiottoSpatEnrichments reading sources... [ 82%] subsections/md_rst/showGiottoSpatGrids reading sources... [ 82%] subsections/md_rst/showGiottoSpatLocs reading sources... [ 83%] subsections/md_rst/showGiottoSpatNetworks reading sources... [ 83%] subsections/md_rst/showGiottoSpatialInfo reading sources... [ 83%] subsections/md_rst/showGrids reading sources... [ 83%] subsections/md_rst/showNetworks reading sources... [ 83%] subsections/md_rst/showPattern reading sources... [ 83%] subsections/md_rst/showPattern2D reading sources... [ 84%] subsections/md_rst/showPattern3D reading sources... [ 84%] subsections/md_rst/showPatternGenes reading sources... [ 84%] subsections/md_rst/showProcessingSteps reading sources... [ 84%] subsections/md_rst/showSaveParameters reading sources... [ 84%] subsections/md_rst/showSpatialCorFeats reading sources... [ 84%] subsections/md_rst/showSpatialCorGenes reading sources... [ 84%] subsections/md_rst/signPCA reading sources... [ 85%] subsections/md_rst/silhouetteRank reading sources... [ 85%] subsections/md_rst/silhouetteRankTest reading sources... [ 85%] subsections/md_rst/simulateOneGenePatternGiottoObject reading sources... [ 85%] subsections/md_rst/smoothGiottoPolygons reading sources... [ 85%] subsections/md_rst/solve_OLS_internal reading sources... [ 85%] subsections/md_rst/solve_dampened_WLSj reading sources... [ 85%] subsections/md_rst/sort_combine_two_DT_columns reading sources... [ 86%] subsections/md_rst/spark reading sources... [ 86%] subsections/md_rst/spatCellCellcom reading sources... [ 86%] subsections/md_rst/spatCellPlot reading sources... [ 86%] subsections/md_rst/spatCellPlot2D reading sources... [ 86%] subsections/md_rst/spatDeconvPlot reading sources... [ 86%] subsections/md_rst/spatDimCellPlot reading sources... [ 86%] subsections/md_rst/spatDimCellPlot2D reading sources... [ 87%] subsections/md_rst/spatDimFeatPlot2D reading sources... [ 87%] subsections/md_rst/spatDimGenePlot reading sources... [ 87%] subsections/md_rst/spatDimGenePlot2D reading sources... [ 87%] subsections/md_rst/spatDimGenePlot3D reading sources... [ 87%] subsections/md_rst/spatDimPlot reading sources... [ 87%] subsections/md_rst/spatDimPlot2D reading sources... [ 88%] subsections/md_rst/spatDimPlot3D reading sources... [ 88%] subsections/md_rst/spatFeatPlot2D reading sources... [ 88%] subsections/md_rst/spatFeatPlot2D_single reading sources... [ 88%] subsections/md_rst/spatGenePlot reading sources... [ 88%] subsections/md_rst/spatGenePlot2D reading sources... [ 88%] subsections/md_rst/spatGenePlot3D reading sources... [ 88%] subsections/md_rst/spatInSituPlotDensity reading sources... [ 89%] subsections/md_rst/spatInSituPlotDensity_single reading sources... [ 89%] subsections/md_rst/spatInSituPlotHex reading sources... [ 89%] subsections/md_rst/spatInSituPlotHex_single reading sources... [ 89%] subsections/md_rst/spatInSituPlotPoints reading sources... [ 89%] subsections/md_rst/spatNetwDistributions reading sources... [ 89%] subsections/md_rst/spatNetwDistributionsDistance reading sources... [ 89%] subsections/md_rst/spatNetwDistributionsKneighbors reading sources... [ 90%] subsections/md_rst/spatPlot reading sources... [ 90%] subsections/md_rst/spatPlot2D reading sources... [ 90%] subsections/md_rst/spatPlot2D_single reading sources... [ 90%] subsections/md_rst/spatPlot3D reading sources... [ 90%] subsections/md_rst/spatPlot_2D_plotly reading sources... [ 90%] subsections/md_rst/spatPlot_3D_plotly reading sources... [ 90%] subsections/md_rst/spatVector_to_dt reading sources... [ 91%] subsections/md_rst/spat_OR_func reading sources... [ 91%] subsections/md_rst/spat_OR_func_DT reading sources... [ 91%] subsections/md_rst/spat_fish_func reading sources... [ 91%] subsections/md_rst/spat_fish_func_DT reading sources... [ 91%] subsections/md_rst/spatialAEH reading sources... [ 91%] subsections/md_rst/spatialDE reading sources... [ 92%] subsections/md_rst/specificCellCellcommunicationScores reading sources... [ 92%] subsections/md_rst/spline_poly reading sources... [ 92%] subsections/md_rst/split_dendrogram_in_two reading sources... [ 92%] subsections/md_rst/spot_deconvolution reading sources... [ 92%] subsections/md_rst/standardise_flex reading sources... [ 92%] subsections/md_rst/stitchFieldCoordinates reading sources... [ 92%] subsections/md_rst/stitchGiottoLargeImage reading sources... [ 93%] subsections/md_rst/stitchTileCoordinates reading sources... [ 93%] subsections/md_rst/subClusterCells reading sources... [ 93%] subsections/md_rst/subsetGiotto reading sources... [ 93%] subsections/md_rst/subsetGiottoLocs reading sources... [ 93%] subsections/md_rst/subsetGiottoLocsMulti reading sources... [ 93%] subsections/md_rst/subset_cell_metadata reading sources... [ 93%] subsections/md_rst/subset_dimension_reduction reading sources... [ 94%] subsections/md_rst/subset_expression_data reading sources... [ 94%] subsections/md_rst/subset_feature_info_data reading sources... [ 94%] subsections/md_rst/subset_feature_metadata reading sources... [ 94%] subsections/md_rst/subset_giotto_points_object reading sources... [ 94%] subsections/md_rst/subset_giotto_polygon_object reading sources... [ 94%] subsections/md_rst/subset_nearest_network reading sources... [ 94%] subsections/md_rst/subset_spatial_enrichment reading sources... [ 95%] subsections/md_rst/subset_spatial_info_data reading sources... [ 95%] subsections/md_rst/subset_spatial_locations reading sources... [ 95%] subsections/md_rst/subset_spatial_network reading sources... [ 95%] subsections/md_rst/t_flex reading sources... [ 95%] subsections/md_rst/trakem2_rigid_transf_extract reading sources... [ 95%] subsections/md_rst/transform_2d_mesh_to_3d_mesh reading sources... [ 96%] subsections/md_rst/trendSceek reading sources... [ 96%] subsections/md_rst/updateGiottoImage reading sources... [ 96%] subsections/md_rst/updateGiottoImageMG reading sources... [ 96%] subsections/md_rst/updateGiottoLargeImage reading sources... [ 96%] subsections/md_rst/update_giotto_params reading sources... [ 96%] subsections/md_rst/viewHMRFresults reading sources... [ 96%] subsections/md_rst/viewHMRFresults2D reading sources... [ 97%] subsections/md_rst/viewHMRFresults3D reading sources... [ 97%] subsections/md_rst/violinPlot reading sources... [ 97%] subsections/md_rst/writeGiottoLargeImage reading sources... [ 97%] subsections/md_rst/writeHMRFresults reading sources... [ 97%] subsections/md_rst/write_giotto_viewer_annotation reading sources... [ 97%] subsections/md_rst/write_giotto_viewer_dim_reduction reading sources... [ 97%] subsections/md_rst/write_giotto_viewer_numeric_annotation reading sources... [ 98%] subsections/md_rst/xy_translate_spatial_locations reading sources... [ 98%] subsections/tipsandtricks/NEWS reading sources... [ 98%] subsections/tipsandtricks/giottoclass reading sources... [ 98%] subsections/tipsandtricks/howtosubsetgiottoobject reading sources... [ 98%] subsections/tipsandtricks/howtovisualizeandsaveplots reading sources... [ 98%] subsections/tipsandtricks/testandstoremultipleanayses reading sources... [ 98%] subsections/tipsandtricks/visualizewithvoronoiplots reading sources... [ 99%] subsections/tipsandtricks/waystovisualizespatialdata reading sources... [ 99%] subsections/tipsandtricks/workingwithimages reading sources... [ 99%] subsections/trygiotto/binder reading sources... [ 99%] subsections/trygiotto/docker reading sources... [ 99%] subsections/trygiotto/terra reading sources... [ 99%] tipsandtricks reading sources... [100%] trygiotto /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/citing_giotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/resolve_bc_210928.rst:159: WARNING: Title overline & underline mismatch. ******************************** Part 7: Process Giotto Object ********************************* /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/DT_removeNA.rst:1: WARNING: malformed hyperlink target. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/DT_removeNA.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addCellsFromPolygon.rst:4: WARNING: duplicate label addcellmetadata, other instance in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addCellMetadata.rst /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addFeatStatistics.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneMetadata.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneStatistics.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGenesPerc.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImageMG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImageToSpatPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPoints.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPolygons.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addHMRF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addNetworkLayout.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocationsLayer.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addStatistics.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/adjustGiottoMatrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/aes_string2.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/all_plots_save_function.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/anndataToGiotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotateGiotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotateSpatialGrid.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotateSpatialNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/average_feat_feat_expression_in_groups.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:10: WARNING: Unexpected section title. Description ----------- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:15: WARNING: Unexpected section title. Usage ----- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:47: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:105: WARNING: Unexpected section title. Value ----- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_group_HVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_loess_HVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_minimum.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_var_HVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateHVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateHVG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateMetaTableCells.rst:4: WARNING: duplicate label calculatemetatable, other instance in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateMetaTable.rst /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapParallel.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapRaster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapSerial.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_centroids_polygons.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_distance_and_weight.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityEnrichment.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityHeatmap.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximitySpatPlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_2D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_3D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/changeGiottoInstructions.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/changeImageBg.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/checkGiottoEnvironment.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/check_spatial_location_data.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterCells.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterSpatialCorFeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterSpatialCorGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cluster_enrich_analysis.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colMeans_flex.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colSums_flex.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combCCcom.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCPG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellData.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes_per_interaction.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureData.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureOverlapData.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineICG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineInteractionChangedGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineMetadata.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellFeatureInfo.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellMetadataInfo.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/compatible_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertEnsemblToGeneSymbol.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertGiottoLargeImageToMG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_mgImage_to_array_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_full_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_reduced_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cor_flex.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createCrossSection.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoInstructions.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImageList.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoObjectSubcellular.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPoints.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromDfr.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromMask.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoVisiumObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createHeatmap_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createMetafeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createMetagenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialDefaultGrid.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialDelaunayNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialEnrich.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialGrid.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialKNNnetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_2d_mesh_grid_line_obj.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_KNNnetwork_dbscan.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_detection_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cell_type_random_cell_IDs.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cluster_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_crossSection_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_RTriangle.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_deldir.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_dimObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_featureNetwork_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_genes_to_use_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_points_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_polygon_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_jackstrawplot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_mesh_grid_lines.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_screeplot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGridObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialNetworkObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatvector_object_from_dfr.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cropGiottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionGenePlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionGenePlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionPlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/decide_cluster_order.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/density_giottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/depth.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialPatterns.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/determine_cores.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimCellPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimCellPlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimFeatPlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D_single.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_2D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_3D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/distGiottoImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doCellSegmentation.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doHMRF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doHclust.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doKmeans.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLeidenCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLeidenSubCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_community.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_multinet.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_community.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_multinet.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doRandomWalkCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doSNNCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doScrubletDetect.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_cell_proximity_test.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_limmatest.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_multi_permuttest_random.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_page_permutation.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_original.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_random.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_rank_permutation.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_grid_averaging.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_knn_smoothing.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_ttest.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_wilctest.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_points.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_polygon.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_analysis.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_deconvolution.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/estimateCellCellDistance.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_expr_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_feat_info.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_provided_spatial_locations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_info.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations_OLD.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/exportGiottoViewer.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/exprCellCellcom.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extend_vector.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extended_gini_fun.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extractNearestNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_points_list.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_polygon_list.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/fDataDT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/featureNetwork-class.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCPG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCellProximityGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCombinations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterDistributions.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterGiotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterICF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterICG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterInteractionChangedFeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterInteractionChangedGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filter_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCPG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityFeats_per_interaction.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findGiniMarkers.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findGiniMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findICF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findICG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findInteractionChangedFeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findInteractionChangedGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMarkers.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMastMarkers.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMastMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findNetworkNeighbors.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findScranMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_dampening_constant.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_x.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_y.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_z.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_terra_writeRaster_dataType.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_x_y_ranges.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runRankEnrich.rst:82: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/stitchGiottoLargeImage.rst:82: WARNING: Block quote ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/Workflow.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/development.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/citing_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/STARmap_mouse_cortex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/human_CyCIF_PDAC.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/merFISH_hypot_preopt_region.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mini_3D_STARmap.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mini_seqFISH.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mini_visium.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mouse_CODEX_spleen.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mouse_visium_brain.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mouse_visium_kidney.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/osmFISH_mouse_SS_cortex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/resolve_bc_210928.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/seqFISH_cortex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/tcyCIF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/vizgen_mouse_brain.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/detailed_workflow.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/license.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/DT_removeNA.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/FSV_show.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/OR_test_fnc.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/PAGEEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/PAGE_DT_method.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/adapt_aspect_ratio.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addCellsFromPolygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneMetadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneStatistics.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGenesPerc.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImageMG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPoints.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPolygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocationsLayer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/add_img_array_alpha.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/aes_string2.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/all_plots_save_function.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/anndataToGiotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/average_feat_feat_expression_in_groups.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_group_HVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_loess_HVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_minimum.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_var_HVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateHVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapParallel.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapRaster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapSerial.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_centroids_polygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_distance_and_weight.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximitySpatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_2D_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_2D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_3D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/check_spatial_location_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cluster_enrich_analysis.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colMeans_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colSums_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combCCcom.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellData.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes_per_interaction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureData.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureOverlapData.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellFeatureInfo.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellMetadataInfo.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/compatible_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertEnsemblToGeneSymbol.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertGiottoLargeImageToMG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_mgImage_to_array_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_full_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_reduced_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cor_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoImageOLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImageList.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPoints.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromDfr.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromMask.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createHeatmap_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createMetafeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialDefaultGrid.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_2d_mesh_grid_line_obj.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_KNNnetwork_dbscan.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_detection_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cell_type_random_cell_IDs.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cluster_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_crossSection_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_RTriangle.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_deldir.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_dimObject.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_featureNetwork_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_genes_to_use_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_points_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_polygon_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_jackstrawplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_mesh_grid_lines.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_screeplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_segm_polygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGridObject.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialNetworkObject.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatvector_object_from_dfr.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cropGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/decide_cluster_order.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/density_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/depth.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialCorFeatsMatrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialPatterns.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/determine_cores.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimCellPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimFeatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_2D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_3D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/distGiottoImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doCellSegmentation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_community.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_multinet.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_community.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_multinet.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doRandomWalkCluster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doSNNCluster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doScrubletDetect.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_cell_proximity_test.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_limmatest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_multi_permuttest_random.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_page_permutation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_original.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_random.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_rank_permutation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_grid_averaging.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_knn_smoothing.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_ttest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_wilctest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_points.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_polygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_analysis.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_deconvolution.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/estimateCellCellDistance.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_expr_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_feat_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_provided_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations_OLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/exportGiottoViewer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extend_vector.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extended_gini_fun.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extractNearestNetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_points_list.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_polygon_list.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/featureNetwork-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCombinations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterDistributions.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filter_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityFeats_per_interaction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_dampening_constant.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_x.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_y.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_z.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_terra_writeRaster_dataType.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_x_y_ranges.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/fix_multipart_geoms.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/flex_lapply.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/general_save_function.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get10XmatrixOLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/getCellsFromPolygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/getDistinctColors.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_adj_rescale_img.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_args.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_cross_section_coordinates.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_distance.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_img_corners.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_img_minmax.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_os.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_sectionThickness.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/ggplot_save_function.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giotto-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoImage-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoLargeImage-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoPoints-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoPolygon-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoToSeurat.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giotto_point.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/heatmSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/hyperGeometricEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/identify_background_range_polygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/install_giotto_environment.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/install_giotto_environment_specific.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/join_cell_meta.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/join_expression_matrices.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/join_spatlocs.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_arma_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_arma_subset_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_binarize_wrapper.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/lapply_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/libNorm_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_cell_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_dim_reductions.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_dim_reductions_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_expression.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_expression_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_feat_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_feature_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_feature_info_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_giotto_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_images.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_images_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_enrichments.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_enrichments_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_grids.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_grids_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_info_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_locations_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_networks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_networks_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/logNorm_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/make_simulated_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mean_expr_det_test.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mean_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/merge_spatial_locs_feat_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mini_giotto_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mini_giotto_multi_cell.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mini_giotto_single_cell.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/my_arowMeans.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/my_growMeans.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/my_rowMeans.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mygini_fun.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/nnDT_to_kNN.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/node_clusters.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/optimize_deconvolute_dwls.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/optimize_solveDampenedWLS.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlapToMatrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlapToMatrixMultiPoly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlap_points_per_polygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlap_points_per_polygon_wrapped.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlap_points_single_polygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/package_check.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/pca_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/pipe.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCCcomHeatmap.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCCcom.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCellCellCommunication.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotICF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotInteractionChangedFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotInteractivePolygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotPCA_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotRecovery_sub.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotTSNE_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotUMAP_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_auto_largeImage_resample.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_cell_polygon_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_feature_hexbin_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_feature_points_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_feature_raster_density_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_network_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_point_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_point_layer_ggplot_noFILL.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_image_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_point_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_point_layer_ggplot_noFILL.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_scatterpie_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_voronoi_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_axis_scale_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_axis_scale_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_grid.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/polygon_to_raster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/processGiotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/projection_fun.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rankEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rank_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rank_binarize_wrapper.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/readPolygonFilesVizgen.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/readPolygonFilesVizgenHDF5.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_crossSection.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_dimension_reduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_expression_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_nearest_networks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_spatial_enrichment.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_spatial_location_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_spatial_networks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnectGiottoImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnect_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnect_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnect_image_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reg_img_minmax_finder.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerGiottoObjectList.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerGiottoObjectListFiji.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerGiottoObjectListRvision.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerImagesFIJI.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reshape_to_data_point.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reshape_to_mesh_grid_obj.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/return_giotto_environment_path.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/return_giotto_environment_path_executable.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rigid_transform_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rna_osmfish_normalization.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rna_pears_resid_normalization.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rna_standard_normalization.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rotate_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rowMeans_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rowSums_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runFijiMacro.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runGiottoHarmony.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPAGEEnrich_OLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPCA_BiocSingular.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPCA_factominer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPCA_prcomp_irlba.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/run_spatial_sim_tests_multi.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/run_spatial_sim_tests_one_rep.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/scale_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/selectPatternGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_NearestNetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_dimReduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_expression_values.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_feature_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_gimage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_polygon_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_spatialGrid.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_spatialNetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_cell_and_feat_IDs.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_cell_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_default_feat_type.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_default_spat_unit.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_feature_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giottoImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giotto_python_path.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/seuratToGiotto_OLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/show-methods.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showGrids.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showNetworks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPattern.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPattern2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPattern3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPatternGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showSaveParameters.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/silhouetteRank.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/silhouetteRankTest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/smoothGiottoPolygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/solve_OLS_internal.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/solve_dampened_WLSj.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/sort_combine_two_DT_columns.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatCellPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDeconvPlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimCellPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimFeatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimGenePlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimGenePlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimGenePlot3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatFeatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatFeatPlot2D_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatGenePlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatGenePlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatGenePlot3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotDensity.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotDensity_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotHex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotHex_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotPoints.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot2D_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot_2D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot_3D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatVector_to_dt.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_OR_func.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_OR_func_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_fish_func.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_fish_func_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/specificCellCellcommunicationScores.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spline_poly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/split_dendrogram_in_two.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spot_deconvolution.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/standardise_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/stitchGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subsetGiottoLocsMulti.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_cell_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_dimension_reduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_expression_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_feature_info_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_feature_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_giotto_points_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_giotto_polygon_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_nearest_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_enrichment.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_info_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/t_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/trakem2_rigid_transf_extract.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/transform_2d_mesh_to_3d_mesh.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/updateGiottoImageMG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/updateGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/update_giotto_params.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/writeGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/write_giotto_viewer_annotation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/write_giotto_viewer_dim_reduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/write_giotto_viewer_numeric_annotation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/xy_translate_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/tipsandtricks/NEWS.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/tipsandtricks.rst: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... gettingstarted documentation subsections/md_rst/installGiottoEnvironment subsections/md_rst/removeGiottoEnvironment subsections/md_rst/checkGiottoEnvironment subsections/md_rst/createGiottoInstructions subsections/md_rst/readGiottoInstructions subsections/md_rst/showGiottoInstructions subsections/md_rst/changeGiottoInstructions subsections/md_rst/replaceGiottoInstructions subsections/md_rst/getSpatialDataset subsections/md_rst/readExprMatrix subsections/md_rst/get10Xmatrix subsections/md_rst/get10Xmatrix_h5 subsections/md_rst/stitchFieldCoordinates subsections/md_rst/stitchTileCoordinates subsections/md_rst/estimateImageBg subsections/md_rst/changeImageBg subsections/md_rst/createGiottoImage subsections/md_rst/addGiottoImage subsections/md_rst/addGiottoImageToSpatPlot subsections/md_rst/showGiottoImageNames subsections/md_rst/updateGiottoImage subsections/md_rst/get_giottoImage subsections/md_rst/plotGiottoImage subsections/md_rst/createGiottoObject subsections/md_rst/createGiottoVisiumObject subsections/md_rst/createGiottoObjectSubcellular subsections/md_rst/pDataDT subsections/md_rst/fDataDT subsections/md_rst/showProcessingSteps subsections/md_rst/calculateMetaTable subsections/md_rst/calculateMetaTableCells subsections/md_rst/combineMetadata subsections/md_rst/createMetagenes subsections/md_rst/findNetworkNeighbors subsections/md_rst/get_expression_values subsections/md_rst/set_expression_values subsections/md_rst/get_spatial_locations subsections/md_rst/set_spatial_locations subsections/md_rst/get_dimReduction subsections/md_rst/set_dimReduction subsections/md_rst/get_NearestNetwork subsections/md_rst/set_NearestNetwork subsections/md_rst/get_spatialNetwork subsections/md_rst/set_spatialNetwork subsections/md_rst/get_spatialGrid subsections/md_rst/set_spatialGrid subsections/md_rst/get_polygon_info subsections/md_rst/set_polygon_info subsections/md_rst/get_feature_info subsections/md_rst/set_feature_info subsections/md_rst/get_spatial_enrichment subsections/md_rst/set_spatial_enrichment subsections/md_rst/showGiottoExpression subsections/md_rst/showGiottoSpatLocs subsections/md_rst/showGiottoDimRed subsections/md_rst/showGiottoSpatNetworks subsections/md_rst/showGiottoSpatGrids subsections/md_rst/showGiottoSpatialInfo subsections/md_rst/showGiottoFeatInfo subsections/md_rst/showGiottoSpatEnrichments subsections/md_rst/filterGiotto subsections/md_rst/subsetGiotto subsections/md_rst/subsetGiottoLocs subsections/md_rst/joinGiottoObjects subsections/md_rst/normalizeGiotto subsections/md_rst/adjustGiottoMatrix subsections/md_rst/annotateGiotto subsections/md_rst/removeCellAnnotation subsections/md_rst/removeFeatAnnotation subsections/md_rst/addCellMetadata subsections/md_rst/addFeatMetadata subsections/md_rst/addFeatStatistics subsections/md_rst/addCellStatistics subsections/md_rst/addStatistics subsections/md_rst/addFeatsPerc subsections/md_rst/addCellIntMetadata subsections/md_rst/calculateHVG subsections/md_rst/signPCA subsections/md_rst/screePlot subsections/md_rst/jackstrawPlot subsections/md_rst/runPCA subsections/md_rst/runUMAP subsections/md_rst/runtSNE subsections/md_rst/createNearestNetwork subsections/md_rst/addNetworkLayout subsections/md_rst/clusterCells subsections/md_rst/doLeidenCluster subsections/md_rst/doLouvainCluster subsections/md_rst/doKmeans subsections/md_rst/doHclust subsections/md_rst/subClusterCells subsections/md_rst/doLeidenSubCluster subsections/md_rst/doLouvainSubCluster subsections/md_rst/getClusterSimilarity subsections/md_rst/mergeClusters subsections/md_rst/getDendrogramSplits subsections/md_rst/findMarkers subsections/md_rst/findMarkers_one_vs_all subsections/md_rst/findGiniMarkers subsections/md_rst/findGiniMarkers_one_vs_all subsections/md_rst/findScranMarkers subsections/md_rst/findScranMarkers_one_vs_all subsections/md_rst/findMastMarkers subsections/md_rst/findMastMarkers_one_vs_all subsections/md_rst/showClusterHeatmap subsections/md_rst/showClusterDendrogram subsections/md_rst/plotHeatmap subsections/md_rst/plotMetaDataHeatmap subsections/md_rst/plotMetaDataCellsHeatmap subsections/md_rst/violinPlot subsections/md_rst/makeSignMatrixPAGE subsections/md_rst/makeSignMatrixRank subsections/md_rst/runSpatialEnrich subsections/md_rst/runPAGEEnrich subsections/md_rst/runRankEnrich subsections/md_rst/runHyperGeometricEnrich subsections/md_rst/makeSignMatrixDWLSfromMatrix subsections/md_rst/makeSignMatrixDWLS subsections/md_rst/runSpatialDeconv subsections/md_rst/runDWLSDeconv subsections/md_rst/spatNetwDistributionsDistance subsections/md_rst/spatNetwDistributionsKneighbors subsections/md_rst/spatNetwDistributions subsections/md_rst/createSpatialDelaunayNetwork subsections/md_rst/plotStatDelaunayNetwork subsections/md_rst/createSpatialKNNnetwork subsections/md_rst/createSpatialNetwork subsections/md_rst/annotateSpatialNetwork subsections/md_rst/annotateSpatialGrid subsections/md_rst/createSpatialGrid subsections/md_rst/binSpectSingleMatrix subsections/md_rst/binSpectMultiMatrix subsections/md_rst/binSpectSingle subsections/md_rst/binSpectMulti subsections/md_rst/binSpect subsections/md_rst/spatialDE subsections/md_rst/spatialAEH subsections/md_rst/trendSceek subsections/md_rst/spark subsections/md_rst/simulateOneGenePatternGiottoObject subsections/md_rst/runPatternSimulation subsections/md_rst/clusterSpatialCorGenes subsections/md_rst/detectSpatialCorGenes subsections/md_rst/heatmSpatialCorGenes subsections/md_rst/showSpatialCorGenes subsections/md_rst/rankSpatialCorGroups subsections/md_rst/doHMRF subsections/md_rst/loadHMRF subsections/md_rst/viewHMRFresults subsections/md_rst/writeHMRFresults subsections/md_rst/addHMRF subsections/md_rst/viewHMRFresults2D subsections/md_rst/viewHMRFresults3D subsections/md_rst/dimPlot subsections/md_rst/plotUMAP subsections/md_rst/plotTSNE subsections/md_rst/plotPCA subsections/md_rst/dimGenePlot subsections/md_rst/dimCellPlot subsections/md_rst/spatPlot subsections/md_rst/spatCellPlot subsections/md_rst/spatDimPlot subsections/md_rst/spatDimCellPlot subsections/md_rst/dimPlot3D subsections/md_rst/plotUMAP_3D subsections/md_rst/plotTSNE_3D subsections/md_rst/plotPCA_3D subsections/md_rst/spatPlot3D subsections/md_rst/spatDimPlot3D subsections/md_rst/createCrossSection subsections/md_rst/crossSectionGenePlot subsections/md_rst/crossSectionPlot subsections/md_rst/crossSectionGenePlot3D subsections/md_rst/crossSectionPlot3D subsections/md_rst/insertCrossSectionSpatPlot3D subsections/md_rst/insertCrossSectionGenePlot3D subsections/md_rst/cellProximityEnrichment subsections/md_rst/cellProximityBarplot subsections/md_rst/cellProximityHeatmap subsections/md_rst/cellProximityNetwork subsections/md_rst/cellProximitySpatPlot subsections/md_rst/cellProximitySpatPlot3D subsections/md_rst/findInteractionChangedFeats subsections/md_rst/findICF subsections/md_rst/filterInteractionChangedFeats subsections/md_rst/filterICF subsections/md_rst/exprCellCellcom subsections/md_rst/spatCellCellcom subsections/md_rst/plotCCcomDotplot subsections/md_rst/plotRankSpatvsExpr subsections/md_rst/plotRecovery subsections/md_rst/seuratToGiotto contribute datasets faqs trygiotto subsections/trygiotto/binder subsections/trygiotto/docker subsections/trygiotto/terra errorsfaqsandtips github_issues done writing... done writing additional files... done copying images... [ 2%] images/GiottoInstallationWorkflow.png copying images... [ 4%] images/getting_started/icons_configuration.png copying images... [ 6%] images/getting_started/icons_giotto.png copying images... [ 8%] images/getting_started/icons_processing.png copying images... [ 10%] images/getting_started/icons_clustering.png copying images... [ 13%] images/getting_started/icons_images.png copying images... [ 15%] images/getting_started/icons_visualizations.png copying images... [ 17%] images/getting_started/icons_saving.png copying images... [ 19%] images/getting_started/icons_distribution.png copying images... [ 21%] images/getting_started/icons_cell_type.png copying images... [ 23%] images/getting_started/icons_deconvolution.png copying images... [ 26%] images/getting_started/icons_interaction.png copying images... [ 28%] images/getting_started/icons_patterns.png copying images... [ 30%] images/getting_started/icons_subcellular.png copying images... [ 32%] images/dataset_page/visium_kidney_image_summary.png copying images... [ 34%] images/dataset_page/visium_prostate_summary.png copying images... [ 36%] images/dataset_page/coming_soon_summary.png copying images... [ 39%] images/dataset_page/cortex_image_summary.png copying images... [ 41%] images/dataset_page/osmFISH_SS_cortex_image_summary.png copying images... [ 43%] images/dataset_page/merFISH_hypoth_image_summary.png copying images... [ 45%] images/dataset_page/starmap_cortex_image_summary.png copying images... [ 47%] images/dataset_page/vizgen_brain_summary.png copying images... [ 50%] images/dataset_page/resolve_bioscience_cancer_summary.png copying images... [ 52%] images/dataset_page/nanostring_overview_icon.png copying images... [ 54%] images/dataset_page/CODEX_spleen_image_summary.png copying images... [ 56%] images/dataset_page/cyCIF_PDAC_image_summary.png copying images... [ 58%] images/dataset_page/SC_RNAseq_standard.png copying images... [ 60%] images/dataset_page/SC_RNAseq_integration.png copying images... [ 63%] images/GitHub_Logo.png copying images... [ 65%] images/img_terra/01_environments.png copying images... [ 67%] images/img_terra/01_vm.png copying images... [ 69%] images/img_terra/02_docker.png copying images... [ 71%] images/img_terra/03_upload.png copying images... [ 73%] images/img_terra/03_view.png copying images... [ 76%] images/img_terra/03_googlecloud.png copying images... [ 78%] images/img_terra/03_url.png copying images... [ 80%] images/img_terra/03_cloud.png copying images... [ 82%] images/img_terra/04_share.png copying images... [ 84%] images/trygiotto/Binder_1.png copying images... [ 86%] images/trygiotto/Binder_2.png copying images... [ 89%] images/trygiotto/Binder_3.png copying images... [ 91%] images/trygiotto/Binder_4.png copying images... [ 93%] images/index/giotto_suite.png copying images... [ 95%] images/index/input_Compatibility.png copying images... [ 97%] images/index/data_structure_Data_Structure.png copying images... [100%] images/index/analysis.png copying static files... done copying extra files... done dumping object inventory... done build succeeded, 693 warnings. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2022-07-14T19:43:33.090092Z, end-time: 2022-07-14T19:43:40.288983Z, duration: 7, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.4.3 loading translations [en]... done making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found processing giotto.tex... index gettingstarted documentation subsections/md_rst/installGiottoEnvironment subsections/md_rst/removeGiottoEnvironment subsections/md_rst/checkGiottoEnvironment subsections/md_rst/createGiottoInstructions subsections/md_rst/readGiottoInstructions subsections/md_rst/showGiottoInstructions subsections/md_rst/changeGiottoInstructions subsections/md_rst/replaceGiottoInstructions subsections/md_rst/getSpatialDataset subsections/md_rst/readExprMatrix subsections/md_rst/get10Xmatrix subsections/md_rst/get10Xmatrix_h5 subsections/md_rst/stitchFieldCoordinates subsections/md_rst/stitchTileCoordinates subsections/md_rst/estimateImageBg subsections/md_rst/changeImageBg subsections/md_rst/createGiottoImage subsections/md_rst/addGiottoImage subsections/md_rst/addGiottoImageToSpatPlot subsections/md_rst/showGiottoImageNames subsections/md_rst/updateGiottoImage subsections/md_rst/get_giottoImage subsections/md_rst/plotGiottoImage subsections/md_rst/createGiottoObject subsections/md_rst/createGiottoVisiumObject subsections/md_rst/createGiottoObjectSubcellular subsections/md_rst/pDataDT subsections/md_rst/fDataDT subsections/md_rst/showProcessingSteps subsections/md_rst/calculateMetaTable subsections/md_rst/calculateMetaTableCells subsections/md_rst/combineMetadata subsections/md_rst/createMetagenes subsections/md_rst/findNetworkNeighbors subsections/md_rst/get_expression_values subsections/md_rst/set_expression_values subsections/md_rst/get_spatial_locations subsections/md_rst/set_spatial_locations subsections/md_rst/get_dimReduction subsections/md_rst/set_dimReduction subsections/md_rst/get_NearestNetwork subsections/md_rst/set_NearestNetwork subsections/md_rst/get_spatialNetwork subsections/md_rst/set_spatialNetwork subsections/md_rst/get_spatialGrid subsections/md_rst/set_spatialGrid subsections/md_rst/get_polygon_info subsections/md_rst/set_polygon_info subsections/md_rst/get_feature_info subsections/md_rst/set_feature_info subsections/md_rst/get_spatial_enrichment subsections/md_rst/set_spatial_enrichment subsections/md_rst/showGiottoExpression subsections/md_rst/showGiottoSpatLocs subsections/md_rst/showGiottoDimRed subsections/md_rst/showGiottoSpatNetworks subsections/md_rst/showGiottoSpatGrids subsections/md_rst/showGiottoSpatialInfo subsections/md_rst/showGiottoFeatInfo subsections/md_rst/showGiottoSpatEnrichments subsections/md_rst/filterGiotto subsections/md_rst/subsetGiotto subsections/md_rst/subsetGiottoLocs subsections/md_rst/joinGiottoObjects subsections/md_rst/normalizeGiotto subsections/md_rst/adjustGiottoMatrix subsections/md_rst/annotateGiotto subsections/md_rst/removeCellAnnotation subsections/md_rst/removeFeatAnnotation subsections/md_rst/addCellMetadata subsections/md_rst/addFeatMetadata subsections/md_rst/addFeatStatistics subsections/md_rst/addCellStatistics subsections/md_rst/addStatistics subsections/md_rst/addFeatsPerc subsections/md_rst/addCellIntMetadata subsections/md_rst/calculateHVG subsections/md_rst/signPCA subsections/md_rst/screePlot subsections/md_rst/jackstrawPlot subsections/md_rst/runPCA subsections/md_rst/runUMAP subsections/md_rst/runtSNE subsections/md_rst/createNearestNetwork subsections/md_rst/addNetworkLayout subsections/md_rst/clusterCells subsections/md_rst/doLeidenCluster subsections/md_rst/doLouvainCluster subsections/md_rst/doKmeans subsections/md_rst/doHclust subsections/md_rst/subClusterCells subsections/md_rst/doLeidenSubCluster subsections/md_rst/doLouvainSubCluster subsections/md_rst/getClusterSimilarity subsections/md_rst/mergeClusters subsections/md_rst/getDendrogramSplits subsections/md_rst/findMarkers subsections/md_rst/findMarkers_one_vs_all subsections/md_rst/findGiniMarkers subsections/md_rst/findGiniMarkers_one_vs_all subsections/md_rst/findScranMarkers subsections/md_rst/findScranMarkers_one_vs_all subsections/md_rst/findMastMarkers subsections/md_rst/findMastMarkers_one_vs_all subsections/md_rst/showClusterHeatmap subsections/md_rst/showClusterDendrogram subsections/md_rst/plotHeatmap subsections/md_rst/plotMetaDataHeatmap subsections/md_rst/plotMetaDataCellsHeatmap subsections/md_rst/violinPlot subsections/md_rst/makeSignMatrixPAGE subsections/md_rst/makeSignMatrixRank subsections/md_rst/runSpatialEnrich subsections/md_rst/runPAGEEnrich subsections/md_rst/runRankEnrich subsections/md_rst/runHyperGeometricEnrich subsections/md_rst/makeSignMatrixDWLSfromMatrix subsections/md_rst/makeSignMatrixDWLS subsections/md_rst/runSpatialDeconv subsections/md_rst/runDWLSDeconv subsections/md_rst/spatNetwDistributionsDistance subsections/md_rst/spatNetwDistributionsKneighbors subsections/md_rst/spatNetwDistributions subsections/md_rst/createSpatialDelaunayNetwork subsections/md_rst/plotStatDelaunayNetwork subsections/md_rst/createSpatialKNNnetwork subsections/md_rst/createSpatialNetwork subsections/md_rst/annotateSpatialNetwork subsections/md_rst/annotateSpatialGrid subsections/md_rst/createSpatialGrid subsections/md_rst/binSpectSingleMatrix subsections/md_rst/binSpectMultiMatrix subsections/md_rst/binSpectSingle subsections/md_rst/binSpectMulti subsections/md_rst/binSpect subsections/md_rst/spatialDE subsections/md_rst/spatialAEH subsections/md_rst/trendSceek subsections/md_rst/spark subsections/md_rst/simulateOneGenePatternGiottoObject subsections/md_rst/runPatternSimulation subsections/md_rst/clusterSpatialCorGenes subsections/md_rst/detectSpatialCorGenes subsections/md_rst/heatmSpatialCorGenes subsections/md_rst/showSpatialCorGenes subsections/md_rst/rankSpatialCorGroups subsections/md_rst/doHMRF subsections/md_rst/loadHMRF subsections/md_rst/viewHMRFresults subsections/md_rst/writeHMRFresults subsections/md_rst/addHMRF subsections/md_rst/viewHMRFresults2D subsections/md_rst/viewHMRFresults3D subsections/md_rst/dimPlot subsections/md_rst/plotUMAP subsections/md_rst/plotTSNE subsections/md_rst/plotPCA subsections/md_rst/dimGenePlot subsections/md_rst/dimCellPlot subsections/md_rst/spatPlot subsections/md_rst/spatCellPlot subsections/md_rst/spatDimPlot subsections/md_rst/spatDimCellPlot subsections/md_rst/dimPlot3D subsections/md_rst/plotUMAP_3D subsections/md_rst/plotTSNE_3D subsections/md_rst/plotPCA_3D subsections/md_rst/spatPlot3D subsections/md_rst/spatDimPlot3D subsections/md_rst/createCrossSection subsections/md_rst/crossSectionGenePlot subsections/md_rst/crossSectionPlot subsections/md_rst/crossSectionGenePlot3D subsections/md_rst/crossSectionPlot3D subsections/md_rst/insertCrossSectionSpatPlot3D subsections/md_rst/insertCrossSectionGenePlot3D subsections/md_rst/cellProximityEnrichment subsections/md_rst/cellProximityBarplot subsections/md_rst/cellProximityHeatmap subsections/md_rst/cellProximityNetwork subsections/md_rst/cellProximitySpatPlot subsections/md_rst/cellProximitySpatPlot3D subsections/md_rst/findInteractionChangedFeats subsections/md_rst/findICF subsections/md_rst/filterInteractionChangedFeats subsections/md_rst/filterICF subsections/md_rst/exprCellCellcom subsections/md_rst/spatCellCellcom subsections/md_rst/plotCCcomDotplot subsections/md_rst/plotRankSpatvsExpr subsections/md_rst/plotRecovery subsections/md_rst/seuratToGiotto contribute datasets faqs trygiotto subsections/trygiotto/binder subsections/trygiotto/docker subsections/trygiotto/terra errorsfaqsandtips github_issues resolving references... /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/index.rst:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/github/last-commit/RubD/Giotto/suite) /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/index.rst:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/readthedocs/giotto/latest?logo=read-the-docs) /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/index.rst:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/v/Giotto) /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/index.rst:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/dm/giotto) /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/index.rst:19: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/maintenance/yes/2022) /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/trygiotto/binder.rst:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/badge/launch-binder-579ACA.svg?logo=data:image/png;base64,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) /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/index.rst:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/github/license/RubD/Giotto) done writing... done copying images... [ 2%] images/GiottoInstallationWorkflow.png copying images... [ 4%] images/getting_started/icons_configuration.png copying images... [ 6%] images/getting_started/icons_giotto.png copying images... [ 8%] images/getting_started/icons_processing.png copying images... [ 10%] images/getting_started/icons_clustering.png copying images... [ 13%] images/getting_started/icons_images.png copying images... [ 15%] images/getting_started/icons_visualizations.png copying images... [ 17%] images/getting_started/icons_saving.png copying images... [ 19%] images/getting_started/icons_distribution.png copying images... [ 21%] images/getting_started/icons_cell_type.png copying images... [ 23%] images/getting_started/icons_deconvolution.png copying images... [ 26%] images/getting_started/icons_interaction.png copying images... [ 28%] images/getting_started/icons_patterns.png copying images... [ 30%] images/getting_started/icons_subcellular.png copying images... [ 32%] images/dataset_page/visium_kidney_image_summary.png copying images... [ 34%] images/dataset_page/visium_prostate_summary.png copying images... [ 36%] images/dataset_page/coming_soon_summary.png copying images... [ 39%] images/dataset_page/cortex_image_summary.png copying images... [ 41%] images/dataset_page/osmFISH_SS_cortex_image_summary.png copying images... [ 43%] images/dataset_page/merFISH_hypoth_image_summary.png copying images... [ 45%] images/dataset_page/starmap_cortex_image_summary.png copying images... [ 47%] images/dataset_page/vizgen_brain_summary.png copying images... [ 50%] images/dataset_page/resolve_bioscience_cancer_summary.png copying images... [ 52%] images/dataset_page/nanostring_overview_icon.png copying images... [ 54%] images/dataset_page/CODEX_spleen_image_summary.png copying images... [ 56%] images/dataset_page/cyCIF_PDAC_image_summary.png copying images... [ 58%] images/dataset_page/SC_RNAseq_standard.png copying images... [ 60%] images/dataset_page/SC_RNAseq_integration.png copying images... [ 63%] images/GitHub_Logo.png copying images... [ 65%] images/img_terra/01_environments.png copying images... [ 67%] images/img_terra/01_vm.png copying images... [ 69%] images/img_terra/02_docker.png copying images... [ 71%] images/img_terra/03_upload.png copying images... [ 73%] images/img_terra/03_view.png copying images... [ 76%] images/img_terra/03_googlecloud.png copying images... [ 78%] images/img_terra/03_url.png copying images... [ 80%] images/img_terra/03_cloud.png copying images... [ 82%] images/img_terra/04_share.png copying images... [ 84%] images/trygiotto/Binder_1.png copying images... [ 86%] images/trygiotto/Binder_2.png copying images... [ 89%] images/trygiotto/Binder_3.png copying images... [ 91%] images/trygiotto/Binder_4.png copying images... [ 93%] images/index/giotto_suite.png copying images... [ 95%] images/index/input_Compatibility.png copying images... [ 97%] images/index/data_structure_Data_Structure.png copying images... [100%] images/index/analysis.png copying TeX support files... copying TeX support files... done build succeeded, 7 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2022-07-14T19:43:46.087175Z, end-time: 2022-07-14T19:43:46.149626Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2022-07-14T19:43:46.339929Z, end-time: 2022-07-14T19:43:48.055149Z, duration: 1, exit-code: 12 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=giottoteam-giotto -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="giottoteam-giotto" "giotto.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./giotto.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file giottoteam-giotto.idx (./giottoteam-giotto.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 95. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 95. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) Overfull \hbox (178.17314pt too wide) in paragraph at lines 95--95 [][] [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.100 ...5f64e44a4e5e13382f608e1d350b/suite}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.100 ...5f64e44a4e5e13382f608e1d350b/suite}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.102 ...5ab667721c2dd09c88ea01daa89/latest}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.102 ...5ab667721c2dd09c88ea01daa89/latest}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.104 ...ac79798faee8dd94282a8479edf/Giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.104 ...ac79798faee8dd94282a8479edf/Giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.106 ...1527fc1957f271b8f1b3cb3fb20/giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.106 ...1527fc1957f271b8f1b3cb3fb20/giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.108 ...97123326fc58f525350273e570ca89/2022}.svg} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.108 ...97123326fc58f525350273e570ca89/2022}.svg} [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) LaTeX Warning: Hyper reference `faqs:faqs' on page 3 undefined on input line 14 2. [3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [4] Overfull \vbox (27.0568pt too high) has occurred while \output is active [5 <./GiottoInstallationWorkflow.png>] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] LaTeX Warning: Hyper reference `subsections/md_rst/createGiottoInstructions:cre ategiottoinstructions' on page 9 undefined on input line 338. [9] [10] ! TeX capacity exceeded, sorry [input stack size=5000]. \curr@fontshape ->\f@encoding /\f@family /\f@series /\f@shape l.441 ...cludegraphics{{icons_configuration}.png}} ^^M ! ==> Fatal error occurred, no output PDF file produced! Transcript written on giottoteam-giotto.log. Latexmk: Index file 'giottoteam-giotto.idx' was written Rule 'makeindex giottoteam-giotto.idx': File changes, etc: Non-existent destination files: 'giottoteam-giotto.ind' ------------ Run number 1 of rule 'makeindex giottoteam-giotto.idx' ------------ ------------ Running 'makeindex -s python.ist -o "giottoteam-giotto.ind" "giottoteam-giotto.idx"' ------------ Latexmk: applying rule 'makeindex giottoteam-giotto.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file giottoteam-giotto.idx...done (0 entries accepted, 0 rejected). Nothing written in giottoteam-giotto.ind. Transcript written in giottoteam-giotto.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'giottoteam-giotto.aux' 'giottoteam-giotto.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="giottoteam-giotto" "giotto.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./giotto.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file giottoteam-giotto.idx (./giottoteam-giotto.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./giottoteam-giotto.out) (./giottoteam-giotto.out) Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 95. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 95. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) Overfull \hbox (178.17314pt too wide) in paragraph at lines 95--95 [][] [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./giottoteam-giotto.toc) [1] [2] ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.100 ...5f64e44a4e5e13382f608e1d350b/suite}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.100 ...5f64e44a4e5e13382f608e1d350b/suite}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.102 ...5ab667721c2dd09c88ea01daa89/latest}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.102 ...5ab667721c2dd09c88ea01daa89/latest}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.104 ...ac79798faee8dd94282a8479edf/Giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.104 ...ac79798faee8dd94282a8479edf/Giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.106 ...1527fc1957f271b8f1b3cb3fb20/giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.106 ...1527fc1957f271b8f1b3cb3fb20/giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.108 ...97123326fc58f525350273e570ca89/2022}.svg} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.108 ...97123326fc58f525350273e570ca89/2022}.svg} [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) LaTeX Warning: Hyper reference `faqs:faqs' on page 3 undefined on input line 14 2. [3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [4] Overfull \vbox (27.0568pt too high) has occurred while \output is active [5 <./GiottoInstallationWorkflow.png>] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] LaTeX Warning: Hyper reference `subsections/md_rst/createGiottoInstructions:cre ategiottoinstructions' on page 9 undefined on input line 338. [9] [10] ! TeX capacity exceeded, sorry [input stack size=5000]. \curr@fontshape ->\f@encoding /\f@family /\f@series /\f@shape l.441 ...cludegraphics{{icons_configuration}.png}} ^^M ! ==> Fatal error occurred, no output PDF file produced! Transcript written on giottoteam-giotto.log. Latexmk: Index file 'giottoteam-giotto.idx' was written Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'giottoteam-giotto.out' 'giottoteam-giotto.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="giottoteam-giotto" "giotto.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./giotto.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file giottoteam-giotto.idx (./giottoteam-giotto.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./giottoteam-giotto.out) (./giottoteam-giotto.out) Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 95. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 95. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) Overfull \hbox (178.17314pt too wide) in paragraph at lines 95--95 [][] [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./giottoteam-giotto.toc) [1] [2] ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.100 ...5f64e44a4e5e13382f608e1d350b/suite}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.100 ...5f64e44a4e5e13382f608e1d350b/suite}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.102 ...5ab667721c2dd09c88ea01daa89/latest}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.102 ...5ab667721c2dd09c88ea01daa89/latest}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.104 ...ac79798faee8dd94282a8479edf/Giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.104 ...ac79798faee8dd94282a8479edf/Giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.106 ...1527fc1957f271b8f1b3cb3fb20/giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.106 ...1527fc1957f271b8f1b3cb3fb20/giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.108 ...97123326fc58f525350273e570ca89/2022}.svg} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.108 ...97123326fc58f525350273e570ca89/2022}.svg} [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) LaTeX Warning: Hyper reference `faqs:faqs' on page 3 undefined on input line 14 2. [3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [4] Overfull \vbox (27.0568pt too high) has occurred while \output is active [5 <./GiottoInstallationWorkflow.png>] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] LaTeX Warning: Hyper reference `subsections/md_rst/createGiottoInstructions:cre ategiottoinstructions' on page 9 undefined on input line 338. [9] [10] ! TeX capacity exceeded, sorry [input stack size=5000]. \curr@fontshape ->\f@encoding /\f@family /\f@series /\f@shape l.441 ...cludegraphics{{icons_configuration}.png}} ^^M ! ==> Fatal error occurred, no output PDF file produced! Transcript written on giottoteam-giotto.log. Latexmk: Index file 'giottoteam-giotto.idx' was written Failure to make 'giottoteam-giotto.pdf' Latexmk: Errors, in force_mode: so I tried finishing targets Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 [rtd-command-info] start-time: 2022-07-14T19:43:48.284730Z, end-time: 2022-07-14T19:44:49.398917Z, duration: 61, exit-code: 0 python -m sphinx -T -E -b epub -d _build/doctrees -D language=en . _build/epub Running Sphinx v3.4.3 loading translations [en]... done making output directory... done WARNING: conf value "version" should not be empty for EPUB3 building [mo]: targets for 0 po files that are out of date building [epub]: targets for 675 source files that are out of date updating environment: [new config] 675 added, 0 changed, 0 removed reading sources... [ 0%] Workflow reading sources... [ 0%] additionalinformation reading sources... [ 0%] contribute reading sources... [ 0%] datasets reading sources... [ 0%] development reading sources... [ 0%] documentation reading sources... [ 1%] errorsfaqsandtips reading sources... [ 1%] faqs reading sources... [ 1%] gettingstarted reading sources... [ 1%] giottoworkflowanalyses reading sources... [ 1%] github_issues reading sources... [ 1%] index reading sources... [ 1%] subsections/citing_giotto reading sources... [ 2%] subsections/code_of_conduct reading sources... [ 2%] subsections/datasets/STARmap_mouse_cortex reading sources... [ 2%] subsections/datasets/human_CyCIF_PDAC reading sources... [ 2%] subsections/datasets/merFISH_hypot_preopt_region reading sources... [ 2%] subsections/datasets/mini_3D_STARmap reading sources... [ 2%] subsections/datasets/mini_seqFISH reading sources... [ 2%] subsections/datasets/mini_visium reading sources... [ 3%] subsections/datasets/mouse_CODEX_spleen reading sources... [ 3%] subsections/datasets/mouse_visium_brain reading sources... [ 3%] subsections/datasets/mouse_visium_kidney reading sources... [ 3%] subsections/datasets/nanostring_lung_12 reading sources... [ 3%] subsections/datasets/nanostring_overview reading sources... [ 3%] subsections/datasets/osmFISH_mouse_SS_cortex reading sources... [ 4%] subsections/datasets/other_technologies_coming_soon reading sources... [ 4%] subsections/datasets/resolve_bc_210928 reading sources... [ 4%] subsections/datasets/seqFISH_cortex reading sources... [ 4%] subsections/datasets/singlecell_prostate_integration reading sources... [ 4%] subsections/datasets/singlecell_prostate_standard reading sources... [ 4%] subsections/datasets/tcyCIF reading sources... [ 4%] subsections/datasets/visium_prostate_integration reading sources... [ 5%] subsections/datasets/vizgen_mouse_brain reading sources... [ 5%] subsections/detailed_workflow reading sources... [ 5%] subsections/license reading sources... [ 5%] subsections/md_rst/DT_removeNA reading sources... [ 5%] subsections/md_rst/FSV_show reading sources... [ 5%] subsections/md_rst/OR_test_fnc reading sources... [ 5%] subsections/md_rst/PAGEEnrich reading sources... [ 6%] subsections/md_rst/PAGE_DT_method reading sources... [ 6%] subsections/md_rst/adapt_aspect_ratio reading sources... [ 6%] subsections/md_rst/addCellIntMetadata reading sources... [ 6%] subsections/md_rst/addCellMetadata reading sources... [ 6%] subsections/md_rst/addCellStatistics reading sources... [ 6%] subsections/md_rst/addCellsFromPolygon reading sources... [ 6%] subsections/md_rst/addFeatMetadata reading sources... [ 7%] subsections/md_rst/addFeatStatistics reading sources... [ 7%] subsections/md_rst/addFeatsPerc reading sources... [ 7%] subsections/md_rst/addGeneMetadata reading sources... [ 7%] subsections/md_rst/addGeneStatistics reading sources... [ 7%] subsections/md_rst/addGenesPerc reading sources... [ 7%] subsections/md_rst/addGiottoImage reading sources... [ 8%] subsections/md_rst/addGiottoImageMG reading sources... [ 8%] subsections/md_rst/addGiottoImageToSpatPlot reading sources... [ 8%] subsections/md_rst/addGiottoLargeImage reading sources... [ 8%] subsections/md_rst/addGiottoPoints reading sources... [ 8%] subsections/md_rst/addGiottoPolygons reading sources... [ 8%] subsections/md_rst/addHMRF reading sources... [ 8%] subsections/md_rst/addNetworkLayout reading sources... [ 9%] subsections/md_rst/addSpatialCentroidLocations reading sources... [ 9%] subsections/md_rst/addSpatialCentroidLocationsLayer reading sources... [ 9%] subsections/md_rst/addStatistics reading sources... [ 9%] subsections/md_rst/add_img_array_alpha reading sources... [ 9%] subsections/md_rst/adjustGiottoMatrix reading sources... [ 9%] subsections/md_rst/aes_string2 reading sources... [ 9%] subsections/md_rst/all_plots_save_function reading sources... [ 10%] subsections/md_rst/anndataToGiotto reading sources... [ 10%] subsections/md_rst/annotateGiotto reading sources... [ 10%] subsections/md_rst/annotateSpatialGrid reading sources... [ 10%] subsections/md_rst/annotateSpatialNetwork reading sources... [ 10%] subsections/md_rst/annotate_spatlocs_with_spatgrid_2D reading sources... [ 10%] subsections/md_rst/annotate_spatlocs_with_spatgrid_3D reading sources... [ 10%] subsections/md_rst/average_feat_feat_expression_in_groups reading sources... [ 11%] subsections/md_rst/binSpect reading sources... [ 11%] subsections/md_rst/binSpectMulti reading sources... [ 11%] subsections/md_rst/binSpectMultiMatrix reading sources... [ 11%] subsections/md_rst/binSpectSingle reading sources... [ 11%] subsections/md_rst/binSpectSingleMatrix reading sources... [ 11%] subsections/md_rst/calc_cov_group_HVF reading sources... [ 12%] subsections/md_rst/calc_cov_loess_HVF reading sources... [ 12%] subsections/md_rst/calc_spatial_enrichment_DT reading sources... [ 12%] subsections/md_rst/calc_spatial_enrichment_matrix reading sources... [ 12%] subsections/md_rst/calc_spatial_enrichment_minimum reading sources... [ 12%] subsections/md_rst/calc_var_HVF reading sources... [ 12%] subsections/md_rst/calculateHVF reading sources... [ 12%] subsections/md_rst/calculateHVG reading sources... [ 13%] subsections/md_rst/calculateMetaTable reading sources... [ 13%] subsections/md_rst/calculateMetaTableCells reading sources... [ 13%] subsections/md_rst/calculateOverlapParallel reading sources... [ 13%] subsections/md_rst/calculateOverlapRaster reading sources... [ 13%] subsections/md_rst/calculateOverlapSerial reading sources... [ 13%] subsections/md_rst/calculate_centroids_polygons reading sources... [ 13%] subsections/md_rst/calculate_distance_and_weight reading sources... [ 14%] subsections/md_rst/cellProximityBarplot reading sources... [ 14%] subsections/md_rst/cellProximityEnrichment reading sources... [ 14%] subsections/md_rst/cellProximityHeatmap reading sources... [ 14%] subsections/md_rst/cellProximityNetwork reading sources... [ 14%] subsections/md_rst/cellProximitySpatPlot reading sources... [ 14%] subsections/md_rst/cellProximitySpatPlot2D reading sources... [ 14%] subsections/md_rst/cellProximitySpatPlot3D reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot_2D_ggplot reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot_2D_plotly reading sources... [ 15%] subsections/md_rst/cellProximityVisPlot_3D_plotly reading sources... [ 15%] subsections/md_rst/changeGiottoInstructions reading sources... [ 15%] subsections/md_rst/changeImageBg reading sources... [ 16%] subsections/md_rst/checkGiottoEnvironment reading sources... [ 16%] subsections/md_rst/check_spatial_location_data reading sources... [ 16%] subsections/md_rst/clusterCells reading sources... [ 16%] subsections/md_rst/clusterSpatialCorFeats reading sources... [ 16%] subsections/md_rst/clusterSpatialCorGenes reading sources... [ 16%] subsections/md_rst/cluster_enrich_analysis reading sources... [ 16%] subsections/md_rst/colMeans_flex reading sources... [ 17%] subsections/md_rst/colSums_flex reading sources... [ 17%] subsections/md_rst/combCCcom reading sources... [ 17%] subsections/md_rst/combineCPG reading sources... [ 17%] subsections/md_rst/combineCellData reading sources... [ 17%] subsections/md_rst/combineCellProximityGenes reading sources... [ 17%] subsections/md_rst/combineCellProximityGenes_per_interaction reading sources... [ 17%] subsections/md_rst/combineFeatureData reading sources... [ 18%] subsections/md_rst/combineFeatureOverlapData reading sources... [ 18%] subsections/md_rst/combineICG reading sources... [ 18%] subsections/md_rst/combineInteractionChangedGenes reading sources... [ 18%] subsections/md_rst/combineMetadata reading sources... [ 18%] subsections/md_rst/combineSpatialCellFeatureInfo reading sources... [ 18%] subsections/md_rst/combineSpatialCellMetadataInfo reading sources... [ 18%] subsections/md_rst/compatible_spatial_network reading sources... [ 19%] subsections/md_rst/convertEnsemblToGeneSymbol reading sources... [ 19%] subsections/md_rst/convertGiottoLargeImageToMG reading sources... [ 19%] subsections/md_rst/convert_mgImage_to_array_DT reading sources... [ 19%] subsections/md_rst/convert_to_full_spatial_network reading sources... [ 19%] subsections/md_rst/convert_to_reduced_spatial_network reading sources... [ 19%] subsections/md_rst/cor_flex reading sources... [ 20%] subsections/md_rst/createCrossSection reading sources... [ 20%] subsections/md_rst/createGiottoImage reading sources... [ 20%] subsections/md_rst/createGiottoImageOLD reading sources... [ 20%] subsections/md_rst/createGiottoInstructions reading sources... [ 20%] subsections/md_rst/createGiottoLargeImage reading sources... [ 20%] subsections/md_rst/createGiottoLargeImageList reading sources... [ 20%] subsections/md_rst/createGiottoObject reading sources... [ 21%] subsections/md_rst/createGiottoObjectSubcellular reading sources... [ 21%] subsections/md_rst/createGiottoPoints reading sources... [ 21%] subsections/md_rst/createGiottoPolygonsFromDfr reading sources... [ 21%] subsections/md_rst/createGiottoPolygonsFromMask reading sources... [ 21%] subsections/md_rst/createGiottoVisiumObject reading sources... [ 21%] subsections/md_rst/createHeatmap_DT reading sources... [ 21%] subsections/md_rst/createMetafeats reading sources... [ 22%] subsections/md_rst/createMetagenes reading sources... [ 22%] subsections/md_rst/createNearestNetwork reading sources... [ 22%] subsections/md_rst/createSpatialDefaultGrid reading sources... [ 22%] subsections/md_rst/createSpatialDelaunayNetwork reading sources... [ 22%] subsections/md_rst/createSpatialEnrich reading sources... [ 22%] subsections/md_rst/createSpatialFeaturesKNNnetwork reading sources... [ 22%] subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan reading sources... [ 23%] subsections/md_rst/createSpatialGrid reading sources... [ 23%] subsections/md_rst/createSpatialKNNnetwork reading sources... [ 23%] subsections/md_rst/createSpatialNetwork reading sources... [ 23%] subsections/md_rst/create_2d_mesh_grid_line_obj reading sources... [ 23%] subsections/md_rst/create_KNNnetwork_dbscan reading sources... [ 23%] subsections/md_rst/create_average_DT reading sources... [ 24%] subsections/md_rst/create_average_detection_DT reading sources... [ 24%] subsections/md_rst/create_cell_type_random_cell_IDs reading sources... [ 24%] subsections/md_rst/create_cluster_matrix reading sources... [ 24%] subsections/md_rst/create_crossSection_object reading sources... [ 24%] subsections/md_rst/create_delaunayNetwork2D reading sources... [ 24%] subsections/md_rst/create_delaunayNetwork3D reading sources... [ 24%] subsections/md_rst/create_delaunayNetwork_RTriangle reading sources... [ 25%] subsections/md_rst/create_delaunayNetwork_deldir reading sources... [ 25%] subsections/md_rst/create_delaunayNetwork_geometry reading sources... [ 25%] subsections/md_rst/create_delaunayNetwork_geometry_3D reading sources... [ 25%] subsections/md_rst/create_dimObject reading sources... [ 25%] subsections/md_rst/create_featureNetwork_object reading sources... [ 25%] subsections/md_rst/create_genes_to_use_matrix reading sources... [ 25%] subsections/md_rst/create_giotto_points_object reading sources... [ 26%] subsections/md_rst/create_giotto_polygon_object reading sources... [ 26%] subsections/md_rst/create_jackstrawplot reading sources... [ 26%] subsections/md_rst/create_mesh_grid_lines reading sources... [ 26%] subsections/md_rst/create_screeplot reading sources... [ 26%] subsections/md_rst/create_segm_polygons reading sources... [ 26%] subsections/md_rst/create_spatialGridObject reading sources... [ 26%] subsections/md_rst/create_spatialGrid_default_2D reading sources... [ 27%] subsections/md_rst/create_spatialGrid_default_3D reading sources... [ 27%] subsections/md_rst/create_spatialNetworkObject reading sources... [ 27%] subsections/md_rst/create_spatvector_object_from_dfr reading sources... [ 27%] subsections/md_rst/cropGiottoLargeImage reading sources... [ 27%] subsections/md_rst/crossSectionGenePlot reading sources... [ 27%] subsections/md_rst/crossSectionGenePlot3D reading sources... [ 28%] subsections/md_rst/crossSectionPlot reading sources... [ 28%] subsections/md_rst/crossSectionPlot3D reading sources... [ 28%] subsections/md_rst/decide_cluster_order reading sources... [ 28%] subsections/md_rst/density_giottoLargeImage reading sources... [ 28%] subsections/md_rst/depth reading sources... [ 28%] subsections/md_rst/detectSpatialCorFeats reading sources... [ 28%] subsections/md_rst/detectSpatialCorFeatsMatrix reading sources... [ 29%] subsections/md_rst/detectSpatialCorGenes reading sources... [ 29%] subsections/md_rst/detectSpatialPatterns reading sources... [ 29%] subsections/md_rst/determine_cores reading sources... [ 29%] subsections/md_rst/dimCellPlot reading sources... [ 29%] subsections/md_rst/dimCellPlot2D reading sources... [ 29%] subsections/md_rst/dimFeatPlot2D reading sources... [ 29%] subsections/md_rst/dimGenePlot reading sources... [ 30%] subsections/md_rst/dimGenePlot2D reading sources... [ 30%] subsections/md_rst/dimGenePlot3D reading sources... [ 30%] subsections/md_rst/dimPlot reading sources... [ 30%] subsections/md_rst/dimPlot2D reading sources... [ 30%] subsections/md_rst/dimPlot2D_single reading sources... [ 30%] subsections/md_rst/dimPlot3D reading sources... [ 30%] subsections/md_rst/dimPlot_2D_plotly reading sources... [ 31%] subsections/md_rst/dimPlot_3D_plotly reading sources... [ 31%] subsections/md_rst/distGiottoImage reading sources... [ 31%] subsections/md_rst/doCellSegmentation reading sources... [ 31%] subsections/md_rst/doHMRF reading sources... [ 31%] subsections/md_rst/doHclust reading sources... [ 31%] subsections/md_rst/doKmeans reading sources... [ 32%] subsections/md_rst/doLeidenCluster reading sources... [ 32%] subsections/md_rst/doLeidenSubCluster reading sources... [ 32%] subsections/md_rst/doLouvainCluster reading sources... [ 32%] subsections/md_rst/doLouvainCluster_community reading sources... [ 32%] subsections/md_rst/doLouvainCluster_multinet reading sources... [ 32%] subsections/md_rst/doLouvainSubCluster reading sources... [ 32%] subsections/md_rst/doLouvainSubCluster_community reading sources... [ 33%] subsections/md_rst/doLouvainSubCluster_multinet reading sources... [ 33%] subsections/md_rst/doRandomWalkCluster reading sources... [ 33%] subsections/md_rst/doSNNCluster reading sources... [ 33%] subsections/md_rst/doScrubletDetect reading sources... [ 33%] subsections/md_rst/do_cell_proximity_test reading sources... [ 33%] subsections/md_rst/do_limmatest reading sources... [ 33%] subsections/md_rst/do_multi_permuttest_random reading sources... [ 34%] subsections/md_rst/do_page_permutation reading sources... [ 34%] subsections/md_rst/do_permuttest_original reading sources... [ 34%] subsections/md_rst/do_permuttest_random reading sources... [ 34%] subsections/md_rst/do_rank_permutation reading sources... [ 34%] subsections/md_rst/do_spatial_grid_averaging reading sources... [ 34%] subsections/md_rst/do_spatial_knn_smoothing reading sources... [ 34%] subsections/md_rst/do_ttest reading sources... [ 35%] subsections/md_rst/do_wilctest reading sources... [ 35%] subsections/md_rst/dt_to_matrix reading sources... [ 35%] subsections/md_rst/dt_to_spatVector_points reading sources... [ 35%] subsections/md_rst/dt_to_spatVector_polygon reading sources... [ 35%] subsections/md_rst/enrich_analysis reading sources... [ 35%] subsections/md_rst/enrich_deconvolution reading sources... [ 36%] subsections/md_rst/estimateCellCellDistance reading sources... [ 36%] subsections/md_rst/estimateImageBg reading sources... [ 36%] subsections/md_rst/evaluate_expr_matrix reading sources... [ 36%] subsections/md_rst/evaluate_feat_info reading sources... [ 36%] subsections/md_rst/evaluate_provided_spatial_locations reading sources... [ 36%] subsections/md_rst/evaluate_spatial_info reading sources... [ 36%] subsections/md_rst/evaluate_spatial_locations reading sources... [ 37%] subsections/md_rst/evaluate_spatial_locations_OLD reading sources... [ 37%] subsections/md_rst/evaluate_spatial_network reading sources... [ 37%] subsections/md_rst/exportGiottoViewer reading sources... [ 37%] subsections/md_rst/exprCellCellcom reading sources... [ 37%] subsections/md_rst/extend_vector reading sources... [ 37%] subsections/md_rst/extended_gini_fun reading sources... [ 37%] subsections/md_rst/extractNearestNetwork reading sources... [ 38%] subsections/md_rst/extract_points_list reading sources... [ 38%] subsections/md_rst/extract_polygon_list reading sources... [ 38%] subsections/md_rst/fDataDT reading sources... [ 38%] subsections/md_rst/featureNetwork-class reading sources... [ 38%] subsections/md_rst/filterCPG reading sources... [ 38%] subsections/md_rst/filterCellProximityGenes reading sources... [ 38%] subsections/md_rst/filterCombinations reading sources... [ 39%] subsections/md_rst/filterDistributions reading sources... [ 39%] subsections/md_rst/filterGiotto reading sources... [ 39%] subsections/md_rst/filterICF reading sources... [ 39%] subsections/md_rst/filterICG reading sources... [ 39%] subsections/md_rst/filterInteractionChangedFeats reading sources... [ 39%] subsections/md_rst/filterInteractionChangedGenes reading sources... [ 40%] subsections/md_rst/filter_network reading sources... [ 40%] subsections/md_rst/findCPG reading sources... [ 40%] subsections/md_rst/findCellProximityFeats_per_interaction reading sources... [ 40%] subsections/md_rst/findCellProximityGenes reading sources... [ 40%] subsections/md_rst/findGiniMarkers reading sources... [ 40%] subsections/md_rst/findGiniMarkers_one_vs_all reading sources... [ 40%] subsections/md_rst/findICF reading sources... [ 41%] subsections/md_rst/findICG reading sources... [ 41%] subsections/md_rst/findInteractionChangedFeats reading sources... [ 41%] subsections/md_rst/findInteractionChangedGenes reading sources... [ 41%] subsections/md_rst/findMarkers reading sources... [ 41%] subsections/md_rst/findMarkers_one_vs_all reading sources... [ 41%] subsections/md_rst/findMastMarkers reading sources... [ 41%] subsections/md_rst/findMastMarkers_one_vs_all reading sources... [ 42%] subsections/md_rst/findNetworkNeighbors reading sources... [ 42%] subsections/md_rst/findScranMarkers reading sources... [ 42%] subsections/md_rst/findScranMarkers_one_vs_all reading sources... [ 42%] subsections/md_rst/find_dampening_constant reading sources... [ 42%] subsections/md_rst/find_grid_2D reading sources... [ 42%] subsections/md_rst/find_grid_3D reading sources... [ 42%] subsections/md_rst/find_grid_x reading sources... [ 43%] subsections/md_rst/find_grid_y reading sources... [ 43%] subsections/md_rst/find_grid_z reading sources... [ 43%] subsections/md_rst/find_terra_writeRaster_dataType reading sources... [ 43%] subsections/md_rst/find_x_y_ranges reading sources... [ 43%] subsections/md_rst/fix_multipart_geoms reading sources... [ 43%] subsections/md_rst/flex_lapply reading sources... [ 44%] subsections/md_rst/general_save_function reading sources... [ 44%] subsections/md_rst/get10Xmatrix reading sources... [ 44%] subsections/md_rst/get10XmatrixOLD reading sources... [ 44%] subsections/md_rst/get10Xmatrix_h5 reading sources... [ 44%] subsections/md_rst/getCellsFromPolygon reading sources... [ 44%] subsections/md_rst/getClusterSimilarity reading sources... [ 44%] subsections/md_rst/getDendrogramSplits reading sources... [ 45%] subsections/md_rst/getDistinctColors reading sources... [ 45%] subsections/md_rst/getSpatialDataset reading sources... [ 45%] subsections/md_rst/get_NearestNetwork reading sources... [ 45%] subsections/md_rst/get_adj_rescale_img reading sources... [ 45%] subsections/md_rst/get_args reading sources... [ 45%] subsections/md_rst/get_cross_section_coordinates reading sources... [ 45%] subsections/md_rst/get_dimReduction reading sources... [ 46%] subsections/md_rst/get_distance reading sources... [ 46%] subsections/md_rst/get_expression_values reading sources... [ 46%] subsections/md_rst/get_feature_info reading sources... [ 46%] subsections/md_rst/get_giottoImage reading sources... [ 46%] subsections/md_rst/get_giottoImage_MG reading sources... [ 46%] subsections/md_rst/get_giottoLargeImage reading sources... [ 46%] subsections/md_rst/get_img_corners reading sources... [ 47%] subsections/md_rst/get_img_minmax reading sources... [ 47%] subsections/md_rst/get_os reading sources... [ 47%] subsections/md_rst/get_polygon_info reading sources... [ 47%] subsections/md_rst/get_sectionThickness reading sources... [ 47%] subsections/md_rst/get_spatialGrid reading sources... [ 47%] subsections/md_rst/get_spatialNetwork reading sources... [ 48%] subsections/md_rst/get_spatial_enrichment reading sources... [ 48%] subsections/md_rst/get_spatial_locations reading sources... [ 48%] subsections/md_rst/ggplot_save_function reading sources... [ 48%] subsections/md_rst/giotto-class reading sources... [ 48%] subsections/md_rst/giottoImage-class reading sources... [ 48%] subsections/md_rst/giottoLargeImage-class reading sources... [ 48%] subsections/md_rst/giottoPoints-class reading sources... [ 49%] subsections/md_rst/giottoPolygon-class reading sources... [ 49%] subsections/md_rst/giottoToSeurat reading sources... [ 49%] subsections/md_rst/giotto_point reading sources... [ 49%] subsections/md_rst/heatmSpatialCorFeats reading sources... [ 49%] subsections/md_rst/heatmSpatialCorGenes reading sources... [ 49%] subsections/md_rst/hyperGeometricEnrich reading sources... [ 49%] subsections/md_rst/identify_background_range_polygons reading sources... [ 50%] subsections/md_rst/insertCrossSectionGenePlot3D reading sources... [ 50%] subsections/md_rst/insertCrossSectionSpatPlot3D reading sources... [ 50%] subsections/md_rst/installGiottoEnvironment reading sources... [ 50%] subsections/md_rst/install_giotto_environment reading sources... [ 50%] subsections/md_rst/install_giotto_environment_specific reading sources... [ 50%] subsections/md_rst/jackstrawPlot reading sources... [ 50%] subsections/md_rst/joinGiottoObjects reading sources... [ 51%] subsections/md_rst/join_cell_meta reading sources... [ 51%] subsections/md_rst/join_expression_matrices reading sources... [ 51%] subsections/md_rst/join_spatlocs reading sources... [ 51%] subsections/md_rst/kmeans_arma_binarize reading sources... [ 51%] subsections/md_rst/kmeans_arma_subset_binarize reading sources... [ 51%] subsections/md_rst/kmeans_binarize reading sources... [ 52%] subsections/md_rst/kmeans_binarize_wrapper reading sources... [ 52%] subsections/md_rst/lapply_flex reading sources... [ 52%] subsections/md_rst/libNorm_giotto reading sources... [ 52%] subsections/md_rst/list_cell_metadata reading sources... [ 52%] subsections/md_rst/list_dim_reductions reading sources... [ 52%] subsections/md_rst/list_dim_reductions_names reading sources... [ 52%] subsections/md_rst/list_expression reading sources... [ 53%] subsections/md_rst/list_expression_names reading sources... [ 53%] subsections/md_rst/list_feat_metadata reading sources... [ 53%] subsections/md_rst/list_feature_info reading sources... [ 53%] subsections/md_rst/list_feature_info_names reading sources... [ 53%] subsections/md_rst/list_giotto_data reading sources... [ 53%] subsections/md_rst/list_images reading sources... [ 53%] subsections/md_rst/list_images_names reading sources... [ 54%] subsections/md_rst/list_spatial_enrichments reading sources... [ 54%] subsections/md_rst/list_spatial_enrichments_names reading sources... [ 54%] subsections/md_rst/list_spatial_grids reading sources... [ 54%] subsections/md_rst/list_spatial_grids_names reading sources... [ 54%] subsections/md_rst/list_spatial_info reading sources... [ 54%] subsections/md_rst/list_spatial_info_names reading sources... [ 54%] subsections/md_rst/list_spatial_locations reading sources... [ 55%] subsections/md_rst/list_spatial_locations_names reading sources... [ 55%] subsections/md_rst/list_spatial_networks reading sources... [ 55%] subsections/md_rst/list_spatial_networks_names reading sources... [ 55%] subsections/md_rst/loadHMRF reading sources... [ 55%] subsections/md_rst/logNorm_giotto reading sources... [ 55%] subsections/md_rst/makeSignMatrixDWLS reading sources... [ 56%] subsections/md_rst/makeSignMatrixDWLSfromMatrix reading sources... [ 56%] subsections/md_rst/makeSignMatrixPAGE reading sources... [ 56%] subsections/md_rst/makeSignMatrixRank reading sources... [ 56%] subsections/md_rst/make_simulated_network reading sources... [ 56%] subsections/md_rst/mean_expr_det_test reading sources... [ 56%] subsections/md_rst/mean_flex reading sources... [ 56%] subsections/md_rst/mergeClusters reading sources... [ 57%] subsections/md_rst/merge_spatial_locs_feat_info reading sources... [ 57%] subsections/md_rst/mini_giotto_3D reading sources... [ 57%] subsections/md_rst/mini_giotto_multi_cell reading sources... [ 57%] subsections/md_rst/mini_giotto_single_cell reading sources... [ 57%] subsections/md_rst/my_arowMeans reading sources... [ 57%] subsections/md_rst/my_growMeans reading sources... [ 57%] subsections/md_rst/my_rowMeans reading sources... [ 58%] subsections/md_rst/mygini_fun reading sources... [ 58%] subsections/md_rst/nnDT_to_kNN reading sources... [ 58%] subsections/md_rst/node_clusters reading sources... [ 58%] subsections/md_rst/normalizeGiotto reading sources... [ 58%] subsections/md_rst/optimize_deconvolute_dwls reading sources... [ 58%] subsections/md_rst/optimize_solveDampenedWLS reading sources... [ 58%] subsections/md_rst/overlapToMatrix reading sources... [ 59%] subsections/md_rst/overlapToMatrixMultiPoly reading sources... [ 59%] subsections/md_rst/overlap_points_per_polygon reading sources... [ 59%] subsections/md_rst/overlap_points_per_polygon_wrapped reading sources... [ 59%] subsections/md_rst/overlap_points_single_polygon reading sources... [ 59%] subsections/md_rst/pDataDT reading sources... [ 59%] subsections/md_rst/package_check reading sources... [ 60%] subsections/md_rst/pca_giotto reading sources... [ 60%] subsections/md_rst/pipe reading sources... [ 60%] subsections/md_rst/plotCCcomDotplot reading sources... [ 60%] subsections/md_rst/plotCCcomHeatmap reading sources... [ 60%] subsections/md_rst/plotCPG reading sources... [ 60%] subsections/md_rst/plotCellProximityGenes reading sources... [ 60%] subsections/md_rst/plotCombineCCcom reading sources... [ 61%] subsections/md_rst/plotCombineCPG reading sources... [ 61%] subsections/md_rst/plotCombineCellCellCommunication reading sources... [ 61%] subsections/md_rst/plotCombineCellProximityGenes reading sources... [ 61%] subsections/md_rst/plotCombineICG reading sources... [ 61%] subsections/md_rst/plotCombineInteractionChangedGenes reading sources... [ 61%] subsections/md_rst/plotGiottoImage reading sources... [ 61%] subsections/md_rst/plotHeatmap reading sources... [ 62%] subsections/md_rst/plotICF reading sources... [ 62%] subsections/md_rst/plotICG reading sources... [ 62%] subsections/md_rst/plotInteractionChangedFeats reading sources... [ 62%] subsections/md_rst/plotInteractionChangedGenes reading sources... [ 62%] subsections/md_rst/plotInteractivePolygons reading sources... [ 62%] subsections/md_rst/plotMetaDataCellsHeatmap reading sources... [ 62%] subsections/md_rst/plotMetaDataHeatmap reading sources... [ 63%] subsections/md_rst/plotPCA reading sources... [ 63%] subsections/md_rst/plotPCA_2D reading sources... [ 63%] subsections/md_rst/plotPCA_3D reading sources... [ 63%] subsections/md_rst/plotRankSpatvsExpr reading sources... [ 63%] subsections/md_rst/plotRecovery reading sources... [ 63%] subsections/md_rst/plotRecovery_sub reading sources... [ 64%] subsections/md_rst/plotStatDelaunayNetwork reading sources... [ 64%] subsections/md_rst/plotTSNE reading sources... [ 64%] subsections/md_rst/plotTSNE_2D reading sources... [ 64%] subsections/md_rst/plotTSNE_3D reading sources... [ 64%] subsections/md_rst/plotUMAP reading sources... [ 64%] subsections/md_rst/plotUMAP_2D reading sources... [ 64%] subsections/md_rst/plotUMAP_3D reading sources... [ 65%] subsections/md_rst/plot_auto_largeImage_resample reading sources... [ 65%] subsections/md_rst/plot_cell_polygon_layer reading sources... [ 65%] subsections/md_rst/plot_feature_hexbin_layer reading sources... [ 65%] subsections/md_rst/plot_feature_points_layer reading sources... [ 65%] subsections/md_rst/plot_feature_raster_density_layer reading sources... [ 65%] subsections/md_rst/plot_giottoImage_MG reading sources... [ 65%] subsections/md_rst/plot_giottoLargeImage reading sources... [ 66%] subsections/md_rst/plot_network_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_point_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_point_layer_ggplot_noFILL reading sources... [ 66%] subsections/md_rst/plot_spat_image_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_spat_point_layer_ggplot reading sources... [ 66%] subsections/md_rst/plot_spat_point_layer_ggplot_noFILL reading sources... [ 66%] subsections/md_rst/plot_spat_scatterpie_layer_ggplot reading sources... [ 67%] subsections/md_rst/plot_spat_voronoi_layer_ggplot reading sources... [ 67%] subsections/md_rst/plotly_axis_scale_2D reading sources... [ 67%] subsections/md_rst/plotly_axis_scale_3D reading sources... [ 67%] subsections/md_rst/plotly_grid reading sources... [ 67%] subsections/md_rst/plotly_network reading sources... [ 67%] subsections/md_rst/polygon_to_raster reading sources... [ 68%] subsections/md_rst/processGiotto reading sources... [ 68%] subsections/md_rst/projection_fun reading sources... [ 68%] subsections/md_rst/rankEnrich reading sources... [ 68%] subsections/md_rst/rankSpatialCorGroups reading sources... [ 68%] subsections/md_rst/rank_binarize reading sources... [ 68%] subsections/md_rst/rank_binarize_wrapper reading sources... [ 68%] subsections/md_rst/readExprMatrix reading sources... [ 69%] subsections/md_rst/readGiottoInstructions reading sources... [ 69%] subsections/md_rst/readPolygonFilesVizgen reading sources... [ 69%] subsections/md_rst/readPolygonFilesVizgenHDF5 reading sources... [ 69%] subsections/md_rst/read_crossSection reading sources... [ 69%] subsections/md_rst/read_dimension_reduction reading sources... [ 69%] subsections/md_rst/read_expression_data reading sources... [ 69%] subsections/md_rst/read_nearest_networks reading sources... [ 70%] subsections/md_rst/read_spatial_enrichment reading sources... [ 70%] subsections/md_rst/read_spatial_location_data reading sources... [ 70%] subsections/md_rst/read_spatial_networks reading sources... [ 70%] subsections/md_rst/reconnectGiottoImage reading sources... [ 70%] subsections/md_rst/reconnect_giottoImage_MG reading sources... [ 70%] subsections/md_rst/reconnect_giottoLargeImage reading sources... [ 70%] subsections/md_rst/reconnect_image_object reading sources... [ 71%] subsections/md_rst/reg_img_minmax_finder reading sources... [ 71%] subsections/md_rst/registerGiottoObjectList reading sources... [ 71%] subsections/md_rst/registerGiottoObjectListFiji reading sources... [ 71%] subsections/md_rst/registerGiottoObjectListRvision reading sources... [ 71%] subsections/md_rst/registerImagesFIJI reading sources... [ 71%] subsections/md_rst/removeCellAnnotation reading sources... [ 72%] subsections/md_rst/removeFeatAnnotation reading sources... [ 72%] subsections/md_rst/removeGiottoEnvironment reading sources... [ 72%] subsections/md_rst/replaceGiottoInstructions reading sources... [ 72%] subsections/md_rst/reshape_to_data_point reading sources... [ 72%] subsections/md_rst/reshape_to_mesh_grid_obj reading sources... [ 72%] subsections/md_rst/return_giotto_environment_path reading sources... [ 72%] subsections/md_rst/return_giotto_environment_path_executable reading sources... [ 73%] subsections/md_rst/rigid_transform_spatial_locations reading sources... [ 73%] subsections/md_rst/rna_osmfish_normalization reading sources... [ 73%] subsections/md_rst/rna_pears_resid_normalization reading sources... [ 73%] subsections/md_rst/rna_standard_normalization reading sources... [ 73%] subsections/md_rst/rotate_spatial_locations reading sources... [ 73%] subsections/md_rst/rowMeans_flex reading sources... [ 73%] subsections/md_rst/rowSums_flex reading sources... [ 74%] subsections/md_rst/runDWLSDeconv reading sources... [ 74%] subsections/md_rst/runFijiMacro reading sources... [ 74%] subsections/md_rst/runGiottoHarmony reading sources... [ 74%] subsections/md_rst/runHyperGeometricEnrich reading sources... [ 74%] subsections/md_rst/runPAGEEnrich reading sources... [ 74%] subsections/md_rst/runPAGEEnrich_OLD reading sources... [ 74%] subsections/md_rst/runPCA reading sources... [ 75%] subsections/md_rst/runPCA_BiocSingular reading sources... [ 75%] subsections/md_rst/runPCA_factominer reading sources... [ 75%] subsections/md_rst/runPCA_prcomp_irlba reading sources... [ 75%] subsections/md_rst/runPatternSimulation reading sources... [ 75%] subsections/md_rst/runRankEnrich reading sources... [ 75%] subsections/md_rst/runSpatialDeconv reading sources... [ 76%] subsections/md_rst/runSpatialEnrich reading sources... [ 76%] subsections/md_rst/runUMAP reading sources... [ 76%] subsections/md_rst/run_spatial_sim_tests_multi reading sources... [ 76%] subsections/md_rst/run_spatial_sim_tests_one_rep reading sources... [ 76%] subsections/md_rst/runtSNE reading sources... [ 76%] subsections/md_rst/scale_spatial_locations reading sources... [ 76%] subsections/md_rst/screePlot reading sources... [ 77%] subsections/md_rst/selectPatternGenes reading sources... [ 77%] subsections/md_rst/select_NearestNetwork reading sources... [ 77%] subsections/md_rst/select_dimReduction reading sources... [ 77%] subsections/md_rst/select_expression_values reading sources... [ 77%] subsections/md_rst/select_feature_info reading sources... [ 77%] subsections/md_rst/select_gimage reading sources... [ 77%] subsections/md_rst/select_polygon_info reading sources... [ 78%] subsections/md_rst/select_spatialGrid reading sources... [ 78%] subsections/md_rst/select_spatialNetwork reading sources... [ 78%] subsections/md_rst/select_spatial_locations reading sources... [ 78%] subsections/md_rst/set_NearestNetwork reading sources... [ 78%] subsections/md_rst/set_cell_and_feat_IDs reading sources... [ 78%] subsections/md_rst/set_cell_metadata reading sources... [ 78%] subsections/md_rst/set_default_feat_type reading sources... [ 79%] subsections/md_rst/set_default_spat_unit reading sources... [ 79%] subsections/md_rst/set_dimReduction reading sources... [ 79%] subsections/md_rst/set_expression_values reading sources... [ 79%] subsections/md_rst/set_feature_info reading sources... [ 79%] subsections/md_rst/set_feature_metadata reading sources... [ 79%] subsections/md_rst/set_giottoImage reading sources... [ 80%] subsections/md_rst/set_giottoImage_MG reading sources... [ 80%] subsections/md_rst/set_giottoLargeImage reading sources... [ 80%] subsections/md_rst/set_giotto_python_path reading sources... [ 80%] subsections/md_rst/set_polygon_info reading sources... [ 80%] subsections/md_rst/set_spatialGrid reading sources... [ 80%] subsections/md_rst/set_spatialNetwork reading sources... [ 80%] subsections/md_rst/set_spatial_enrichment reading sources... [ 81%] subsections/md_rst/set_spatial_locations reading sources... [ 81%] subsections/md_rst/seuratToGiotto reading sources... [ 81%] subsections/md_rst/seuratToGiotto_OLD reading sources... [ 81%] subsections/md_rst/show-methods reading sources... [ 81%] subsections/md_rst/showClusterDendrogram reading sources... [ 81%] subsections/md_rst/showClusterHeatmap reading sources... [ 81%] subsections/md_rst/showGiottoDimRed reading sources... [ 82%] subsections/md_rst/showGiottoExpression reading sources... [ 82%] subsections/md_rst/showGiottoFeatInfo reading sources... [ 82%] subsections/md_rst/showGiottoImageNames reading sources... [ 82%] subsections/md_rst/showGiottoInstructions reading sources... [ 82%] subsections/md_rst/showGiottoSpatEnrichments reading sources... [ 82%] subsections/md_rst/showGiottoSpatGrids reading sources... [ 82%] subsections/md_rst/showGiottoSpatLocs reading sources... [ 83%] subsections/md_rst/showGiottoSpatNetworks reading sources... [ 83%] subsections/md_rst/showGiottoSpatialInfo reading sources... [ 83%] subsections/md_rst/showGrids reading sources... [ 83%] subsections/md_rst/showNetworks reading sources... [ 83%] subsections/md_rst/showPattern reading sources... [ 83%] subsections/md_rst/showPattern2D reading sources... [ 84%] subsections/md_rst/showPattern3D reading sources... [ 84%] subsections/md_rst/showPatternGenes reading sources... [ 84%] subsections/md_rst/showProcessingSteps reading sources... [ 84%] subsections/md_rst/showSaveParameters reading sources... [ 84%] subsections/md_rst/showSpatialCorFeats reading sources... [ 84%] subsections/md_rst/showSpatialCorGenes reading sources... [ 84%] subsections/md_rst/signPCA reading sources... [ 85%] subsections/md_rst/silhouetteRank reading sources... [ 85%] subsections/md_rst/silhouetteRankTest reading sources... [ 85%] subsections/md_rst/simulateOneGenePatternGiottoObject reading sources... [ 85%] subsections/md_rst/smoothGiottoPolygons reading sources... [ 85%] subsections/md_rst/solve_OLS_internal reading sources... [ 85%] subsections/md_rst/solve_dampened_WLSj reading sources... [ 85%] subsections/md_rst/sort_combine_two_DT_columns reading sources... [ 86%] subsections/md_rst/spark reading sources... [ 86%] subsections/md_rst/spatCellCellcom reading sources... [ 86%] subsections/md_rst/spatCellPlot reading sources... [ 86%] subsections/md_rst/spatCellPlot2D reading sources... [ 86%] subsections/md_rst/spatDeconvPlot reading sources... [ 86%] subsections/md_rst/spatDimCellPlot reading sources... [ 86%] subsections/md_rst/spatDimCellPlot2D reading sources... [ 87%] subsections/md_rst/spatDimFeatPlot2D reading sources... [ 87%] subsections/md_rst/spatDimGenePlot reading sources... [ 87%] subsections/md_rst/spatDimGenePlot2D reading sources... [ 87%] subsections/md_rst/spatDimGenePlot3D reading sources... [ 87%] subsections/md_rst/spatDimPlot reading sources... [ 87%] subsections/md_rst/spatDimPlot2D reading sources... [ 88%] subsections/md_rst/spatDimPlot3D reading sources... [ 88%] subsections/md_rst/spatFeatPlot2D reading sources... [ 88%] subsections/md_rst/spatFeatPlot2D_single reading sources... [ 88%] subsections/md_rst/spatGenePlot reading sources... [ 88%] subsections/md_rst/spatGenePlot2D reading sources... [ 88%] subsections/md_rst/spatGenePlot3D reading sources... [ 88%] subsections/md_rst/spatInSituPlotDensity reading sources... [ 89%] subsections/md_rst/spatInSituPlotDensity_single reading sources... [ 89%] subsections/md_rst/spatInSituPlotHex reading sources... [ 89%] subsections/md_rst/spatInSituPlotHex_single reading sources... [ 89%] subsections/md_rst/spatInSituPlotPoints reading sources... [ 89%] subsections/md_rst/spatNetwDistributions reading sources... [ 89%] subsections/md_rst/spatNetwDistributionsDistance reading sources... [ 89%] subsections/md_rst/spatNetwDistributionsKneighbors reading sources... [ 90%] subsections/md_rst/spatPlot reading sources... [ 90%] subsections/md_rst/spatPlot2D reading sources... [ 90%] subsections/md_rst/spatPlot2D_single reading sources... [ 90%] subsections/md_rst/spatPlot3D reading sources... [ 90%] subsections/md_rst/spatPlot_2D_plotly reading sources... [ 90%] subsections/md_rst/spatPlot_3D_plotly reading sources... [ 90%] subsections/md_rst/spatVector_to_dt reading sources... [ 91%] subsections/md_rst/spat_OR_func reading sources... [ 91%] subsections/md_rst/spat_OR_func_DT reading sources... [ 91%] subsections/md_rst/spat_fish_func reading sources... [ 91%] subsections/md_rst/spat_fish_func_DT reading sources... [ 91%] subsections/md_rst/spatialAEH reading sources... [ 91%] subsections/md_rst/spatialDE reading sources... [ 92%] subsections/md_rst/specificCellCellcommunicationScores reading sources... [ 92%] subsections/md_rst/spline_poly reading sources... [ 92%] subsections/md_rst/split_dendrogram_in_two reading sources... [ 92%] subsections/md_rst/spot_deconvolution reading sources... [ 92%] subsections/md_rst/standardise_flex reading sources... [ 92%] subsections/md_rst/stitchFieldCoordinates reading sources... [ 92%] subsections/md_rst/stitchGiottoLargeImage reading sources... [ 93%] subsections/md_rst/stitchTileCoordinates reading sources... [ 93%] subsections/md_rst/subClusterCells reading sources... [ 93%] subsections/md_rst/subsetGiotto reading sources... [ 93%] subsections/md_rst/subsetGiottoLocs reading sources... [ 93%] subsections/md_rst/subsetGiottoLocsMulti reading sources... [ 93%] subsections/md_rst/subset_cell_metadata reading sources... [ 93%] subsections/md_rst/subset_dimension_reduction reading sources... [ 94%] subsections/md_rst/subset_expression_data reading sources... [ 94%] subsections/md_rst/subset_feature_info_data reading sources... [ 94%] subsections/md_rst/subset_feature_metadata reading sources... [ 94%] subsections/md_rst/subset_giotto_points_object reading sources... [ 94%] subsections/md_rst/subset_giotto_polygon_object reading sources... [ 94%] subsections/md_rst/subset_nearest_network reading sources... [ 94%] subsections/md_rst/subset_spatial_enrichment reading sources... [ 95%] subsections/md_rst/subset_spatial_info_data reading sources... [ 95%] subsections/md_rst/subset_spatial_locations reading sources... [ 95%] subsections/md_rst/subset_spatial_network reading sources... [ 95%] subsections/md_rst/t_flex reading sources... [ 95%] subsections/md_rst/trakem2_rigid_transf_extract reading sources... [ 95%] subsections/md_rst/transform_2d_mesh_to_3d_mesh reading sources... [ 96%] subsections/md_rst/trendSceek reading sources... [ 96%] subsections/md_rst/updateGiottoImage reading sources... [ 96%] subsections/md_rst/updateGiottoImageMG reading sources... [ 96%] subsections/md_rst/updateGiottoLargeImage reading sources... [ 96%] subsections/md_rst/update_giotto_params reading sources... [ 96%] subsections/md_rst/viewHMRFresults reading sources... [ 96%] subsections/md_rst/viewHMRFresults2D reading sources... [ 97%] subsections/md_rst/viewHMRFresults3D reading sources... [ 97%] subsections/md_rst/violinPlot reading sources... [ 97%] subsections/md_rst/writeGiottoLargeImage reading sources... [ 97%] subsections/md_rst/writeHMRFresults reading sources... [ 97%] subsections/md_rst/write_giotto_viewer_annotation reading sources... [ 97%] subsections/md_rst/write_giotto_viewer_dim_reduction reading sources... [ 97%] subsections/md_rst/write_giotto_viewer_numeric_annotation reading sources... [ 98%] subsections/md_rst/xy_translate_spatial_locations reading sources... [ 98%] subsections/tipsandtricks/NEWS reading sources... [ 98%] subsections/tipsandtricks/giottoclass reading sources... [ 98%] subsections/tipsandtricks/howtosubsetgiottoobject reading sources... [ 98%] subsections/tipsandtricks/howtovisualizeandsaveplots reading sources... [ 98%] subsections/tipsandtricks/testandstoremultipleanayses reading sources... [ 98%] subsections/tipsandtricks/visualizewithvoronoiplots reading sources... [ 99%] subsections/tipsandtricks/waystovisualizespatialdata reading sources... [ 99%] subsections/tipsandtricks/workingwithimages reading sources... [ 99%] subsections/trygiotto/binder reading sources... [ 99%] subsections/trygiotto/docker reading sources... [ 99%] subsections/trygiotto/terra reading sources... [ 99%] tipsandtricks reading sources... [100%] trygiotto /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/citing_giotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/resolve_bc_210928.rst:159: WARNING: Title overline & underline mismatch. ******************************** Part 7: Process Giotto Object ********************************* /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/DT_removeNA.rst:1: WARNING: malformed hyperlink target. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/DT_removeNA.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addCellsFromPolygon.rst:4: WARNING: duplicate label addcellmetadata, other instance in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addCellMetadata.rst /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addFeatStatistics.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneMetadata.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneStatistics.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGenesPerc.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImageMG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImageToSpatPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPoints.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPolygons.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addHMRF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addNetworkLayout.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocationsLayer.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addStatistics.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/adjustGiottoMatrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/aes_string2.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/all_plots_save_function.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/anndataToGiotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotateGiotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotateSpatialGrid.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotateSpatialNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/average_feat_feat_expression_in_groups.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:10: WARNING: Unexpected section title. Description ----------- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:15: WARNING: Unexpected section title. Usage ----- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:47: WARNING: Unexpected section title. Arguments --------- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/binSpectMultiMatrix.rst:105: WARNING: Unexpected section title. Value ----- /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_group_HVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_loess_HVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_minimum.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_var_HVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateHVF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateHVG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateMetaTableCells.rst:4: WARNING: duplicate label calculatemetatable, other instance in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateMetaTable.rst /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapParallel.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapRaster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapSerial.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_centroids_polygons.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_distance_and_weight.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityEnrichment.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityHeatmap.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximitySpatPlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_2D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_3D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/changeGiottoInstructions.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/changeImageBg.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/checkGiottoEnvironment.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/check_spatial_location_data.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterCells.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterSpatialCorFeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterSpatialCorGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cluster_enrich_analysis.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colMeans_flex.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colSums_flex.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combCCcom.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCPG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellData.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes_per_interaction.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureData.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureOverlapData.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineICG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineInteractionChangedGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineMetadata.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellFeatureInfo.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellMetadataInfo.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/compatible_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertEnsemblToGeneSymbol.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertGiottoLargeImageToMG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_mgImage_to_array_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_full_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_reduced_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cor_flex.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createCrossSection.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoInstructions.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImageList.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoObjectSubcellular.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPoints.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromDfr.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromMask.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoVisiumObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createHeatmap_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createMetafeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createMetagenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialDefaultGrid.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialDelaunayNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialEnrich.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialGrid.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialKNNnetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_2d_mesh_grid_line_obj.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_KNNnetwork_dbscan.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_detection_DT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cell_type_random_cell_IDs.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cluster_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_crossSection_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_RTriangle.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_deldir.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_dimObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_featureNetwork_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_genes_to_use_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_points_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_polygon_object.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_jackstrawplot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_mesh_grid_lines.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_screeplot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGridObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialNetworkObject.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatvector_object_from_dfr.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cropGiottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionGenePlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionGenePlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/crossSectionPlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/decide_cluster_order.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/density_giottoLargeImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/depth.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialPatterns.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/determine_cores.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimCellPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimCellPlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimFeatPlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D_single.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_2D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_3D_plotly.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/distGiottoImage.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doCellSegmentation.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doHMRF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doHclust.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doKmeans.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLeidenCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLeidenSubCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_community.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_multinet.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_community.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_multinet.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doRandomWalkCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doSNNCluster.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doScrubletDetect.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_cell_proximity_test.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_limmatest.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_multi_permuttest_random.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_page_permutation.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_original.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_random.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_rank_permutation.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_grid_averaging.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_knn_smoothing.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_ttest.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_wilctest.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_points.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_polygon.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_analysis.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_deconvolution.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/estimateCellCellDistance.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_expr_matrix.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_feat_info.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_provided_spatial_locations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_info.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations_OLD.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/exportGiottoViewer.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/exprCellCellcom.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extend_vector.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extended_gini_fun.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extractNearestNetwork.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_points_list.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_polygon_list.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/fDataDT.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/featureNetwork-class.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCPG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCellProximityGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCombinations.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterDistributions.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterGiotto.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterICF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterICG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterInteractionChangedFeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterInteractionChangedGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filter_network.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCPG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityFeats_per_interaction.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findGiniMarkers.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findGiniMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findICF.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findICG.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findInteractionChangedFeats.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findInteractionChangedGenes.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMarkers.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMastMarkers.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findMastMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findNetworkNeighbors.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findScranMarkers_one_vs_all.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_dampening_constant.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_2D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_3D.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_x.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_y.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_z.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_terra_writeRaster_dataType.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_x_y_ranges.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runRankEnrich.rst:82: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/stitchGiottoLargeImage.rst:82: WARNING: Block quote ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/Workflow.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/development.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/citing_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/STARmap_mouse_cortex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/human_CyCIF_PDAC.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/merFISH_hypot_preopt_region.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mini_3D_STARmap.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mini_seqFISH.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mini_visium.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mouse_CODEX_spleen.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mouse_visium_brain.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/mouse_visium_kidney.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/osmFISH_mouse_SS_cortex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/resolve_bc_210928.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/seqFISH_cortex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/tcyCIF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/vizgen_mouse_brain.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/detailed_workflow.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/license.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/DT_removeNA.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/FSV_show.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/OR_test_fnc.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/PAGEEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/PAGE_DT_method.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/adapt_aspect_ratio.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addCellsFromPolygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneMetadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGeneStatistics.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGenesPerc.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoImageMG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPoints.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addGiottoPolygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/addSpatialCentroidLocationsLayer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/add_img_array_alpha.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/aes_string2.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/all_plots_save_function.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/anndataToGiotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/annotate_spatlocs_with_spatgrid_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/average_feat_feat_expression_in_groups.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_group_HVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_cov_loess_HVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_spatial_enrichment_minimum.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calc_var_HVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateHVF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapParallel.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapRaster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculateOverlapSerial.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_centroids_polygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/calculate_distance_and_weight.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximitySpatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_2D_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_2D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cellProximityVisPlot_3D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/check_spatial_location_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/clusterSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cluster_enrich_analysis.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colMeans_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/colSums_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combCCcom.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellData.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineCellProximityGenes_per_interaction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureData.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineFeatureOverlapData.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellFeatureInfo.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/combineSpatialCellMetadataInfo.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/compatible_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertEnsemblToGeneSymbol.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convertGiottoLargeImageToMG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_mgImage_to_array_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_full_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/convert_to_reduced_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cor_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoImageOLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoLargeImageList.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPoints.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromDfr.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createGiottoPolygonsFromMask.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createHeatmap_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createMetafeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialDefaultGrid.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_2d_mesh_grid_line_obj.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_KNNnetwork_dbscan.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_average_detection_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cell_type_random_cell_IDs.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_cluster_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_crossSection_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_RTriangle.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_deldir.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_delaunayNetwork_geometry_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_dimObject.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_featureNetwork_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_genes_to_use_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_points_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_giotto_polygon_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_jackstrawplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_mesh_grid_lines.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_screeplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_segm_polygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGridObject.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialGrid_default_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatialNetworkObject.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/create_spatvector_object_from_dfr.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/cropGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/decide_cluster_order.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/density_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/depth.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialCorFeatsMatrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/detectSpatialPatterns.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/determine_cores.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimCellPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimFeatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimGenePlot3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot2D_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_2D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dimPlot_3D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/distGiottoImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doCellSegmentation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_community.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainCluster_multinet.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_community.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doLouvainSubCluster_multinet.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doRandomWalkCluster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doSNNCluster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/doScrubletDetect.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_cell_proximity_test.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_limmatest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_multi_permuttest_random.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_page_permutation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_original.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_permuttest_random.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_rank_permutation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_grid_averaging.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_spatial_knn_smoothing.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_ttest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/do_wilctest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_points.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/dt_to_spatVector_polygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_analysis.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/enrich_deconvolution.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/estimateCellCellDistance.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_expr_matrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_feat_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_provided_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_locations_OLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/evaluate_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/exportGiottoViewer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extend_vector.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extended_gini_fun.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extractNearestNetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_points_list.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/extract_polygon_list.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/featureNetwork-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterCombinations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterDistributions.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filterInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/filter_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityFeats_per_interaction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/findInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_dampening_constant.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_x.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_y.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_grid_z.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_terra_writeRaster_dataType.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/find_x_y_ranges.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/fix_multipart_geoms.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/flex_lapply.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/general_save_function.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get10XmatrixOLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/getCellsFromPolygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/getDistinctColors.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_adj_rescale_img.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_args.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_cross_section_coordinates.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_distance.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_img_corners.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_img_minmax.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_os.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/get_sectionThickness.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/ggplot_save_function.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giotto-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoImage-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoLargeImage-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoPoints-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoPolygon-class.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giottoToSeurat.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/giotto_point.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/heatmSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/hyperGeometricEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/identify_background_range_polygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/install_giotto_environment.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/install_giotto_environment_specific.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/join_cell_meta.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/join_expression_matrices.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/join_spatlocs.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_arma_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_arma_subset_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/kmeans_binarize_wrapper.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/lapply_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/libNorm_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_cell_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_dim_reductions.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_dim_reductions_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_expression.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_expression_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_feat_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_feature_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_feature_info_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_giotto_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_images.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_images_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_enrichments.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_enrichments_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_grids.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_grids_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_info_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_locations_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_networks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/list_spatial_networks_names.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/logNorm_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/make_simulated_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mean_expr_det_test.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mean_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/merge_spatial_locs_feat_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mini_giotto_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mini_giotto_multi_cell.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mini_giotto_single_cell.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/my_arowMeans.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/my_growMeans.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/my_rowMeans.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/mygini_fun.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/nnDT_to_kNN.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/node_clusters.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/optimize_deconvolute_dwls.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/optimize_solveDampenedWLS.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlapToMatrix.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlapToMatrixMultiPoly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlap_points_per_polygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlap_points_per_polygon_wrapped.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/overlap_points_single_polygon.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/package_check.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/pca_giotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/pipe.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCCcomHeatmap.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCCcom.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCPG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCellCellCommunication.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineCellProximityGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotCombineInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotICF.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotICG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotInteractionChangedFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotInteractionChangedGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotInteractivePolygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotPCA_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotRecovery_sub.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotTSNE_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotUMAP_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_auto_largeImage_resample.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_cell_polygon_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_feature_hexbin_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_feature_points_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_feature_raster_density_layer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_network_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_point_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_point_layer_ggplot_noFILL.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_image_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_point_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_point_layer_ggplot_noFILL.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_scatterpie_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plot_spat_voronoi_layer_ggplot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_axis_scale_2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_axis_scale_3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_grid.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/plotly_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/polygon_to_raster.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/processGiotto.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/projection_fun.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rankEnrich.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rank_binarize.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rank_binarize_wrapper.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/readPolygonFilesVizgen.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/readPolygonFilesVizgenHDF5.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_crossSection.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_dimension_reduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_expression_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_nearest_networks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_spatial_enrichment.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_spatial_location_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/read_spatial_networks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnectGiottoImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnect_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnect_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reconnect_image_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reg_img_minmax_finder.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerGiottoObjectList.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerGiottoObjectListFiji.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerGiottoObjectListRvision.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/registerImagesFIJI.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reshape_to_data_point.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/reshape_to_mesh_grid_obj.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/return_giotto_environment_path.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/return_giotto_environment_path_executable.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rigid_transform_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rna_osmfish_normalization.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rna_pears_resid_normalization.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rna_standard_normalization.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rotate_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rowMeans_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/rowSums_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runFijiMacro.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runGiottoHarmony.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPAGEEnrich_OLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPCA_BiocSingular.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPCA_factominer.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/runPCA_prcomp_irlba.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/run_spatial_sim_tests_multi.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/run_spatial_sim_tests_one_rep.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/scale_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/selectPatternGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_NearestNetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_dimReduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_expression_values.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_feature_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_gimage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_polygon_info.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_spatialGrid.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_spatialNetwork.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/select_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_cell_and_feat_IDs.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_cell_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_default_feat_type.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_default_spat_unit.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_feature_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giottoImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giottoImage_MG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/set_giotto_python_path.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/seuratToGiotto_OLD.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/show-methods.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showGrids.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showNetworks.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPattern.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPattern2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPattern3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showPatternGenes.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showSaveParameters.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/showSpatialCorFeats.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/silhouetteRank.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/silhouetteRankTest.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/smoothGiottoPolygons.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/solve_OLS_internal.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/solve_dampened_WLSj.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/sort_combine_two_DT_columns.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatCellPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDeconvPlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimCellPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimFeatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimGenePlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimGenePlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimGenePlot3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatDimPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatFeatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatFeatPlot2D_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatGenePlot.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatGenePlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatGenePlot3D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotDensity.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotDensity_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotHex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotHex_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatInSituPlotPoints.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot2D.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot2D_single.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot_2D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatPlot_3D_plotly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spatVector_to_dt.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_OR_func.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_OR_func_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_fish_func.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spat_fish_func_DT.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/specificCellCellcommunicationScores.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spline_poly.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/split_dendrogram_in_two.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/spot_deconvolution.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/standardise_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/stitchGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subsetGiottoLocsMulti.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_cell_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_dimension_reduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_expression_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_feature_info_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_feature_metadata.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_giotto_points_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_giotto_polygon_object.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_nearest_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_enrichment.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_info_data.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/subset_spatial_network.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/t_flex.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/trakem2_rigid_transf_extract.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/transform_2d_mesh_to_3d_mesh.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/updateGiottoImageMG.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/updateGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/update_giotto_params.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/writeGiottoLargeImage.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/write_giotto_viewer_annotation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/write_giotto_viewer_dim_reduction.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/write_giotto_viewer_numeric_annotation.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/md_rst/xy_translate_spatial_locations.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/tipsandtricks/NEWS.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/tipsandtricks.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] Workflow writing output... [ 0%] additionalinformation writing output... [ 0%] contribute writing output... [ 0%] datasets writing output... [ 0%] development writing output... [ 0%] documentation writing output... [ 1%] errorsfaqsandtips writing output... [ 1%] faqs writing output... [ 1%] gettingstarted writing output... [ 1%] giottoworkflowanalyses writing output... [ 1%] github_issues writing output... [ 1%] index writing output... [ 1%] subsections/citing_giotto writing output... [ 2%] subsections/code_of_conduct writing output... [ 2%] subsections/datasets/STARmap_mouse_cortex writing output... [ 2%] subsections/datasets/human_CyCIF_PDAC writing output... [ 2%] subsections/datasets/merFISH_hypot_preopt_region writing output... [ 2%] subsections/datasets/mini_3D_STARmap writing output... [ 2%] subsections/datasets/mini_seqFISH writing output... [ 2%] subsections/datasets/mini_visium writing output... [ 3%] subsections/datasets/mouse_CODEX_spleen writing output... [ 3%] subsections/datasets/mouse_visium_brain writing output... [ 3%] subsections/datasets/mouse_visium_kidney writing output... [ 3%] subsections/datasets/nanostring_lung_12 writing output... [ 3%] subsections/datasets/nanostring_overview writing output... [ 3%] subsections/datasets/osmFISH_mouse_SS_cortex writing output... [ 4%] subsections/datasets/other_technologies_coming_soon writing output... [ 4%] subsections/datasets/resolve_bc_210928 writing output... [ 4%] subsections/datasets/seqFISH_cortex writing output... [ 4%] subsections/datasets/singlecell_prostate_integration writing output... [ 4%] subsections/datasets/singlecell_prostate_standard writing output... [ 4%] subsections/datasets/tcyCIF writing output... [ 4%] subsections/datasets/visium_prostate_integration writing output... [ 5%] subsections/datasets/vizgen_mouse_brain writing output... [ 5%] subsections/detailed_workflow writing output... [ 5%] subsections/license writing output... [ 5%] subsections/md_rst/DT_removeNA writing output... [ 5%] subsections/md_rst/FSV_show writing output... [ 5%] subsections/md_rst/OR_test_fnc writing output... [ 5%] subsections/md_rst/PAGEEnrich writing output... [ 6%] subsections/md_rst/PAGE_DT_method writing output... [ 6%] subsections/md_rst/adapt_aspect_ratio writing output... [ 6%] subsections/md_rst/addCellIntMetadata writing output... [ 6%] subsections/md_rst/addCellMetadata writing output... [ 6%] subsections/md_rst/addCellStatistics writing output... [ 6%] subsections/md_rst/addCellsFromPolygon writing output... [ 6%] subsections/md_rst/addFeatMetadata writing output... [ 7%] subsections/md_rst/addFeatStatistics writing output... [ 7%] subsections/md_rst/addFeatsPerc writing output... [ 7%] subsections/md_rst/addGeneMetadata writing output... [ 7%] subsections/md_rst/addGeneStatistics writing output... [ 7%] subsections/md_rst/addGenesPerc writing output... [ 7%] subsections/md_rst/addGiottoImage writing output... [ 8%] subsections/md_rst/addGiottoImageMG writing output... [ 8%] subsections/md_rst/addGiottoImageToSpatPlot writing output... [ 8%] subsections/md_rst/addGiottoLargeImage writing output... [ 8%] subsections/md_rst/addGiottoPoints writing output... [ 8%] subsections/md_rst/addGiottoPolygons writing output... [ 8%] subsections/md_rst/addHMRF writing output... [ 8%] subsections/md_rst/addNetworkLayout writing output... [ 9%] subsections/md_rst/addSpatialCentroidLocations writing output... [ 9%] subsections/md_rst/addSpatialCentroidLocationsLayer writing output... [ 9%] subsections/md_rst/addStatistics writing output... [ 9%] subsections/md_rst/add_img_array_alpha writing output... [ 9%] subsections/md_rst/adjustGiottoMatrix writing output... [ 9%] subsections/md_rst/aes_string2 writing output... [ 9%] subsections/md_rst/all_plots_save_function writing output... [ 10%] subsections/md_rst/anndataToGiotto writing output... [ 10%] subsections/md_rst/annotateGiotto writing output... [ 10%] subsections/md_rst/annotateSpatialGrid writing output... [ 10%] subsections/md_rst/annotateSpatialNetwork writing output... [ 10%] subsections/md_rst/annotate_spatlocs_with_spatgrid_2D writing output... [ 10%] subsections/md_rst/annotate_spatlocs_with_spatgrid_3D writing output... [ 10%] subsections/md_rst/average_feat_feat_expression_in_groups writing output... [ 11%] subsections/md_rst/binSpect writing output... [ 11%] subsections/md_rst/binSpectMulti writing output... [ 11%] subsections/md_rst/binSpectMultiMatrix writing output... [ 11%] subsections/md_rst/binSpectSingle writing output... [ 11%] subsections/md_rst/binSpectSingleMatrix writing output... [ 11%] subsections/md_rst/calc_cov_group_HVF writing output... [ 12%] subsections/md_rst/calc_cov_loess_HVF writing output... [ 12%] subsections/md_rst/calc_spatial_enrichment_DT writing output... [ 12%] subsections/md_rst/calc_spatial_enrichment_matrix writing output... [ 12%] subsections/md_rst/calc_spatial_enrichment_minimum writing output... [ 12%] subsections/md_rst/calc_var_HVF writing output... [ 12%] subsections/md_rst/calculateHVF writing output... [ 12%] subsections/md_rst/calculateHVG writing output... [ 13%] subsections/md_rst/calculateMetaTable writing output... [ 13%] subsections/md_rst/calculateMetaTableCells writing output... [ 13%] subsections/md_rst/calculateOverlapParallel writing output... [ 13%] subsections/md_rst/calculateOverlapRaster writing output... [ 13%] subsections/md_rst/calculateOverlapSerial writing output... [ 13%] subsections/md_rst/calculate_centroids_polygons writing output... [ 13%] subsections/md_rst/calculate_distance_and_weight writing output... [ 14%] subsections/md_rst/cellProximityBarplot writing output... [ 14%] subsections/md_rst/cellProximityEnrichment writing output... [ 14%] subsections/md_rst/cellProximityHeatmap writing output... [ 14%] subsections/md_rst/cellProximityNetwork writing output... [ 14%] subsections/md_rst/cellProximitySpatPlot writing output... [ 14%] subsections/md_rst/cellProximitySpatPlot2D writing output... [ 14%] subsections/md_rst/cellProximitySpatPlot3D writing output... [ 15%] subsections/md_rst/cellProximityVisPlot writing output... [ 15%] subsections/md_rst/cellProximityVisPlot_2D_ggplot writing output... [ 15%] subsections/md_rst/cellProximityVisPlot_2D_plotly writing output... [ 15%] subsections/md_rst/cellProximityVisPlot_3D_plotly writing output... [ 15%] subsections/md_rst/changeGiottoInstructions writing output... [ 15%] subsections/md_rst/changeImageBg writing output... [ 16%] subsections/md_rst/checkGiottoEnvironment writing output... [ 16%] subsections/md_rst/check_spatial_location_data writing output... [ 16%] subsections/md_rst/clusterCells writing output... [ 16%] subsections/md_rst/clusterSpatialCorFeats writing output... [ 16%] subsections/md_rst/clusterSpatialCorGenes writing output... [ 16%] subsections/md_rst/cluster_enrich_analysis writing output... [ 16%] subsections/md_rst/colMeans_flex writing output... [ 17%] subsections/md_rst/colSums_flex writing output... [ 17%] subsections/md_rst/combCCcom writing output... [ 17%] subsections/md_rst/combineCPG writing output... [ 17%] subsections/md_rst/combineCellData writing output... [ 17%] subsections/md_rst/combineCellProximityGenes writing output... [ 17%] subsections/md_rst/combineCellProximityGenes_per_interaction writing output... [ 17%] subsections/md_rst/combineFeatureData writing output... [ 18%] subsections/md_rst/combineFeatureOverlapData writing output... [ 18%] subsections/md_rst/combineICG writing output... [ 18%] subsections/md_rst/combineInteractionChangedGenes writing output... [ 18%] subsections/md_rst/combineMetadata writing output... [ 18%] subsections/md_rst/combineSpatialCellFeatureInfo writing output... [ 18%] subsections/md_rst/combineSpatialCellMetadataInfo writing output... [ 18%] subsections/md_rst/compatible_spatial_network writing output... [ 19%] subsections/md_rst/convertEnsemblToGeneSymbol writing output... [ 19%] subsections/md_rst/convertGiottoLargeImageToMG writing output... [ 19%] subsections/md_rst/convert_mgImage_to_array_DT writing output... [ 19%] subsections/md_rst/convert_to_full_spatial_network writing output... [ 19%] subsections/md_rst/convert_to_reduced_spatial_network writing output... [ 19%] subsections/md_rst/cor_flex writing output... [ 20%] subsections/md_rst/createCrossSection writing output... [ 20%] subsections/md_rst/createGiottoImage writing output... [ 20%] subsections/md_rst/createGiottoImageOLD writing output... [ 20%] subsections/md_rst/createGiottoInstructions writing output... [ 20%] subsections/md_rst/createGiottoLargeImage writing output... [ 20%] subsections/md_rst/createGiottoLargeImageList writing output... [ 20%] subsections/md_rst/createGiottoObject writing output... [ 21%] subsections/md_rst/createGiottoObjectSubcellular writing output... [ 21%] subsections/md_rst/createGiottoPoints writing output... [ 21%] subsections/md_rst/createGiottoPolygonsFromDfr writing output... [ 21%] subsections/md_rst/createGiottoPolygonsFromMask writing output... [ 21%] subsections/md_rst/createGiottoVisiumObject writing output... [ 21%] subsections/md_rst/createHeatmap_DT writing output... [ 21%] subsections/md_rst/createMetafeats writing output... [ 22%] subsections/md_rst/createMetagenes writing output... [ 22%] subsections/md_rst/createNearestNetwork writing output... [ 22%] subsections/md_rst/createSpatialDefaultGrid writing output... [ 22%] subsections/md_rst/createSpatialDelaunayNetwork writing output... [ 22%] subsections/md_rst/createSpatialEnrich writing output... [ 22%] subsections/md_rst/createSpatialFeaturesKNNnetwork writing output... [ 22%] subsections/md_rst/createSpatialFeaturesKNNnetwork_dbscan writing output... [ 23%] subsections/md_rst/createSpatialGrid writing output... [ 23%] subsections/md_rst/createSpatialKNNnetwork writing output... [ 23%] subsections/md_rst/createSpatialNetwork writing output... [ 23%] subsections/md_rst/create_2d_mesh_grid_line_obj writing output... [ 23%] subsections/md_rst/create_KNNnetwork_dbscan writing output... [ 23%] subsections/md_rst/create_average_DT writing output... [ 24%] subsections/md_rst/create_average_detection_DT writing output... [ 24%] subsections/md_rst/create_cell_type_random_cell_IDs writing output... [ 24%] subsections/md_rst/create_cluster_matrix writing output... [ 24%] subsections/md_rst/create_crossSection_object writing output... [ 24%] subsections/md_rst/create_delaunayNetwork2D writing output... [ 24%] subsections/md_rst/create_delaunayNetwork3D writing output... [ 24%] subsections/md_rst/create_delaunayNetwork_RTriangle writing output... [ 25%] subsections/md_rst/create_delaunayNetwork_deldir writing output... [ 25%] subsections/md_rst/create_delaunayNetwork_geometry writing output... [ 25%] subsections/md_rst/create_delaunayNetwork_geometry_3D writing output... [ 25%] subsections/md_rst/create_dimObject writing output... [ 25%] subsections/md_rst/create_featureNetwork_object writing output... [ 25%] subsections/md_rst/create_genes_to_use_matrix writing output... [ 25%] subsections/md_rst/create_giotto_points_object writing output... [ 26%] subsections/md_rst/create_giotto_polygon_object writing output... [ 26%] subsections/md_rst/create_jackstrawplot writing output... [ 26%] subsections/md_rst/create_mesh_grid_lines writing output... [ 26%] subsections/md_rst/create_screeplot writing output... [ 26%] subsections/md_rst/create_segm_polygons writing output... [ 26%] subsections/md_rst/create_spatialGridObject writing output... [ 26%] subsections/md_rst/create_spatialGrid_default_2D writing output... [ 27%] subsections/md_rst/create_spatialGrid_default_3D writing output... [ 27%] subsections/md_rst/create_spatialNetworkObject writing output... [ 27%] subsections/md_rst/create_spatvector_object_from_dfr writing output... [ 27%] subsections/md_rst/cropGiottoLargeImage writing output... [ 27%] subsections/md_rst/crossSectionGenePlot writing output... [ 27%] subsections/md_rst/crossSectionGenePlot3D writing output... [ 28%] subsections/md_rst/crossSectionPlot writing output... [ 28%] subsections/md_rst/crossSectionPlot3D writing output... [ 28%] subsections/md_rst/decide_cluster_order writing output... [ 28%] subsections/md_rst/density_giottoLargeImage writing output... [ 28%] subsections/md_rst/depth writing output... [ 28%] subsections/md_rst/detectSpatialCorFeats writing output... [ 28%] subsections/md_rst/detectSpatialCorFeatsMatrix writing output... [ 29%] subsections/md_rst/detectSpatialCorGenes writing output... [ 29%] subsections/md_rst/detectSpatialPatterns writing output... [ 29%] subsections/md_rst/determine_cores writing output... [ 29%] subsections/md_rst/dimCellPlot writing output... [ 29%] subsections/md_rst/dimCellPlot2D writing output... [ 29%] subsections/md_rst/dimFeatPlot2D writing output... [ 29%] subsections/md_rst/dimGenePlot writing output... [ 30%] subsections/md_rst/dimGenePlot2D writing output... [ 30%] subsections/md_rst/dimGenePlot3D writing output... [ 30%] subsections/md_rst/dimPlot writing output... [ 30%] subsections/md_rst/dimPlot2D writing output... [ 30%] subsections/md_rst/dimPlot2D_single writing output... [ 30%] subsections/md_rst/dimPlot3D writing output... [ 30%] subsections/md_rst/dimPlot_2D_plotly writing output... [ 31%] subsections/md_rst/dimPlot_3D_plotly writing output... [ 31%] subsections/md_rst/distGiottoImage writing output... [ 31%] subsections/md_rst/doCellSegmentation writing output... [ 31%] subsections/md_rst/doHMRF writing output... [ 31%] subsections/md_rst/doHclust writing output... [ 31%] subsections/md_rst/doKmeans writing output... [ 32%] subsections/md_rst/doLeidenCluster writing output... [ 32%] subsections/md_rst/doLeidenSubCluster writing output... [ 32%] subsections/md_rst/doLouvainCluster writing output... [ 32%] subsections/md_rst/doLouvainCluster_community writing output... [ 32%] subsections/md_rst/doLouvainCluster_multinet writing output... [ 32%] subsections/md_rst/doLouvainSubCluster writing output... [ 32%] subsections/md_rst/doLouvainSubCluster_community writing output... [ 33%] subsections/md_rst/doLouvainSubCluster_multinet writing output... [ 33%] subsections/md_rst/doRandomWalkCluster writing output... [ 33%] subsections/md_rst/doSNNCluster writing output... [ 33%] subsections/md_rst/doScrubletDetect writing output... [ 33%] subsections/md_rst/do_cell_proximity_test writing output... [ 33%] subsections/md_rst/do_limmatest writing output... [ 33%] subsections/md_rst/do_multi_permuttest_random writing output... [ 34%] subsections/md_rst/do_page_permutation writing output... [ 34%] subsections/md_rst/do_permuttest_original writing output... [ 34%] subsections/md_rst/do_permuttest_random writing output... [ 34%] subsections/md_rst/do_rank_permutation writing output... [ 34%] subsections/md_rst/do_spatial_grid_averaging writing output... [ 34%] subsections/md_rst/do_spatial_knn_smoothing writing output... [ 34%] subsections/md_rst/do_ttest writing output... [ 35%] subsections/md_rst/do_wilctest writing output... [ 35%] subsections/md_rst/dt_to_matrix writing output... [ 35%] subsections/md_rst/dt_to_spatVector_points writing output... [ 35%] subsections/md_rst/dt_to_spatVector_polygon writing output... [ 35%] subsections/md_rst/enrich_analysis writing output... [ 35%] subsections/md_rst/enrich_deconvolution writing output... [ 36%] subsections/md_rst/estimateCellCellDistance writing output... [ 36%] subsections/md_rst/estimateImageBg writing output... [ 36%] subsections/md_rst/evaluate_expr_matrix writing output... [ 36%] subsections/md_rst/evaluate_feat_info writing output... [ 36%] subsections/md_rst/evaluate_provided_spatial_locations writing output... [ 36%] subsections/md_rst/evaluate_spatial_info writing output... [ 36%] subsections/md_rst/evaluate_spatial_locations writing output... [ 37%] subsections/md_rst/evaluate_spatial_locations_OLD writing output... [ 37%] subsections/md_rst/evaluate_spatial_network writing output... [ 37%] subsections/md_rst/exportGiottoViewer writing output... [ 37%] subsections/md_rst/exprCellCellcom writing output... [ 37%] subsections/md_rst/extend_vector writing output... [ 37%] subsections/md_rst/extended_gini_fun writing output... [ 37%] subsections/md_rst/extractNearestNetwork writing output... [ 38%] subsections/md_rst/extract_points_list writing output... [ 38%] subsections/md_rst/extract_polygon_list writing output... [ 38%] subsections/md_rst/fDataDT writing output... [ 38%] subsections/md_rst/featureNetwork-class writing output... [ 38%] subsections/md_rst/filterCPG writing output... [ 38%] subsections/md_rst/filterCellProximityGenes writing output... [ 38%] subsections/md_rst/filterCombinations writing output... [ 39%] subsections/md_rst/filterDistributions writing output... [ 39%] subsections/md_rst/filterGiotto writing output... [ 39%] subsections/md_rst/filterICF writing output... [ 39%] subsections/md_rst/filterICG writing output... [ 39%] subsections/md_rst/filterInteractionChangedFeats writing output... [ 39%] subsections/md_rst/filterInteractionChangedGenes writing output... [ 40%] subsections/md_rst/filter_network writing output... [ 40%] subsections/md_rst/findCPG writing output... [ 40%] subsections/md_rst/findCellProximityFeats_per_interaction writing output... [ 40%] subsections/md_rst/findCellProximityGenes writing output... [ 40%] subsections/md_rst/findGiniMarkers writing output... [ 40%] subsections/md_rst/findGiniMarkers_one_vs_all writing output... [ 40%] subsections/md_rst/findICF writing output... [ 41%] subsections/md_rst/findICG writing output... [ 41%] subsections/md_rst/findInteractionChangedFeats writing output... [ 41%] subsections/md_rst/findInteractionChangedGenes writing output... [ 41%] subsections/md_rst/findMarkers writing output... [ 41%] subsections/md_rst/findMarkers_one_vs_all writing output... [ 41%] subsections/md_rst/findMastMarkers writing output... [ 41%] subsections/md_rst/findMastMarkers_one_vs_all writing output... [ 42%] subsections/md_rst/findNetworkNeighbors writing output... [ 42%] subsections/md_rst/findScranMarkers writing output... [ 42%] subsections/md_rst/findScranMarkers_one_vs_all writing output... [ 42%] subsections/md_rst/find_dampening_constant writing output... [ 42%] subsections/md_rst/find_grid_2D writing output... [ 42%] subsections/md_rst/find_grid_3D writing output... [ 42%] subsections/md_rst/find_grid_x writing output... [ 43%] subsections/md_rst/find_grid_y writing output... [ 43%] subsections/md_rst/find_grid_z writing output... [ 43%] subsections/md_rst/find_terra_writeRaster_dataType writing output... [ 43%] subsections/md_rst/find_x_y_ranges writing output... [ 43%] subsections/md_rst/fix_multipart_geoms writing output... [ 43%] subsections/md_rst/flex_lapply writing output... [ 44%] subsections/md_rst/general_save_function writing output... [ 44%] subsections/md_rst/get10Xmatrix writing output... [ 44%] subsections/md_rst/get10XmatrixOLD writing output... [ 44%] subsections/md_rst/get10Xmatrix_h5 writing output... [ 44%] subsections/md_rst/getCellsFromPolygon writing output... [ 44%] subsections/md_rst/getClusterSimilarity writing output... [ 44%] subsections/md_rst/getDendrogramSplits writing output... [ 45%] subsections/md_rst/getDistinctColors writing output... [ 45%] subsections/md_rst/getSpatialDataset writing output... [ 45%] subsections/md_rst/get_NearestNetwork writing output... [ 45%] subsections/md_rst/get_adj_rescale_img writing output... [ 45%] subsections/md_rst/get_args writing output... [ 45%] subsections/md_rst/get_cross_section_coordinates writing output... [ 45%] subsections/md_rst/get_dimReduction writing output... [ 46%] subsections/md_rst/get_distance writing output... [ 46%] subsections/md_rst/get_expression_values writing output... [ 46%] subsections/md_rst/get_feature_info writing output... [ 46%] subsections/md_rst/get_giottoImage writing output... [ 46%] subsections/md_rst/get_giottoImage_MG writing output... [ 46%] subsections/md_rst/get_giottoLargeImage writing output... [ 46%] subsections/md_rst/get_img_corners writing output... [ 47%] subsections/md_rst/get_img_minmax writing output... [ 47%] subsections/md_rst/get_os writing output... [ 47%] subsections/md_rst/get_polygon_info writing output... [ 47%] subsections/md_rst/get_sectionThickness writing output... [ 47%] subsections/md_rst/get_spatialGrid writing output... [ 47%] subsections/md_rst/get_spatialNetwork writing output... [ 48%] subsections/md_rst/get_spatial_enrichment writing output... [ 48%] subsections/md_rst/get_spatial_locations writing output... [ 48%] subsections/md_rst/ggplot_save_function writing output... [ 48%] subsections/md_rst/giotto-class writing output... [ 48%] subsections/md_rst/giottoImage-class writing output... [ 48%] subsections/md_rst/giottoLargeImage-class writing output... [ 48%] subsections/md_rst/giottoPoints-class writing output... [ 49%] subsections/md_rst/giottoPolygon-class writing output... [ 49%] subsections/md_rst/giottoToSeurat writing output... [ 49%] subsections/md_rst/giotto_point writing output... [ 49%] subsections/md_rst/heatmSpatialCorFeats writing output... [ 49%] subsections/md_rst/heatmSpatialCorGenes writing output... [ 49%] subsections/md_rst/hyperGeometricEnrich writing output... [ 49%] subsections/md_rst/identify_background_range_polygons writing output... [ 50%] subsections/md_rst/insertCrossSectionGenePlot3D writing output... [ 50%] subsections/md_rst/insertCrossSectionSpatPlot3D writing output... [ 50%] subsections/md_rst/installGiottoEnvironment writing output... [ 50%] subsections/md_rst/install_giotto_environment writing output... [ 50%] subsections/md_rst/install_giotto_environment_specific writing output... [ 50%] subsections/md_rst/jackstrawPlot writing output... [ 50%] subsections/md_rst/joinGiottoObjects writing output... [ 51%] subsections/md_rst/join_cell_meta writing output... [ 51%] subsections/md_rst/join_expression_matrices writing output... [ 51%] subsections/md_rst/join_spatlocs writing output... [ 51%] subsections/md_rst/kmeans_arma_binarize writing output... [ 51%] subsections/md_rst/kmeans_arma_subset_binarize writing output... [ 51%] subsections/md_rst/kmeans_binarize writing output... [ 52%] subsections/md_rst/kmeans_binarize_wrapper writing output... [ 52%] subsections/md_rst/lapply_flex writing output... [ 52%] subsections/md_rst/libNorm_giotto writing output... [ 52%] subsections/md_rst/list_cell_metadata writing output... [ 52%] subsections/md_rst/list_dim_reductions writing output... [ 52%] subsections/md_rst/list_dim_reductions_names writing output... [ 52%] subsections/md_rst/list_expression writing output... [ 53%] subsections/md_rst/list_expression_names writing output... [ 53%] subsections/md_rst/list_feat_metadata writing output... [ 53%] subsections/md_rst/list_feature_info writing output... [ 53%] subsections/md_rst/list_feature_info_names writing output... [ 53%] subsections/md_rst/list_giotto_data writing output... [ 53%] subsections/md_rst/list_images writing output... [ 53%] subsections/md_rst/list_images_names writing output... [ 54%] subsections/md_rst/list_spatial_enrichments writing output... [ 54%] subsections/md_rst/list_spatial_enrichments_names writing output... [ 54%] subsections/md_rst/list_spatial_grids writing output... [ 54%] subsections/md_rst/list_spatial_grids_names writing output... [ 54%] subsections/md_rst/list_spatial_info writing output... [ 54%] subsections/md_rst/list_spatial_info_names writing output... [ 54%] subsections/md_rst/list_spatial_locations writing output... [ 55%] subsections/md_rst/list_spatial_locations_names writing output... [ 55%] subsections/md_rst/list_spatial_networks writing output... [ 55%] subsections/md_rst/list_spatial_networks_names writing output... [ 55%] subsections/md_rst/loadHMRF writing output... [ 55%] subsections/md_rst/logNorm_giotto writing output... [ 55%] subsections/md_rst/makeSignMatrixDWLS writing output... [ 56%] subsections/md_rst/makeSignMatrixDWLSfromMatrix writing output... [ 56%] subsections/md_rst/makeSignMatrixPAGE writing output... [ 56%] subsections/md_rst/makeSignMatrixRank writing output... [ 56%] subsections/md_rst/make_simulated_network writing output... [ 56%] subsections/md_rst/mean_expr_det_test writing output... [ 56%] subsections/md_rst/mean_flex writing output... [ 56%] subsections/md_rst/mergeClusters writing output... [ 57%] subsections/md_rst/merge_spatial_locs_feat_info writing output... [ 57%] subsections/md_rst/mini_giotto_3D writing output... [ 57%] subsections/md_rst/mini_giotto_multi_cell writing output... [ 57%] subsections/md_rst/mini_giotto_single_cell writing output... [ 57%] subsections/md_rst/my_arowMeans writing output... [ 57%] subsections/md_rst/my_growMeans writing output... [ 57%] subsections/md_rst/my_rowMeans writing output... [ 58%] subsections/md_rst/mygini_fun writing output... [ 58%] subsections/md_rst/nnDT_to_kNN writing output... [ 58%] subsections/md_rst/node_clusters writing output... [ 58%] subsections/md_rst/normalizeGiotto writing output... [ 58%] subsections/md_rst/optimize_deconvolute_dwls writing output... [ 58%] subsections/md_rst/optimize_solveDampenedWLS writing output... [ 58%] subsections/md_rst/overlapToMatrix writing output... [ 59%] subsections/md_rst/overlapToMatrixMultiPoly writing output... [ 59%] subsections/md_rst/overlap_points_per_polygon writing output... [ 59%] subsections/md_rst/overlap_points_per_polygon_wrapped writing output... [ 59%] subsections/md_rst/overlap_points_single_polygon writing output... [ 59%] subsections/md_rst/pDataDT writing output... [ 59%] subsections/md_rst/package_check writing output... [ 60%] subsections/md_rst/pca_giotto writing output... [ 60%] subsections/md_rst/pipe writing output... [ 60%] subsections/md_rst/plotCCcomDotplot writing output... [ 60%] subsections/md_rst/plotCCcomHeatmap writing output... [ 60%] subsections/md_rst/plotCPG writing output... [ 60%] subsections/md_rst/plotCellProximityGenes writing output... [ 60%] subsections/md_rst/plotCombineCCcom writing output... [ 61%] subsections/md_rst/plotCombineCPG writing output... [ 61%] subsections/md_rst/plotCombineCellCellCommunication writing output... [ 61%] subsections/md_rst/plotCombineCellProximityGenes writing output... [ 61%] subsections/md_rst/plotCombineICG writing output... [ 61%] subsections/md_rst/plotCombineInteractionChangedGenes writing output... [ 61%] subsections/md_rst/plotGiottoImage writing output... [ 61%] subsections/md_rst/plotHeatmap writing output... [ 62%] subsections/md_rst/plotICF writing output... [ 62%] subsections/md_rst/plotICG writing output... [ 62%] subsections/md_rst/plotInteractionChangedFeats writing output... [ 62%] subsections/md_rst/plotInteractionChangedGenes writing output... [ 62%] subsections/md_rst/plotInteractivePolygons writing output... [ 62%] subsections/md_rst/plotMetaDataCellsHeatmap writing output... [ 62%] subsections/md_rst/plotMetaDataHeatmap writing output... [ 63%] subsections/md_rst/plotPCA writing output... [ 63%] subsections/md_rst/plotPCA_2D writing output... [ 63%] subsections/md_rst/plotPCA_3D writing output... [ 63%] subsections/md_rst/plotRankSpatvsExpr writing output... [ 63%] subsections/md_rst/plotRecovery writing output... [ 63%] subsections/md_rst/plotRecovery_sub writing output... [ 64%] subsections/md_rst/plotStatDelaunayNetwork writing output... [ 64%] subsections/md_rst/plotTSNE writing output... [ 64%] subsections/md_rst/plotTSNE_2D writing output... [ 64%] subsections/md_rst/plotTSNE_3D writing output... [ 64%] subsections/md_rst/plotUMAP writing output... [ 64%] subsections/md_rst/plotUMAP_2D writing output... [ 64%] subsections/md_rst/plotUMAP_3D writing output... [ 65%] subsections/md_rst/plot_auto_largeImage_resample writing output... [ 65%] subsections/md_rst/plot_cell_polygon_layer writing output... [ 65%] subsections/md_rst/plot_feature_hexbin_layer writing output... [ 65%] subsections/md_rst/plot_feature_points_layer writing output... [ 65%] subsections/md_rst/plot_feature_raster_density_layer writing output... [ 65%] subsections/md_rst/plot_giottoImage_MG writing output... [ 65%] subsections/md_rst/plot_giottoLargeImage writing output... [ 66%] subsections/md_rst/plot_network_layer_ggplot writing output... [ 66%] subsections/md_rst/plot_point_layer_ggplot writing output... [ 66%] subsections/md_rst/plot_point_layer_ggplot_noFILL writing output... [ 66%] subsections/md_rst/plot_spat_image_layer_ggplot writing output... [ 66%] subsections/md_rst/plot_spat_point_layer_ggplot writing output... [ 66%] subsections/md_rst/plot_spat_point_layer_ggplot_noFILL writing output... [ 66%] subsections/md_rst/plot_spat_scatterpie_layer_ggplot writing output... [ 67%] subsections/md_rst/plot_spat_voronoi_layer_ggplot writing output... [ 67%] subsections/md_rst/plotly_axis_scale_2D writing output... [ 67%] subsections/md_rst/plotly_axis_scale_3D writing output... [ 67%] subsections/md_rst/plotly_grid writing output... [ 67%] subsections/md_rst/plotly_network writing output... [ 67%] subsections/md_rst/polygon_to_raster writing output... [ 68%] subsections/md_rst/processGiotto writing output... [ 68%] subsections/md_rst/projection_fun writing output... [ 68%] subsections/md_rst/rankEnrich writing output... [ 68%] subsections/md_rst/rankSpatialCorGroups writing output... [ 68%] subsections/md_rst/rank_binarize writing output... [ 68%] subsections/md_rst/rank_binarize_wrapper writing output... [ 68%] subsections/md_rst/readExprMatrix writing output... [ 69%] subsections/md_rst/readGiottoInstructions writing output... [ 69%] subsections/md_rst/readPolygonFilesVizgen writing output... [ 69%] subsections/md_rst/readPolygonFilesVizgenHDF5 writing output... [ 69%] subsections/md_rst/read_crossSection writing output... [ 69%] subsections/md_rst/read_dimension_reduction writing output... [ 69%] subsections/md_rst/read_expression_data writing output... [ 69%] subsections/md_rst/read_nearest_networks writing output... [ 70%] subsections/md_rst/read_spatial_enrichment writing output... [ 70%] subsections/md_rst/read_spatial_location_data writing output... [ 70%] subsections/md_rst/read_spatial_networks writing output... [ 70%] subsections/md_rst/reconnectGiottoImage writing output... [ 70%] subsections/md_rst/reconnect_giottoImage_MG writing output... [ 70%] subsections/md_rst/reconnect_giottoLargeImage writing output... [ 70%] subsections/md_rst/reconnect_image_object writing output... [ 71%] subsections/md_rst/reg_img_minmax_finder writing output... [ 71%] subsections/md_rst/registerGiottoObjectList writing output... [ 71%] subsections/md_rst/registerGiottoObjectListFiji writing output... [ 71%] subsections/md_rst/registerGiottoObjectListRvision writing output... [ 71%] subsections/md_rst/registerImagesFIJI writing output... [ 71%] subsections/md_rst/removeCellAnnotation writing output... [ 72%] subsections/md_rst/removeFeatAnnotation writing output... [ 72%] subsections/md_rst/removeGiottoEnvironment writing output... [ 72%] subsections/md_rst/replaceGiottoInstructions writing output... [ 72%] subsections/md_rst/reshape_to_data_point writing output... [ 72%] subsections/md_rst/reshape_to_mesh_grid_obj writing output... [ 72%] subsections/md_rst/return_giotto_environment_path writing output... [ 72%] subsections/md_rst/return_giotto_environment_path_executable writing output... [ 73%] subsections/md_rst/rigid_transform_spatial_locations writing output... [ 73%] subsections/md_rst/rna_osmfish_normalization writing output... [ 73%] subsections/md_rst/rna_pears_resid_normalization writing output... [ 73%] subsections/md_rst/rna_standard_normalization writing output... [ 73%] subsections/md_rst/rotate_spatial_locations writing output... [ 73%] subsections/md_rst/rowMeans_flex writing output... [ 73%] subsections/md_rst/rowSums_flex writing output... [ 74%] subsections/md_rst/runDWLSDeconv writing output... [ 74%] subsections/md_rst/runFijiMacro writing output... [ 74%] subsections/md_rst/runGiottoHarmony writing output... [ 74%] subsections/md_rst/runHyperGeometricEnrich writing output... [ 74%] subsections/md_rst/runPAGEEnrich writing output... [ 74%] subsections/md_rst/runPAGEEnrich_OLD writing output... [ 74%] subsections/md_rst/runPCA writing output... [ 75%] subsections/md_rst/runPCA_BiocSingular writing output... [ 75%] subsections/md_rst/runPCA_factominer writing output... [ 75%] subsections/md_rst/runPCA_prcomp_irlba writing output... [ 75%] subsections/md_rst/runPatternSimulation writing output... [ 75%] subsections/md_rst/runRankEnrich writing output... [ 75%] subsections/md_rst/runSpatialDeconv writing output... [ 76%] subsections/md_rst/runSpatialEnrich writing output... [ 76%] subsections/md_rst/runUMAP writing output... [ 76%] subsections/md_rst/run_spatial_sim_tests_multi writing output... [ 76%] subsections/md_rst/run_spatial_sim_tests_one_rep writing output... [ 76%] subsections/md_rst/runtSNE writing output... [ 76%] subsections/md_rst/scale_spatial_locations writing output... [ 76%] subsections/md_rst/screePlot writing output... [ 77%] subsections/md_rst/selectPatternGenes writing output... [ 77%] subsections/md_rst/select_NearestNetwork writing output... [ 77%] subsections/md_rst/select_dimReduction writing output... [ 77%] subsections/md_rst/select_expression_values writing output... [ 77%] subsections/md_rst/select_feature_info writing output... [ 77%] subsections/md_rst/select_gimage writing output... [ 77%] subsections/md_rst/select_polygon_info writing output... [ 78%] subsections/md_rst/select_spatialGrid writing output... [ 78%] subsections/md_rst/select_spatialNetwork writing output... [ 78%] subsections/md_rst/select_spatial_locations writing output... [ 78%] subsections/md_rst/set_NearestNetwork writing output... [ 78%] subsections/md_rst/set_cell_and_feat_IDs writing output... [ 78%] subsections/md_rst/set_cell_metadata writing output... [ 78%] subsections/md_rst/set_default_feat_type writing output... [ 79%] subsections/md_rst/set_default_spat_unit writing output... [ 79%] subsections/md_rst/set_dimReduction writing output... [ 79%] subsections/md_rst/set_expression_values writing output... [ 79%] subsections/md_rst/set_feature_info writing output... [ 79%] subsections/md_rst/set_feature_metadata writing output... [ 79%] subsections/md_rst/set_giottoImage writing output... [ 80%] subsections/md_rst/set_giottoImage_MG writing output... [ 80%] subsections/md_rst/set_giottoLargeImage writing output... [ 80%] subsections/md_rst/set_giotto_python_path writing output... [ 80%] subsections/md_rst/set_polygon_info writing output... [ 80%] subsections/md_rst/set_spatialGrid writing output... [ 80%] subsections/md_rst/set_spatialNetwork writing output... [ 80%] subsections/md_rst/set_spatial_enrichment writing output... [ 81%] subsections/md_rst/set_spatial_locations writing output... [ 81%] subsections/md_rst/seuratToGiotto writing output... [ 81%] subsections/md_rst/seuratToGiotto_OLD writing output... [ 81%] subsections/md_rst/show-methods writing output... [ 81%] subsections/md_rst/showClusterDendrogram writing output... [ 81%] subsections/md_rst/showClusterHeatmap writing output... [ 81%] subsections/md_rst/showGiottoDimRed writing output... [ 82%] subsections/md_rst/showGiottoExpression writing output... [ 82%] subsections/md_rst/showGiottoFeatInfo writing output... [ 82%] subsections/md_rst/showGiottoImageNames writing output... [ 82%] subsections/md_rst/showGiottoInstructions writing output... [ 82%] subsections/md_rst/showGiottoSpatEnrichments writing output... [ 82%] subsections/md_rst/showGiottoSpatGrids writing output... [ 82%] subsections/md_rst/showGiottoSpatLocs writing output... [ 83%] subsections/md_rst/showGiottoSpatNetworks writing output... [ 83%] subsections/md_rst/showGiottoSpatialInfo writing output... [ 83%] subsections/md_rst/showGrids writing output... [ 83%] subsections/md_rst/showNetworks writing output... [ 83%] subsections/md_rst/showPattern writing output... [ 83%] subsections/md_rst/showPattern2D writing output... [ 84%] subsections/md_rst/showPattern3D writing output... [ 84%] subsections/md_rst/showPatternGenes writing output... [ 84%] subsections/md_rst/showProcessingSteps writing output... [ 84%] subsections/md_rst/showSaveParameters writing output... [ 84%] subsections/md_rst/showSpatialCorFeats writing output... [ 84%] subsections/md_rst/showSpatialCorGenes writing output... [ 84%] subsections/md_rst/signPCA writing output... [ 85%] subsections/md_rst/silhouetteRank writing output... [ 85%] subsections/md_rst/silhouetteRankTest writing output... [ 85%] subsections/md_rst/simulateOneGenePatternGiottoObject writing output... [ 85%] subsections/md_rst/smoothGiottoPolygons writing output... [ 85%] subsections/md_rst/solve_OLS_internal writing output... [ 85%] subsections/md_rst/solve_dampened_WLSj writing output... [ 85%] subsections/md_rst/sort_combine_two_DT_columns writing output... [ 86%] subsections/md_rst/spark writing output... [ 86%] subsections/md_rst/spatCellCellcom writing output... [ 86%] subsections/md_rst/spatCellPlot writing output... [ 86%] subsections/md_rst/spatCellPlot2D writing output... [ 86%] subsections/md_rst/spatDeconvPlot writing output... [ 86%] subsections/md_rst/spatDimCellPlot writing output... [ 86%] subsections/md_rst/spatDimCellPlot2D writing output... [ 87%] subsections/md_rst/spatDimFeatPlot2D writing output... [ 87%] subsections/md_rst/spatDimGenePlot writing output... [ 87%] subsections/md_rst/spatDimGenePlot2D writing output... [ 87%] subsections/md_rst/spatDimGenePlot3D writing output... [ 87%] subsections/md_rst/spatDimPlot writing output... [ 87%] subsections/md_rst/spatDimPlot2D writing output... [ 88%] subsections/md_rst/spatDimPlot3D writing output... [ 88%] subsections/md_rst/spatFeatPlot2D writing output... [ 88%] subsections/md_rst/spatFeatPlot2D_single writing output... [ 88%] subsections/md_rst/spatGenePlot writing output... [ 88%] subsections/md_rst/spatGenePlot2D writing output... [ 88%] subsections/md_rst/spatGenePlot3D writing output... [ 88%] subsections/md_rst/spatInSituPlotDensity writing output... [ 89%] subsections/md_rst/spatInSituPlotDensity_single writing output... [ 89%] subsections/md_rst/spatInSituPlotHex writing output... [ 89%] subsections/md_rst/spatInSituPlotHex_single writing output... [ 89%] subsections/md_rst/spatInSituPlotPoints writing output... [ 89%] subsections/md_rst/spatNetwDistributions writing output... [ 89%] subsections/md_rst/spatNetwDistributionsDistance writing output... [ 89%] subsections/md_rst/spatNetwDistributionsKneighbors writing output... [ 90%] subsections/md_rst/spatPlot writing output... [ 90%] subsections/md_rst/spatPlot2D writing output... [ 90%] subsections/md_rst/spatPlot2D_single writing output... [ 90%] subsections/md_rst/spatPlot3D writing output... [ 90%] subsections/md_rst/spatPlot_2D_plotly writing output... [ 90%] subsections/md_rst/spatPlot_3D_plotly writing output... [ 90%] subsections/md_rst/spatVector_to_dt writing output... [ 91%] subsections/md_rst/spat_OR_func writing output... [ 91%] subsections/md_rst/spat_OR_func_DT writing output... [ 91%] subsections/md_rst/spat_fish_func writing output... [ 91%] subsections/md_rst/spat_fish_func_DT writing output... [ 91%] subsections/md_rst/spatialAEH writing output... [ 91%] subsections/md_rst/spatialDE writing output... [ 92%] subsections/md_rst/specificCellCellcommunicationScores writing output... [ 92%] subsections/md_rst/spline_poly writing output... [ 92%] subsections/md_rst/split_dendrogram_in_two writing output... [ 92%] subsections/md_rst/spot_deconvolution writing output... [ 92%] subsections/md_rst/standardise_flex writing output... [ 92%] subsections/md_rst/stitchFieldCoordinates writing output... [ 92%] subsections/md_rst/stitchGiottoLargeImage writing output... [ 93%] subsections/md_rst/stitchTileCoordinates writing output... [ 93%] subsections/md_rst/subClusterCells writing output... [ 93%] subsections/md_rst/subsetGiotto writing output... [ 93%] subsections/md_rst/subsetGiottoLocs writing output... [ 93%] subsections/md_rst/subsetGiottoLocsMulti writing output... [ 93%] subsections/md_rst/subset_cell_metadata writing output... [ 93%] subsections/md_rst/subset_dimension_reduction writing output... [ 94%] subsections/md_rst/subset_expression_data writing output... [ 94%] subsections/md_rst/subset_feature_info_data writing output... [ 94%] subsections/md_rst/subset_feature_metadata writing output... [ 94%] subsections/md_rst/subset_giotto_points_object writing output... [ 94%] subsections/md_rst/subset_giotto_polygon_object writing output... [ 94%] subsections/md_rst/subset_nearest_network writing output... [ 94%] subsections/md_rst/subset_spatial_enrichment writing output... [ 95%] subsections/md_rst/subset_spatial_info_data writing output... [ 95%] subsections/md_rst/subset_spatial_locations writing output... [ 95%] subsections/md_rst/subset_spatial_network writing output... [ 95%] subsections/md_rst/t_flex writing output... [ 95%] subsections/md_rst/trakem2_rigid_transf_extract writing output... [ 95%] subsections/md_rst/transform_2d_mesh_to_3d_mesh writing output... [ 96%] subsections/md_rst/trendSceek writing output... [ 96%] subsections/md_rst/updateGiottoImage writing output... [ 96%] subsections/md_rst/updateGiottoImageMG writing output... [ 96%] subsections/md_rst/updateGiottoLargeImage writing output... [ 96%] subsections/md_rst/update_giotto_params writing output... [ 96%] subsections/md_rst/viewHMRFresults writing output... [ 96%] subsections/md_rst/viewHMRFresults2D writing output... [ 97%] subsections/md_rst/viewHMRFresults3D writing output... [ 97%] subsections/md_rst/violinPlot writing output... [ 97%] subsections/md_rst/writeGiottoLargeImage writing output... [ 97%] subsections/md_rst/writeHMRFresults writing output... [ 97%] subsections/md_rst/write_giotto_viewer_annotation writing output... [ 97%] subsections/md_rst/write_giotto_viewer_dim_reduction writing output... [ 97%] subsections/md_rst/write_giotto_viewer_numeric_annotation writing output... [ 98%] subsections/md_rst/xy_translate_spatial_locations writing output... [ 98%] subsections/tipsandtricks/NEWS writing output... [ 98%] subsections/tipsandtricks/giottoclass writing output... [ 98%] subsections/tipsandtricks/howtosubsetgiottoobject writing output... [ 98%] subsections/tipsandtricks/howtovisualizeandsaveplots writing output... [ 98%] subsections/tipsandtricks/testandstoremultipleanayses writing output... [ 98%] subsections/tipsandtricks/visualizewithvoronoiplots writing output... [ 99%] subsections/tipsandtricks/waystovisualizespatialdata writing output... [ 99%] subsections/tipsandtricks/workingwithimages writing output... [ 99%] subsections/trygiotto/binder writing output... [ 99%] subsections/trygiotto/docker writing output... [ 99%] subsections/trygiotto/terra writing output... [ 99%] tipsandtricks writing output... [100%] trygiotto /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/subsections/datasets/nanostring_overview.rst:10: WARNING: unknown document: subsections/datasets/nanostring_lung_12 generating indices... genindex done writing additional pages... done copying images... [ 0%] images/dataset_page/visium_kidney_image_summary.png copying images... [ 0%] images/dataset_page/visium_prostate_summary.png copying images... [ 0%] images/dataset_page/coming_soon_summary.png copying images... [ 0%] images/dataset_page/cortex_image_summary.png copying images... [ 0%] images/dataset_page/osmFISH_SS_cortex_image_summary.png copying images... [ 1%] images/dataset_page/merFISH_hypoth_image_summary.png copying images... [ 1%] images/dataset_page/starmap_cortex_image_summary.png copying images... [ 1%] images/dataset_page/vizgen_brain_summary.png copying images... [ 1%] images/dataset_page/resolve_bioscience_cancer_summary.png copying images... [ 1%] images/dataset_page/nanostring_overview_icon.png copying images... [ 2%] images/dataset_page/CODEX_spleen_image_summary.png copying images... [ 2%] images/dataset_page/cyCIF_PDAC_image_summary.png copying images... [ 2%] images/dataset_page/SC_RNAseq_standard.png copying images... [ 2%] images/dataset_page/SC_RNAseq_integration.png copying images... [ 2%] images/GiottoInstallationWorkflow.png copying images... [ 3%] images/getting_started/icons_configuration.png copying images... [ 3%] images/getting_started/icons_giotto.png copying images... [ 3%] images/getting_started/icons_processing.png copying images... [ 3%] images/getting_started/icons_clustering.png copying images... [ 3%] images/getting_started/icons_images.png copying images... [ 3%] images/getting_started/icons_visualizations.png copying images... [ 4%] images/getting_started/icons_saving.png copying images... [ 4%] images/getting_started/icons_distribution.png copying images... [ 4%] images/getting_started/icons_cell_type.png copying images... [ 4%] images/getting_started/icons_deconvolution.png copying images... [ 4%] images/getting_started/icons_interaction.png copying images... [ 5%] images/getting_started/icons_patterns.png copying images... [ 5%] images/getting_started/icons_subcellular.png copying images... [ 5%] images/diagram_giotto_workflow.png copying images... [ 5%] https://img.shields.io/github/last-commit/RubD/Giotto/suite copying images... [ 5%] https://img.shields.io/readthedocs/giotto/latest?logo=read-the-docs copying images... [ 6%] https://img.shields.io/pypi/v/Giotto copying images... [ 6%] https://img.shields.io/pypi/dm/giotto copying images... [ 6%] https://img.shields.io/maintenance/yes/2022 copying images... [ 6%] images/index/giotto_suite.png copying images... [ 6%] images/index/input_Compatibility.png copying images... [ 6%] images/index/data_structure_Data_Structure.png copying images... [ 7%] images/index/analysis.png copying images... [ 7%] https://img.shields.io/github/license/RubD/Giotto copying images... [ 7%] images/other/mouse_starmap_cortex/vignette_200917/2_a_distribution_genes.png copying images... [ 7%] images/other/mouse_starmap_cortex/vignette_200917/2_b_distribution_cells.png copying images... [ 7%] images/other/mouse_starmap_cortex/vignette_200917/2_c_distribution_filters.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/2_d_spatial_locations.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/3_a_hvg.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/3_b_signPCs.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/3_c_umap.png copying images... [ 8%] images/other/mouse_starmap_cortex/vignette_200917/4_leiden_0.2.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/5_a_covisualize_leiden_0.2.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/6_a_violinplot.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/6_b_heatmap_leiden_0.2.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/7_a_general_cell_type.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/7_b_dim_plot_detailed_cell_type.png copying images... [ 9%] images/other/mouse_starmap_cortex/vignette_200917/7_c_cluster_annotation_heatmap.png copying images... [ 10%] images/other/mouse_starmap_cortex/vignette_200917/8_cell_type_co_vis.png copying images... [ 10%] images/other/mouse_starmap_cortex/vignette_200917/9_a_Rorb_dim_plot.png copying images... [ 10%] images/other/mouse_starmap_cortex/vignette_200917/9_b_Pcp4_dim_plot.png copying images... [ 10%] images/other/mouse_starmap_cortex/vignette_200917/9_c_Pcp4_spat_plot.png copying images... [ 10%] images/other/mouse_starmap_cortex/vignette_200917/9_d_Cux2_dim_plot.png copying images... [ 11%] images/other/mouse_starmap_cortex/vignette_200917/9_e_detailed_cell_types.png copying images... [ 11%] images/other/mouse_starmap_cortex/vignette_200917/9_f_Cux2_spat_plot.png copying images... [ 11%] images/other/mouse_starmap_cortex/vignette_200917/9_g_Ctgf_dim_plot.png copying images... [ 11%] images/other/mouse_starmap_cortex/vignette_200917/9_h_Ctgf_spat_plot.png copying images... [ 11%] images/other/mouse_starmap_cortex/vignette_200917/10_a_insert_cross_section_cell_types.png copying images... [ 12%] images/other/mouse_starmap_cortex/vignette_200917/10_b_insert_cross_section_Slc17a7.png copying images... [ 12%] images/other/mouse_starmap_cortex/vignette_200917/10_c_cross_section_spat.png copying images... [ 12%] images/other/mouse_starmap_cortex/vignette_200917/10_d_cross_section_spat3d.png copying images... [ 12%] images/other/mouse_starmap_cortex/vignette_200917/10_e_Slc17a7_cross_section_gene3d.png copying images... [ 12%] images/other/human_cycif_PDAC/vignette_200916/2_a_spatPlot.png copying images... [ 12%] images/other/human_cycif_PDAC/vignette_200916/2_b_spatPlot_column.png copying images... [ 13%] images/other/human_cycif_PDAC/vignette_200916/2_c_spatPlot_row.png copying images... [ 13%] images/other/human_cycif_PDAC/vignette_200916/2_d_spatPlot_hist.png copying images... [ 13%] images/other/human_cycif_PDAC/vignette_200916/2_e_spatPlot_hist2.png copying images... [ 13%] images/other/human_cycif_PDAC/vignette_200916/3_a_signPCA.png copying images... [ 13%] images/other/human_cycif_PDAC/vignette_200916/3_b_PCAplot.png copying images... [ 14%] images/other/human_cycif_PDAC/vignette_200916/3_c_UMAP.png copying images... [ 14%] images/other/human_cycif_PDAC/vignette_200916/4_a_UMAP.png copying images... [ 14%] images/other/human_cycif_PDAC/vignette_200916/4_b_UMAP.png copying images... [ 14%] images/other/human_cycif_PDAC/vignette_200916/4_c_spatplot.png copying images... [ 14%] images/other/human_cycif_PDAC/vignette_200916/4_d_spatPlot.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/5_a_spatdimplot.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/5_b_spatdimplot.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/5_c_spatdimplot.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/6_a_metaheatmap.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/6_b_violinplot_gini.png copying images... [ 15%] images/other/human_cycif_PDAC/vignette_200916/7_a_metaheatmap.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_b_metaheatmap.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_c_spatplot.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_d_spatplot.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_e_spatplot.png copying images... [ 16%] images/other/human_cycif_PDAC/vignette_200916/7_f_spatplot.png copying images... [ 17%] images/other/human_cycif_PDAC/vignette_200916/7_g_spatplot_1.png copying images... [ 17%] images/other/human_cycif_PDAC/vignette_200916/7_g_spatplot_2.png copying images... [ 17%] images/other/human_cycif_PDAC/vignette_200916/7_h_spatdimplot.png copying images... [ 17%] images/other/human_cycif_PDAC/vignette_200916/7_i_spatplot.png copying images... [ 17%] images/other/human_cycif_PDAC/vignette_200916/7_j_umap.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/8_a_spatplot.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/12_a_barplot.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/12_b_network.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/12_c_proxspatplot.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/xx_a_metaheatmap.png copying images... [ 18%] images/other/human_cycif_PDAC/vignette_200916/xx_b_spatplot.png copying images... [ 19%] images/other/human_cycif_PDAC/vignette_200916/xx_c_spatgeneplot.png copying images... [ 19%] images/other/human_cycif_PDAC/vignette_200916/xx_d_umap.png copying images... [ 19%] images/other/human_cycif_PDAC/vignette_200916/xx_e_dimGeneplot.png copying images... [ 19%] images/other/human_cycif_PDAC/vignette_200916/xx_f_spatplot.png copying images... [ 19%] images/other/human_cycif_PDAC/vignette_200916/xx_g_spatGeneplot.png copying images... [ 20%] images/other/human_cycif_PDAC/vignette_200916/xx_h_umap.png copying images... [ 20%] images/other/human_cycif_PDAC/vignette_200916/xx_i_dimGeneplot.png copying images... [ 20%] images/other/mouse_merFISH_hypoth/vignette_200909/2_a_distribution_genes.png copying images... [ 20%] images/other/mouse_merFISH_hypoth/vignette_200909/2_b_distribution_cells.png copying images... [ 20%] images/other/mouse_merFISH_hypoth/vignette_200909/2_c_filter_combos.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/2_d_spatial_locations2D.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/2_e_spatial_locations3D.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/3_a_screeplot.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/3_b_UMAP_reduction.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/4_a_UMAP_leiden.png copying images... [ 21%] images/other/mouse_merFISH_hypoth/vignette_200909/5_b_leiden_2D.png copying images... [ 22%] images/other/mouse_merFISH_hypoth/vignette_200909/6_a_violinplot.png copying images... [ 22%] images/other/mouse_merFISH_hypoth/vignette_200909/6_b_clusterheatmap_markers.png copying images... [ 22%] images/other/mouse_merFISH_hypoth/vignette_200909/7_a_clusterheatmap_markers.png copying images... [ 22%] images/other/mouse_merFISH_hypoth/vignette_200909/7_b_clusterheatmap_markers_celltypes.png copying images... [ 22%] images/other/mouse_merFISH_hypoth/vignette_200909/7_c_umap_cell_types.png copying images... [ 23%] images/other/mouse_merFISH_hypoth/vignette_200909/7_d_spatPlot_cell_types_all.png copying images... [ 23%] images/other/mouse_merFISH_hypoth/vignette_200909/7_e_spatPlot2D_cell_types_all.png copying images... [ 23%] images/other/mouse_merFISH_hypoth/vignette_200909/7_f_spatPlot_cell_types_excit.png copying images... [ 23%] images/other/mouse_merFISH_hypoth/vignette_200909/7_g_spatPlot2D_cell_types_excit.png copying images... [ 23%] images/other/mouse_merFISH_hypoth/vignette_200909/7_h_spatPlot_cell_types_inhib.png copying images... [ 24%] images/other/mouse_merFISH_hypoth/vignette_200909/7_i_spatPlot2D_cell_types_inhib.png copying images... [ 24%] images/other/mouse_merFISH_hypoth/vignette_200909/7_j_spatPlot_cell_types_ODandAstro.png copying images... [ 24%] images/other/mouse_merFISH_hypoth/vignette_200909/7_k_spatPlot2D_cell_types_ODandAstro.png copying images... [ 24%] images/other/mouse_merFISH_hypoth/vignette_200909/7_l_spatPlot_cell_types_other.png copying images... [ 24%] images/other/mouse_merFISH_hypoth/vignette_200909/7_m_spatPlot2D_cell_types_other.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/2_a_filtergenes.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/2_b_filtercells.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/2_c_filtercombos.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/3_a_screeplot.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/3_b_PCA.png copying images... [ 25%] images/other/mini_datasets/mini_starmap/vignette_200922/3_d_UMAP_3D.png copying images... [ 26%] images/other/mini_datasets/mini_starmap/vignette_200922/3_e_TSNE.png copying images... [ 26%] images/other/mini_datasets/mini_starmap/vignette_200922/4_a_UMAP.png copying images... [ 26%] images/other/mini_datasets/mini_starmap/vignette_200922/4_b_UMAP_3D.png copying images... [ 26%] images/other/mini_datasets/mini_starmap/vignette_200922/4_c_spatdimplot.png copying images... [ 26%] images/other/mini_datasets/mini_starmap/vignette_200922/4_e_clusterheatmap.png copying images... [ 27%] images/other/mini_datasets/mini_starmap/vignette_200922/4_f_clusterdendrogram.png copying images... [ 27%] images/other/mini_datasets/mini_starmap/vignette_200922/5_a_violinplot.png copying images... [ 27%] images/other/mini_datasets/mini_starmap/vignette_200922/5_b_metaheatmap.png copying images... [ 27%] images/other/mini_datasets/mini_starmap/vignette_200922/6_a_spatdimplot.png copying images... [ 27%] images/other/mini_datasets/mini_starmap/vignette_200922/6_b_dimgeneplot.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/6_c_spatgeneplot.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/7_a_spatplot.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/8_a_plotStatDelaunayNetwork.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/8_b_spatplot.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/8_c_spatplot.png copying images... [ 28%] images/other/mini_datasets/mini_starmap/vignette_200922/9_a_spatgeneplot.png copying images... [ 29%] images/other/mini_datasets/mini_starmap/vignette_200922/9_b_spatgeneplot.png copying images... [ 29%] images/other/mini_datasets/mini_starmap/vignette_200922/10_a_heatmspatcor.png copying images... [ 29%] images/other/mini_datasets/mini_starmap/vignette_200922/10_b_rankcorgroup.png copying images... [ 29%] images/other/mini_datasets/mini_starmap/vignette_200922/10_c_spatcellplot.png copying images... [ 29%] images/other/mini_datasets/mini_starmap/vignette_200922/12_a_barplot.png copying images... [ 30%] images/other/mini_datasets/mini_starmap/vignette_200922/12_b_heatmap.png copying images... [ 30%] images/other/mini_datasets/mini_starmap/vignette_200922/12_c_network.png copying images... [ 30%] images/other/mini_datasets/mini_starmap/vignette_200922/12_d_network.png copying images... [ 30%] images/other/mini_datasets/mini_starmap/vignette_200922/12_e_spatplot.png copying images... [ 30%] images/other/mini_datasets/mini_starmap/vignette_200922/12_e_cellproximity.png copying images... [ 31%] images/other/mini_datasets/mini_starmap/vignette_200922/13_a_insert.png copying images... [ 31%] images/other/mini_datasets/mini_starmap/vignette_200922/13_b_crossplot.png copying images... [ 31%] images/other/mini_datasets/mini_starmap/vignette_200922/13_c_cross.png copying images... [ 31%] images/other/mini_datasets/mini_starmap/vignette_200922/13_d_crossgeneplot.png copying images... [ 31%] images/other/mini_datasets/mini_starmap/vignette_200922/13_e_crossgene.png copying images... [ 31%] images/other/mini_datasets/mini_seqfish/vignette_200921/3.1_HVGplot.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/3.2_screePlot.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/3.3_jackstrawPlot.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/3.4_PCA.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/3.5_tSNE.png copying images... [ 32%] images/other/mini_datasets/mini_seqfish/vignette_200921/4.1_UMAP.png copying images... [ 33%] images/other/mini_datasets/mini_seqfish/vignette_200921/4.2_showClusterHeatmap.png copying images... [ 33%] images/other/mini_datasets/mini_seqfish/vignette_200921/4.3_showClusterDendrogram.png copying images... [ 33%] images/other/mini_datasets/mini_seqfish/vignette_200921/5.1_violinPlot.png copying images... [ 33%] images/other/mini_datasets/mini_seqfish/vignette_200921/5.2_plotMetaDataHeatmap.png copying images... [ 33%] images/other/mini_datasets/mini_seqfish/vignette_200921/6.1_spatDimPlot2D.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/9.1_spatGenePlot2D.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/10.1_heatmSpatialCorGenes.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/10.2_spatCellPlot2D.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.1_cellProximityBarplot.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.2_spatCellPlot2D.png copying images... [ 34%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.3_cellProximityHeatmap.png copying images... [ 35%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.4_cellProximityNetwork.png copying images... [ 35%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.5_cellProximitySpatPlot2D.png copying images... [ 35%] images/other/mini_datasets/mini_seqfish/vignette_200921/12.6_spatPlot2D.png copying images... [ 35%] images/other/mini_datasets/mini_seqfish/vignette_200921/13.1_plotCellProximityGenes.png copying images... [ 35%] images/other/mini_datasets/mini_seqfish/vignette_200921/13.2_plotICG.png copying images... [ 36%] images/other/mini_datasets/mini_seqfish/vignette_200921/14.1_plotCCcomHeatmap.png copying images... [ 36%] images/other/mini_datasets/mini_seqfish/vignette_200921/14.2_plotCCcomDotplot.png copying images... [ 36%] images/other/mini_datasets/mini_seqfish/vignette_200921/14.3_plotRankSpatvsExpr.png copying images... [ 36%] images/other/mini_datasets/mini_seqfish/vignette_200921/14.4_plotRecovery.png copying images... [ 36%] images/other/mouse_codex_spleen/vignette_200921/2_a_spatPlot.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/2_b_spatPlot.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/3_a_spatPlot.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/3_b_PCA.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/3_c_UMAP.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/4_a_UMAP.png copying images... [ 37%] images/other/mouse_codex_spleen/vignette_200921/4_b_spatplot.png copying images... [ 38%] images/other/mouse_codex_spleen/vignette_200921/5_a_spatdimplot.png copying images... [ 38%] images/other/mouse_codex_spleen/vignette_200921/6_a_metaheatmap.png copying images... [ 38%] images/other/mouse_codex_spleen/vignette_200921/6_b_violinplot.png copying images... [ 38%] images/other/mouse_codex_spleen/vignette_200921/6_c_metaheatmap.png copying images... [ 38%] images/other/mouse_codex_spleen/vignette_200921/6_d_violinplot.png copying images... [ 39%] images/other/mouse_codex_spleen/vignette_200921/7_a_metaheatmap.png copying images... [ 39%] images/other/mouse_codex_spleen/vignette_200921/7_b_umap.png copying images... [ 39%] images/other/mouse_codex_spleen/vignette_200921/7_c_spatplot.png copying images... [ 39%] images/other/mouse_codex_spleen/vignette_200921/8_a_umap.png copying images... [ 39%] images/other/mouse_codex_spleen/vignette_200921/8_b_spatplot.png copying images... [ 40%] images/other/mouse_codex_spleen/vignette_200921/8_c_spatdimplot.png copying images... [ 40%] images/other/mouse_codex_spleen/vignette_200921/8_d_umap.png copying images... [ 40%] images/other/mouse_codex_spleen/vignette_200921/8_e_spatPlot.png copying images... [ 40%] images/other/mouse_codex_spleen/vignette_200921/8_f_spatdimgeneplot.png copying images... [ 40%] images/other/general_figs/visium_technology.png copying images... [ 40%] images/other/general_figs/visium_brain_image_summary.png copying images... [ 41%] images/other/mouse_Visium_brain/vignette_201226/2_a_spatplot_image.png copying images... [ 41%] images/other/mouse_Visium_brain/vignette_201226/2_b_spatplot_image_adjusted.png copying images... [ 41%] images/other/mouse_Visium_brain/vignette_201226/2_c_in_tissue.png copying images... [ 41%] images/other/mouse_Visium_brain/vignette_201226/2_d_spatial_locations.png copying images... [ 41%] images/other/mouse_Visium_brain/vignette_201226/2_e_nr_genes.png copying images... [ 42%] images/other/mouse_Visium_brain/vignette_201226/3_a_HVGplot.png copying images... [ 42%] images/other/mouse_Visium_brain/vignette_201226/3_b_screeplot.png copying images... [ 42%] images/other/mouse_Visium_brain/vignette_201226/3_c_PCA_reduction.png copying images... [ 42%] images/other/mouse_Visium_brain/vignette_201226/3_d_UMAP_reduction.png copying images... [ 42%] images/other/mouse_Visium_brain/vignette_201226/3_e_tSNE_reduction.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/4_a_UMAP_leiden.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/5_a_covis_leiden.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/5_b_nr_genes.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/5_c_DEG_subset.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/6_a_violinplot_gini.png copying images... [ 43%] images/other/mouse_Visium_brain/vignette_201226/6_b_metaheatmap_gini.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/6_c_gini_umap.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/6_d_violinplot_scran.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/6_e_metaheatmap_scran.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/6_f_scran_umap.png copying images... [ 44%] images/other/mouse_Visium_brain/vignette_201226/7_a_metaheatmap.png copying images... [ 45%] images/other/mouse_Visium_brain/vignette_201226/7_b_spatcellplot.png copying images... [ 45%] images/other/mouse_Visium_brain/vignette_201226/7_c_spatcellplot.png copying images... [ 45%] images/other/mouse_Visium_brain/vignette_201226/7_d_spatDimCellPlot.png copying images... [ 45%] images/other/mouse_Visium_brain/vignette_201226/8_grid.png copying images... [ 45%] images/other/mouse_Visium_brain/vignette_201226/9_a_knn_network.png copying images... [ 46%] images/other/mouse_Visium_brain/vignette_201226/10_a_spatial_genes_km.png copying images... [ 46%] images/other/mouse_Visium_brain/vignette_201226/10_b_spatial_genes_rank.png copying images... [ 46%] images/other/mouse_Visium_brain/vignette_201226/10_c_heatmap.png copying images... [ 46%] images/other/mouse_Visium_brain/vignette_201226/10_d_spatPlot2D_HMRF.png copying images... [ 46%] images/other/mouse_Visium_kidney/mouse_kidney_highres.png copying images... [ 46%] images/other/mouse_Visium_kidney/vignette_200916/2_a_spatplot_image.png copying images... [ 47%] images/other/mouse_Visium_kidney/vignette_200916/2_b_spatplot_image_adjusted.png copying images... [ 47%] images/other/mouse_Visium_kidney/vignette_200916/2_c_in_tissue.png copying images... [ 47%] images/other/mouse_Visium_kidney/vignette_200916/2_d_spatial_locations.png copying images... [ 47%] images/other/mouse_Visium_kidney/vignette_200916/2_e_nr_genes.png copying images... [ 47%] images/other/mouse_Visium_kidney/vignette_200916/3_a_HVGplot.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/3_b_screeplot.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/3_c_PCA_reduction.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/3_d_UMAP_reduction.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/3_e_tSNE_reduction.png copying images... [ 48%] images/other/mouse_Visium_kidney/vignette_200916/4_a_UMAP_leiden.png copying images... [ 49%] images/other/mouse_Visium_kidney/vignette_200916/5_a_covis_leiden.png copying images... [ 49%] images/other/mouse_Visium_kidney/vignette_200916/5_b_nr_genes.png copying images... [ 49%] images/other/mouse_Visium_kidney/vignette_200916/6_a_violinplot_gini.png copying images... [ 49%] images/other/mouse_Visium_kidney/vignette_200916/6_b_metaheatmap_gini.png copying images... [ 49%] images/other/mouse_Visium_kidney/vignette_200916/6_c_gini_umap.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/6_d_violinplot_scran.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/6_e_metaheatmap_scran.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/6_f_scran_umap.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/8_grid.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/9_a_delaunay_network.png copying images... [ 50%] images/other/mouse_Visium_kidney/vignette_200916/9_b_delaunay_network.png copying images... [ 51%] images/other/mouse_Visium_kidney/vignette_200916/10_a_spatial_genes_km.png copying images... [ 51%] images/other/mouse_Visium_kidney/vignette_200916/10_b_spatial_genes_rank.png copying images... [ 51%] images/other/mouse_Visium_kidney/vignette_200916/10_d_Napsa_correlated_genes.png copying images... [ 51%] images/other/mouse_Visium_kidney/vignette_200916/10_e_heatmap_correlated_genes.png copying images... [ 51%] images/other/mouse_Visium_kidney/vignette_200916/10_f_rank_correlated_groups.png copying images... [ 52%] images/other/mouse_Visium_kidney/vignette_200916/10_g_spat_enrichment_score_plots.png copying images... [ 52%] images/other/mouse_Visium_kidney/vignette_200916/10_h_spat_enrichment_score_plots_genes.png copying images... [ 52%] images/other/nanostring_cosmx_subcellular_lung_cancer/Rplot1.png copying images... [ 52%] images/other/nanostring_cosmx_subcellular_lung_cancer/Rplot2.png copying images... [ 52%] images/other/nanostring_cosmx_subcellular_lung_cancer/Rplothist.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/Rplot3.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/Rplot5.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/4-HVFplot.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/5-HVFplot.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/6-screePlot.png copying images... [ 53%] images/other/nanostring_cosmx_subcellular_lung_cancer/7-PCA.png copying images... [ 54%] images/other/nanostring_cosmx_subcellular_lung_cancer/8-UMAP.png copying images... [ 54%] images/other/nanostring_cosmx_subcellular_lung_cancer/9-UMAP.png copying images... [ 54%] images/other/nanostring_cosmx_subcellular_lung_cancer/10-spatDimPlot2D.png copying images... [ 54%] images/other/nanostring_cosmx_subcellular_lung_cancer/spatinsituclustered.png copying images... [ 54%] images/other/nanostring_cosmx_subcellular_lung_cancer/12-spatInSituPlotPoints.png copying images... [ 55%] images/other/nanostring_cosmx_subcellular_lung_cancer/13-spatFeatPlot2D.png copying images... [ 55%] images/other/nanostring_cosmx_subcellular_lung_cancer/14-violinPlot.png copying images... [ 55%] images/other/nanostring_cosmx_subcellular_lung_cancer/6-plotMetaDataHeatmap.png copying images... [ 55%] images/other/nanostring_cosmx_subcellular_lung_cancer/15-UMAP.png copying images... [ 55%] images/other/nanostring_cosmx_subcellular_lung_cancer/16-spatDimPlot2D.png copying images... [ 56%] images/other/nanostring_cosmx_subcellular_lung_cancer/17-spatInSituPlotPoints.png copying images... [ 56%] images/other/nanostring_cosmx_subcellular_lung_cancer/18-spatInSituPlotPoints.png copying images... [ 56%] images/other/general_figs/osmfish_image_demo.png copying images... [ 56%] images/other//mouse_osmfish_ss_cortex/vignette_200915/2_a_original_clusters.png copying images... [ 56%] images/other/mouse_osmfish_ss_cortex/vignette_200915/2_b_original_regions.png copying images... [ 56%] images/other/mouse_osmfish_ss_cortex/vignette_200915/2_c_clusterID.png copying images... [ 57%] images/other/mouse_osmfish_ss_cortex/vignette_200915/2_d_total_expr_limits.png copying images... [ 57%] images/other/mouse_osmfish_ss_cortex/vignette_200915/3_a_screeplot.png copying images... [ 57%] images/other/mouse_osmfish_ss_cortex/vignette_200915/3_b_PCA_reduction.png copying images... [ 57%] images/other/mouse_osmfish_ss_cortex/vignette_200915/3_c_UMAP_reduction.png copying images... [ 57%] images/other/mouse_osmfish_ss_cortex/vignette_200915/3_d_UMAP_reduction_expression.png copying images... [ 58%] images/other/mouse_osmfish_ss_cortex/vignette_200915/3_e_tSNE_reduction.png copying images... [ 58%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_a_UMAP_hclust.png copying images... [ 58%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_b_UMAP_kmeans.png copying images... [ 58%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_c_UMAP_leiden.png copying images... [ 58%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_d_UMAP_leiden_merged.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_e_heatmap.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915/4_f_dendro.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915//5_a_covis_leiden.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915/5_b_covis_leiden_m.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915/5_c_covis_leiden_merged_selected.png copying images... [ 59%] images/other/mouse_osmfish_ss_cortex/vignette_200915/5_d_total_expr.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/6_a_violinplot.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/6_b_metaheatmap.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/6_e_metaheatmap_all_genes.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/6_f_metaheatmap_all_genes_names.png copying images... [ 60%] images/other/mouse_osmfish_ss_cortex/vignette_200915/7_a_annotation_leiden_merged_detailed.png copying images... [ 61%] images/other/mouse_osmfish_ss_cortex/vignette_200915/7_b_annotation_leiden_merged_coarse.png copying images... [ 61%] images/other/mouse_osmfish_ss_cortex/vignette_200915/7_c_clusterHeatmap_det_cell_types.png copying images... [ 61%] images/other/mouse_osmfish_ss_cortex/vignette_200915/7_d_heatamp_det_cell_types.png copying images... [ 61%] images/other/mouse_osmfish_ss_cortex/vignette_200915/7_e_metaheatmap.png copying images... [ 61%] images/other/mouse_osmfish_ss_cortex/vignette_200915/8_grid_det_cell_types.png copying images... [ 62%] images/other/mouse_osmfish_ss_cortex/vignette_200915/9_spatial_network_k10.png copying images... [ 62%] images/other/mouse_osmfish_ss_cortex/vignette_200915/10_a_spatial_genes_km.png copying images... [ 62%] images/other/mouse_osmfish_ss_cortex/vignette_200915/11_a_barplot_cell_cell_enrichment.png copying images... [ 62%] images/other/mouse_osmfish_ss_cortex/vignette_200915/11_b_heatmap_cell_cell_enrichment.png copying images... [ 62%] images/other/mouse_osmfish_ss_cortex/vignette_200915/11_c_network_cell_cell_enrichment.png copying images... [ 62%] images/other/mouse_osmfish_ss_cortex/vignette_200915/11_d_cell_cell_enrichment_selected.png copying images... [ 63%] images/other/general_figs/construction-boy.png copying images... [ 63%] images/other/resolve_bc_subcellular/0-spatPlot2D.png copying images... [ 63%] images/other/resolve_bc_subcellular/1-spatPlot2D.png copying images... [ 63%] images/other/resolve_bc_subcellular/69-spatPlot2D.png copying images... [ 63%] images/other/resolve_bc_subcellular/4-HVFplot.png copying images... [ 64%] images/other/resolve_bc_subcellular/5-HVFplot.png copying images... [ 64%] images/other/resolve_bc_subcellular/6-screePlot.png copying images... [ 64%] images/other/resolve_bc_subcellular/7-PCA.png copying images... [ 64%] images/other/resolve_bc_subcellular/8-UMAP.png copying images... [ 64%] images/other/resolve_bc_subcellular/39-UMAP.png copying images... [ 65%] images/other/resolve_bc_subcellular/51-spatDimPlot2D.png copying images... [ 65%] images/other/resolve_bc_subcellular/72-Heatmap.png copying images... [ 65%] images/other/resolve_bc_subcellular/12-showClusterDendrogram.png copying images... [ 65%] images/other/resolve_bc_subcellular/13-spatPlot2D.png copying images... [ 65%] images/other/resolve_bc_subcellular/54-spatInSituPlotPoints.png copying images... [ 65%] images/other/resolve_bc_subcellular/16-spatInSituPlotPoints.png copying images... [ 66%] images/other/resolve_bc_subcellular/17-spatInSituPlotPoints.png copying images... [ 66%] images/other/resolve_bc_subcellular/18-spatInSituPlotPoints.png copying images... [ 66%] images/other/resolve_bc_subcellular/19-spatInSituPlotPoints.png copying images... [ 66%] images/other/resolve_bc_subcellular/21-spatInSituPlotPoints.png copying images... [ 66%] images/other/resolve_bc_subcellular/61-spatInSituPlotPoints.png copying images... [ 67%] images/other/resolve_bc_subcellular/22-spatInSituPlotPoints.png copying images... [ 67%] images/other/resolve_bc_subcellular/66-spatInSituPlotPoints.png copying images... [ 67%] images/other/resolve_bc_subcellular/43-spatInSituPlotPoints.png copying images... [ 67%] images/other/general_figs/cortex_svz_location_fields.png copying images... [ 67%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/2_a_spatplot.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/3_a_HVGplot.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/3_b_screeplot.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/3_c_PCA_reduction.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/3_d_UMAP_reduction.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/3_e_tSNE_reduction.png copying images... [ 68%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/4_a_UMAP_leiden.png copying images... [ 69%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/4_b_UMAP_leiden_subcluster.png copying images... [ 69%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/4_c_heatmap.png copying images... [ 69%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/4_d_dendro.png copying images... [ 69%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/5_a_covis_leiden.png copying images... [ 69%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/5_b_covis_leiden_selected.png copying images... [ 70%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/6_a_violinplot_gini.png copying images... [ 70%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/6_b_metaheatmap_gini.png copying images... [ 70%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/7_a_violinplot.png copying images... [ 70%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/7_b_covisualization.png copying images... [ 70%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/7_c_heatmap.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/7_d_heatmap_selected.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/8_a_grid.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/9_a_spatial_network_delaunay.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/9_b_spatial_network_k3.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/9_c_spatial_network_k10.png copying images... [ 71%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/9_d_spatial_network_dist.png copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/10_a_spatialgenes_km.png copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/10_b_spatialcoexpression_heatmap.png copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/10_c_spatialcoexpression_rank.png copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/10_d_spatialcoexpression_metagenes.png copying images... [ 72%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/11_HMRF_2_k9_b.28.pdf copying images... [ 73%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_a_barplot_cell_cell_enrichment.png copying images... [ 73%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_b_heatmap_cell_cell_enrichment.png copying images... [ 73%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_c_network_cell_cell_enrichment.png copying images... [ 73%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_d_network_cell_cell_enrichment_self.pdf copying images... [ 73%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_e_cell_cell_enrichment_selected.png copying images... [ 74%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/12_f_cell_cell_enrichment_sel_vs_not.png copying images... [ 74%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/13_a_CPG_dotplot.png copying images... [ 74%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/13_b_ICG_barplot.png copying images... [ 74%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/14_a_communication_dotplot.png copying images... [ 74%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/14_b_expr_vs_spatial_expression_rank.png copying images... [ 75%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/14_c_spatial_recovery_expression_rank.png copying images... [ 75%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/14_d_expr_vs_spatial_activity.png copying images... [ 75%] images/other/mouse_seqFISH_SS_cortex/vignette_200914/14_e_spatial_recovery_activity.png copying images... [ 75%] images/other/singlecell_rna_seq_integration/4_cluster_without_integration.png copying images... [ 75%] images/other/singlecell_rna_seq_integration/4_list_without_integration.png copying images... [ 75%] images/other/singlecell_rna_seq_integration/4_cluster_with_integration.png copying images... [ 76%] images/other/singlecell_rna_seq_integration/4_list_with_integration.png copying images... [ 76%] images/other/singlecell_rna_seq/3_scree_plot.png copying images... [ 76%] images/other/singlecell_rna_seq/4_Cluster.png copying images... [ 76%] images/other/singlecell_rna_seq/5_a_metaheatmap.png copying images... [ 76%] images/other/singlecell_rna_seq/5_b_violinplot_scran.png copying images... [ 77%] images/other/singlecell_rna_seq/6_featureplot.png copying images... [ 77%] images/other/singlecell_rna_seq/7_Annotation.png copying images... [ 77%] images/other/singlecell_rna_seq/8a_scree_plot.png copying images... [ 77%] images/other/singlecell_rna_seq/8b_Cluster.png copying images... [ 77%] images/other/singlecell_rna_seq/8_c_metaheatmap.png copying images... [ 78%] images/other/singlecell_rna_seq/8d_Annotation.png copying images... [ 78%] images/other/visium_prostate_integration/Visium_FFPE_Human_Normal_Prostate_image.png copying images... [ 78%] images/other/visium_prostate_integration/Visium_FFPE_Human_Prostate_Cancer_image.png copying images... [ 78%] images/other/visium_prostate_integration/1a_plot.png copying images... [ 78%] images/other/visium_prostate_integration/1b_plot.png copying images... [ 78%] images/other/visium_prostate_integration/1c_plot.png copying images... [ 79%] images/other/visium_prostate_integration/2a_plot.png copying images... [ 79%] images/other/visium_prostate_integration/2b_plot.png copying images... [ 79%] images/other/visium_prostate_integration/2c_plot.png copying images... [ 79%] images/other/visium_prostate_integration/3a_screeplot.png copying images... [ 79%] images/other/visium_prostate_integration/4.1a_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4.1b_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4.1c_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4.2a_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4.2b_plot.png copying images... [ 80%] images/other/visium_prostate_integration/4.2c_plot.png copying images... [ 81%] images/other/visium_prostate_integration/4_w_o_integration_plot.png copying images... [ 81%] images/other/visium_prostate_integration/5a_PAGE_plot.png copying images... [ 81%] images/other/visium_prostate_integration/5b_HyperGeometric_plot.png copying images... [ 81%] images/other/visium_prostate_integration/5c_Rank_plot.png copying images... [ 81%] images/other/visium_prostate_integration/5d_DWLS_plot.png copying images... [ 81%] images/other/vizgen_mouse_brain/0-spatPlot2D.png copying images... [ 82%] images/other/vizgen_mouse_brain/1-spatPlot2D.png copying images... [ 82%] images/other/vizgen_mouse_brain/2-spatPlot2D.png copying images... [ 82%] images/other/vizgen_mouse_brain/3-screePlot.png copying images... [ 82%] images/other/vizgen_mouse_brain/4-PCA.png copying images... [ 82%] images/other/vizgen_mouse_brain/5-UMAP.png copying images... [ 83%] images/other/vizgen_mouse_brain/6-UMAP.png copying images... [ 83%] images/other/vizgen_mouse_brain/7-spatPlot2D.png copying images... [ 83%] images/other/vizgen_mouse_brain/8-spatPlot2D.png copying images... [ 83%] images/other/vizgen_mouse_brain/9-spatFeatPlot2D.png copying images... [ 83%] images/other/vizgen_mouse_brain/10-spatPlot2D.png copying images... [ 84%] images/other/vizgen_mouse_brain/11-spatInSituPlotPoints.png copying images... [ 84%] images/other/vizgen_mouse_brain/12-spatInSituPlotPoints.png copying images... [ 84%] subsections/../images/detailed_workflow/giotto_ip.png copying images... [ 84%] subsections/../images/detailed_workflow/giotto_ds.png copying images... [ 84%] subsections/../images/detailed_workflow/giotto_analysis.png copying images... [ 84%] subsections/../images/detailed_workflow/giotto_viz.png copying images... [ 85%] images/howtos/subset_giotto/vignette_1/1_whole_brain.png copying images... [ 85%] images/howtos/subset_giotto/vignette_1/2_whole_brain_clus4.png copying images... [ 85%] images/howtos/subset_giotto/vignette_1/3_whole_brain_clus4_noOther.png copying images... [ 85%] images/howtos/subset_giotto/vignette_1/4_whole_brain_by_group_leiden_1.png copying images... [ 85%] images/howtos/subset_giotto/vignette_1/4_whole_brain_by_group_leiden_2.png copying images... [ 86%] images/howtos/subset_giotto/vignette_1/5_whole_brain_HMRF.png copying images... [ 86%] images/howtos/subset_giotto/vignette_1/5_whole_brain_by_group_HMRF_1.png copying images... [ 86%] images/howtos/subset_giotto/vignette_1/5_whole_brain_by_group_HMRF_2.png copying images... [ 86%] images/howtos/subset_giotto/vignette_1/6_subset_brain.png copying images... [ 86%] images/howtos/subset_giotto/vignette_1/6_subset_brain_nr_genes.png copying images... [ 87%] images/howtos/subset_giotto/vignette_1/7_DG_loc_subset.png copying images... [ 87%] images/howtos/instructions_and_plotting/vignette_1/original_clusters_black.png copying images... [ 87%] images/howtos/work_with_multiple_analyses/ppt_store_multiple_analyses2.png copying images... [ 87%] images/howtos/work_with_multiple_analyses/vignette_1/1_loess_hvg.png copying images... [ 87%] images/howtos/work_with_multiple_analyses/vignette_1/1_group_hvg.png copying images... [ 87%] images/howtos/work_with_multiple_analyses/vignette_1/1_hvg_table.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/2_loess_pca.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/2_group_pca.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/3_loess_umap.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/3_group_umap.png copying images... [ 88%] images/howtos/work_with_multiple_analyses/vignette_1/4_spatial_network.png copying images... [ 89%] images/howtos/work_with_multiple_analyses/vignette_1/4_large_network.png copying images... [ 89%] images/howtos/work_with_multiple_analyses/vignette_1/4_distance_network.png copying images... [ 89%] images/howtos/work_with_multiple_analyses/vignette_1/5_large_network_genes.png copying images... [ 89%] images/howtos/work_with_multiple_analyses/vignette_1/5_large_distance_network_genes.png copying images... [ 89%] images/howtos/voronoi_plots/vignette_1/1_voronoi.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/2_voronoi_no_others.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/3_voronoi_no_others_black_border.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/4_voronoi_spat_dim.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/5_voronoi_neighbors.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/6_original_points.png copying images... [ 90%] images/howtos/voronoi_plots/vignette_1/7_voronoi_genes.png copying images... [ 91%] images/howtos/voronoi_plots/vignette_1/8_voronoi_gene_black_bg.png copying images... [ 91%] images/howtos/giotto_images/vignette_1/2_a_spatplot.png copying images... [ 91%] images/howtos/giotto_images/vignette_1/2_b_spatplot_image.png copying images... [ 91%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_1.png copying images... [ 91%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_2.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_3.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_4.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_5.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_6.png copying images... [ 92%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_7.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_8.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_9.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_10.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/2_c_spatplot_image_adjusted_11.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/2_d_original_plot.png copying images... [ 93%] images/howtos/giotto_images/vignette_1/3_a_background_colors.png copying images... [ 94%] images/howtos/giotto_images/vignette_1/3_b_black_background.png copying images... [ 94%] images/howtos/giotto_images/vignette_1/3_c_white_background.png copying images... [ 94%] images/howtos/giotto_images/vignette_1/4_a_external_image_negated.png copying images... [ 94%] images/howtos/giotto_images/vignette_1/4_b_external_image_charcoal.png copying images... [ 94%] images/howtos/giotto_images/vignette_1/5_1_a_spatial_locations.png copying images... [ 95%] images/howtos/giotto_images/vignette_1/5_1_b_nr_genes.png copying images... [ 95%] images/howtos/giotto_images/vignette_1/5_1_c_nr_genes_black_bg.png copying images... [ 95%] images/howtos/giotto_images/vignette_1/5_1_d_nr_genes_charc_bg.png copying images... [ 95%] images/howtos/giotto_images/vignette_1/5_2_a_UMAP_reduction.png copying images... [ 95%] images/howtos/giotto_images/vignette_1/5_3_a_UMAP_leiden.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_4_a_covis_leiden_black.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_4_b_covis_leiden_negated.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_4_c_covis_leiden_charc.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_5_a_spatgene_charc_vor.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_5_b_spatgene_charc_vor.png copying images... [ 96%] images/howtos/giotto_images/vignette_1/5_6_a_subset_spatgene_charc.png copying images... [ 97%] images/howtos/giotto_images/vignette_1/5_6_b_subset_spatgene_charc_vor.png copying images... [ 97%] https://img.shields.io/badge/launch-binder-579ACA.svg?logo=data:image/png;base64,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 copying images... [ 97%] images/GitHub_Logo.png copying images... [ 97%] images/img_terra/01_environments.png copying images... [ 97%] images/img_terra/01_vm.png copying images... [ 98%] images/img_terra/02_docker.png copying images... [ 98%] images/img_terra/03_upload.png copying images... [ 98%] images/img_terra/03_view.png copying images... [ 98%] images/img_terra/03_googlecloud.png copying images... [ 98%] images/img_terra/03_url.png copying images... [ 99%] images/img_terra/03_cloud.png copying images... [ 99%] images/img_terra/04_share.png copying images... [ 99%] images/trygiotto/Binder_1.png copying images... [ 99%] images/trygiotto/Binder_2.png copying images... [ 99%] images/trygiotto/Binder_3.png copying images... [100%] images/trygiotto/Binder_4.png copying static files... done copying extra files... done writing mimetype file... writing META-INF/container.xml file... writing content.opf file... WARNING: unknown mimetype for _images/11_HMRF_2_k9_b.28.pdf, ignoring WARNING: unknown mimetype for _images/12_d_network_cell_cell_enrichment_self.pdf, ignoring WARNING: unknown mimetype for _static/css/fonts/Roboto-Slab-Bold.woff2, ignoring WARNING: unknown mimetype for _static/css/fonts/Roboto-Slab-Regular.woff2, ignoring WARNING: unknown mimetype for _static/css/fonts/fontawesome-webfont.eot, ignoring WARNING: unknown mimetype for _static/css/fonts/fontawesome-webfont.woff2, ignoring WARNING: unknown mimetype for _static/css/fonts/lato-bold-italic.woff2, ignoring WARNING: unknown mimetype for _static/css/fonts/lato-bold.woff2, ignoring WARNING: unknown mimetype for _static/css/fonts/lato-normal-italic.woff2, ignoring WARNING: unknown mimetype for _static/css/fonts/lato-normal.woff2, ignoring WARNING: unknown mimetype for _static/fonts/fontawesome-webfont.eot, ignoring WARNING: unknown mimetype for _static/fonts/fontawesome-webfont.woff2, ignoring WARNING: unknown mimetype for _static/fonts/Lato/lato-bold.eot, ignoring WARNING: unknown mimetype for _static/fonts/Lato/lato-bold.woff2, ignoring WARNING: unknown mimetype for _static/fonts/Lato/lato-bolditalic.eot, ignoring WARNING: unknown mimetype for _static/fonts/Lato/lato-bolditalic.woff2, ignoring WARNING: unknown mimetype for _static/fonts/Lato/lato-italic.eot, ignoring WARNING: unknown mimetype for _static/fonts/Lato/lato-italic.woff2, ignoring WARNING: unknown mimetype for _static/fonts/Lato/lato-regular.eot, ignoring WARNING: unknown mimetype for _static/fonts/Lato/lato-regular.woff2, ignoring WARNING: unknown mimetype for _static/fonts/RobotoSlab/roboto-slab-v7-bold 2.woff2, ignoring WARNING: unknown mimetype for _static/fonts/RobotoSlab/roboto-slab-v7-bold 3.woff2, ignoring WARNING: unknown mimetype for _static/fonts/RobotoSlab/roboto-slab-v7-bold 4.woff2, ignoring WARNING: unknown mimetype for _static/fonts/RobotoSlab/roboto-slab-v7-bold.eot, ignoring WARNING: unknown mimetype for _static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2, ignoring WARNING: unknown mimetype for _static/fonts/RobotoSlab/roboto-slab-v7-regular 2.woff2, ignoring WARNING: unknown mimetype for _static/fonts/RobotoSlab/roboto-slab-v7-regular 3.woff2, ignoring WARNING: unknown mimetype for _static/fonts/RobotoSlab/roboto-slab-v7-regular 4.woff2, ignoring WARNING: unknown mimetype for _static/fonts/RobotoSlab/roboto-slab-v7-regular.eot, ignoring WARNING: unknown mimetype for _static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2, ignoring WARNING: unknown mimetype for _static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.map, ignoring writing nav.xhtml file... writing toc.ncx file... writing Giotto.epub file... build succeeded, 726 warnings. The ePub file is in _build/epub. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2022-07-14T19:44:49.769773Z, end-time: 2022-07-14T19:44:49.865141Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/_build/epub/Giotto.epub /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/artifacts/suite/sphinx_epub/giottoteam-giotto.epub