Read the Docs build information Build id: 994217 Project: giottoteam-giotto Version: suite Commit: 1daf317e2b3a82f36b760b4e00c36ce87782caa8 Date: 2022-06-28T18:53:43.654199Z State: finished Success: True [rtd-command-info] start-time: 2022-06-28T18:54:44.591365Z, end-time: 2022-06-28T18:56:45.046755Z, duration: 120, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/sistia01/Giotto.git . Cloning into '.'... [rtd-command-info] start-time: 2022-06-28T18:56:45.328128Z, end-time: 2022-06-28T18:57:07.416020Z, duration: 22, 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 1daf317e updated sphinx version back to 3.4.3 [rtd-command-info] start-time: 2022-06-28T18:57:07.604800Z, end-time: 2022-06-28T18:57:07.704361Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-06-28T18:57:17.046321Z, end-time: 2022-06-28T18:57:21.691364Z, 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: 2022-06-28T18:57:21.887675Z, end-time: 2022-06-28T18:57:23.714392Z, 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 35.1 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 62.6.0 Uninstalling setuptools-62.6.0: Successfully uninstalled setuptools-62.6.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-06-28T18:57:23.904363Z, end-time: 2022-06-28T18:57:32.427916Z, 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 21.5 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 116.6 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 187.4 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 178.0 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 219.3 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 255.0 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-0.18.1-py2.py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 kB 259.9 MB/s eta 0:00:00 Collecting importlib-metadata>=4.4 Downloading importlib_metadata-4.12.0-py3-none-any.whl (21 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 kB 194.1 MB/s eta 0:00:00 Collecting imagesize Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 173.3 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 261.3 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 208.8 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 216.7 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 214.7 MB/s eta 0:00:00 Collecting sphinxcontrib-htmlhelp>=2.0.0 Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.5/100.5 kB 204.9 MB/s eta 0:00:00 Collecting requests>=2.5.0 Downloading requests-2.28.0-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 200.9 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 218.9 MB/s eta 0:00:00 Collecting babel>=1.3 Downloading Babel-2.10.3-py3-none-any.whl (9.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 170.7 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 233.9 MB/s eta 0:00:00 Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 253.4 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 239.9 MB/s eta 0:00:00 Collecting typing-extensions>=3.6.4 Downloading typing_extensions-4.2.0-py3-none-any.whl (24 kB) Collecting zipp>=0.5 Downloading zipp-3.8.0-py3-none-any.whl (5.4 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~=2.0.0 Downloading charset_normalizer-2.0.12-py3-none-any.whl (39 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.9-py2.py3-none-any.whl (138 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 139.0/139.0 kB 224.1 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 207.4 MB/s eta 0:00:00 Collecting certifi>=2017.4.17 Downloading certifi-2022.6.15-py3-none-any.whl (160 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 160.2/160.2 kB 235.7 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 210.9 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=15e41dd3fa076ba729fff0916715db294bddc5c26aa2f03653c0e00a9506ff7d Stored in directory: /tmp/pip-ephem-wheel-cache-7_f0chgc/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=5e5787fb5277c17fe8873bf7267acf48affe2da5e234cdd038c19016ac70fff5 Stored in directory: /tmp/pip-ephem-wheel-cache-7_f0chgc/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-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 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-2.28.0 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-4.2.0 urllib3-1.26.9 zipp-3.8.0 [rtd-command-info] start-time: 2022-06-28T18:57:32.765489Z, end-time: 2022-06-28T18:57:44.247422Z, duration: 11, 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 12.0 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 106.1 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 188.3 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 195.2 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 248.7 MB/s eta 0:00:00 Collecting m2r2 Downloading m2r2-0.3.2-py3-none-any.whl (11 kB) 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: 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 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(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)) (3.8.0) 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=554814 sha256=206387b441687045d1aeeb558498ba3b8d52335956b20a907f7e9962549b4fd5 Stored in directory: /tmp/pip-ephem-wheel-cache-rcph77t9/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-2.4.2 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: 2022-06-28T18:57:46.105599Z, end-time: 2022-06-28T18:57:46.165778Z, 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', #'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. exclude_patterns = [] suppress_warnings = [ #'Unknown directive type dropdown', 'autosectionlabel.*', 'epub.duplicated_toc_entry'] # -- 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 = ['subsections/datasets'] ########################################################################### # 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': [ ], 'downloads': [ ("pdf", "//giottoteam-giotto.readthedocs-hosted.com/_/downloads/en/suite/pdf/"), ("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/latest/', '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': '1daf317e', } # 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/994217/' 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: 2022-06-28T18:57:46.514237Z, end-time: 2022-06-28T18:58:37.735396Z, duration: 51, 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 652 source files that are out of date updating environment: [new config] 652 added, 0 changed, 0 removed reading sources... 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[ 25%] subsections/md_rst/crossSectionGenePlot reading sources... [ 25%] subsections/md_rst/crossSectionGenePlot3D reading sources... [ 25%] subsections/md_rst/crossSectionPlot reading sources... [ 25%] subsections/md_rst/crossSectionPlot3D reading sources... [ 25%] subsections/md_rst/decide_cluster_order reading sources... [ 25%] subsections/md_rst/density_giottoLargeImage reading sources... [ 26%] subsections/md_rst/depth reading sources... [ 26%] subsections/md_rst/detectSpatialCorFeats reading sources... [ 26%] subsections/md_rst/detectSpatialCorFeatsMatrix reading sources... [ 26%] subsections/md_rst/detectSpatialCorGenes reading sources... [ 26%] subsections/md_rst/detectSpatialPatterns reading sources... [ 26%] subsections/md_rst/determine_cores reading sources... [ 26%] subsections/md_rst/dimCellPlot reading sources... [ 27%] subsections/md_rst/dimCellPlot2D reading sources... [ 27%] subsections/md_rst/dimFeatPlot2D reading sources... 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[rtd-command-info] start-time: 2022-06-28T18:58:58.968182Z, end-time: 2022-06-28T18:59:04.887944Z, duration: 5, 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 development additionalinformation contribute subsections/tipsandtricks/NEWS subsections/detailed_workflow tipsandtricks subsections/tipsandtricks/giottoclass subsections/tipsandtricks/howtosubsetgiottoobject subsections/tipsandtricks/howtovisualizeandsaveplots subsections/tipsandtricks/testandstoremultipleanayses subsections/tipsandtricks/waystovisualizespatialdata subsections/tipsandtricks/workingwithimages subsections/tipsandtricks/visualizewithvoronoiplots datasets 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/subsections/trygiotto/binder.rst:: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] 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' %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: 2022-06-28T18:59:19.178240Z, end-time: 2022-06-28T19:01:49.131136Z, duration: 149, exit-code: 0 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. 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\TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ ptm/m/n/10 <#ge-t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS 1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_feature_info\TS1/ptm/m/it/10 ` \T1/ptm/m/n/ 10 <#get-fea-ture-info>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [58] Underfull \hbox (badness 10000) in paragraph at lines 4416--4426 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set-di m-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4416--4426 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ ptm/m/n/10 <#se-t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS 1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_feature_info\TS1/ptm/m/it/10 ` \T1/ptm/m/n/ 10 <#set-fea-ture-info>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [59] Underfull \hbox (badness 10000) in paragraph at lines 4501--4511 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [60] Underfull \hbox (badness 10000) in paragraph at lines 4591--4601 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4591--4601 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [61] Underfull \hbox (badness 10000) in paragraph at lines 4676--4686 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [62] Underfull \hbox (badness 10000) in paragraph at lines 4766--4776 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4766--4776 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4835--4845 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [63] Underfull \hbox (badness 10000) in paragraph at lines 4909--4919 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4909--4919 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 7203) in paragraph at lines 4909--4919 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_feature_info\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-fea-ture-info>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_giottoImage\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set-giot-t oim-age>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_spatialGrid\TS1/ptm/m/it/10 ` [64] Underfull \hbox (badness 10000) in paragraph at lines 4973--4983 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [65] Underfull \hbox (badness 10000) in paragraph at lines 5047--5057 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 5047--5057 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 5131--5141 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [66] Underfull \hbox (badness 10000) in paragraph at lines 5221--5231 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 5221--5231 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , LaTeX Warning: Hyper reference `subsections/md_rst/get_expression_values::doc' on page 67 undefined on input line 5245. 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[108] Overfull \hbox (266.03615pt too wide) in paragraph at lines 9559--9562 [] Underfull \hbox (badness 10000) in paragraph at lines 9559--9562 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 doLouvainCluster\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#dolou-vain-clus-ter>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 do-Ran-domWalk-Clus-ter\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <# do-ran-domwalk-clus-ter>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [109] Overfull \hbox (44.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 nn_network_to_use| Overfull \hbox (14.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 network_name| Overfull \hbox (8.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 python_path| Overfull \hbox (2.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 resolution| Overfull \hbox (2.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 weight_col| Overfull \hbox (26.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 partition_type| Overfull \hbox (32.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 init_membership| Overfull \hbox (14.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 n_iterations| Overfull \hbox (26.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 return_gobject| Overfull \hbox (8.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 seed_number| [110] Overfull \hbox (28.52188pt too wide) in paragraph at lines 9841--9841 []\T1/pcr/m/n/10 nn_network_to_use| Overfull \hbox (10.52188pt too wide) in paragraph at lines 9841--9841 []\T1/pcr/m/n/10 return_gobject| [111] [112] [113] [114] [115] [116] Overfull \hbox (82.97841pt too wide) in paragraph at lines 10391--10393 [] [117] [118] [119] Underfull \hbox (badness 10000) in paragraph at lines 10804--10806 []\T1/ptm/m/n/10 The sys-tem-atic steps [120] [121] [122] [123] LaTeX Warning: Hyper reference `subsections/md_rst/createNearestNetwork::doc' o n page 124 undefined on input line 11202. 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Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on giottoteam-giotto.pdf (377 pages, 82148083 bytes). Transcript written on giottoteam-giotto.log. Latexmk: Index file 'giottoteam-giotto.idx' was written Latexmk: Missing input file: 'giottoteam-giotto.ind' from line 'No file giottoteam-giotto.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'giottoteam-giotto.pdf' 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' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="giottoteam-giotto" "giotto.tex"' ------------ 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. 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[7] [8] [9 <./icons_configuration.png>] [10 <./icons_giotto.png> <./icons_proce ssing.png>] [11 <./icons_clustering.png>] [12 <./icons_images.png> <./icons_vis ualizations.png>] [13 <./icons_saving.png> <./icons_image_analysis.png>] [14 <./icons_cell_type.png> <./icons_deconvolution.png>] [15 <./icons_distribut ion.png> <./icons_interaction.png>] [16 <./icons_patterns.png> <./icons_subcell ular.png>] [17] [18] Chapter 2. [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 730--732 []\T1/ptm/m/n/10 See \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 in-stall-Giot-toEn-vi-r on-ment\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#in-stall-giot-toen-vi-ron- [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] Underfull \hbox (badness 10000) in paragraph at lines 1920--1920 []\T1/pcr/m/n/10 xmax_adj, xmin_adj, Underfull \hbox (badness 10000) in paragraph at lines 1920--1920 []\T1/pcr/m/n/10 xmin_set, xmax_set, [32] [33] Overfull \hbox (9.24567pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/10 largeImages| Overfull \hbox (21.24567pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/10 spat_loc_name| Overfull \hbox (15.24567pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/10 scale_factor| Overfull \hbox (3.24567pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/10 negative_y| [34] Underfull \hbox (badness 10000) in paragraph at lines 2082--2082 []\T1/phv/m/n/10 Ar-gu- Overfull \hbox (4.43025pt too wide) in paragraph at lines 2082--2082 []\T1/pcr/m/n/10 spatpl| Overfull \hbox (4.43025pt too wide) in paragraph at lines 2082--2082 []\T1/pcr/m/n/10 gimage| [35] [36] Underfull \hbox (badness 10000) in paragraph at lines 2260--2260 []\T1/pcr/m/n/10 xmax_adj, xmin_adj, Underfull \hbox (badness 10000) in paragraph at lines 2260--2260 []\T1/pcr/m/n/10 xmin_set, xmax_set, [37] Underfull \hbox (badness 10000) in paragraph at lines 2349--2359 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [38] Overfull \hbox (41.216pt too wide) in paragraph at lines 2448--2448 []\T1/pcr/m/n/10 largeImage_crop_params_list| Overfull \hbox (23.216pt too wide) in paragraph at lines 2448--2448 []\T1/pcr/m/n/10 largeImage_max_intensity| [39] 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`\T1/ptm/m/n/10 _ , [59] Underfull \hbox (badness 10000) in paragraph at lines 4501--4511 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [60] Underfull \hbox (badness 10000) in paragraph at lines 4591--4601 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4591--4601 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [61] Underfull \hbox (badness 10000) in paragraph at lines 4676--4686 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [62] Underfull \hbox (badness 10000) in paragraph at lines 4766--4776 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4766--4776 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4835--4845 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [63] Underfull \hbox (badness 10000) in paragraph at lines 4909--4919 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4909--4919 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 7203) in paragraph at lines 4909--4919 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_feature_info\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-fea-ture-info>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_giottoImage\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set-giot-t oim-age>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_spatialGrid\TS1/ptm/m/it/10 ` [64] Underfull \hbox (badness 10000) in paragraph at lines 4973--4983 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [65] Underfull \hbox (badness 10000) in paragraph at lines 5047--5057 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 5047--5057 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 5131--5141 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [66] Underfull \hbox (badness 10000) in paragraph at lines 5221--5231 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 5221--5231 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 10000) in paragraph at lines 6121--6121 []\T1/pcr/m/n/10 x_max, x_min, y_max, [76] Underfull \hbox (badness 10000) in paragraph at lines 6220--6220 []\T1/pcr/m/n/10 x_max, x_min, y_max, y_min, z_max, [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] Overfull \hbox (9.8002pt too wide) in paragraph at lines 7442--7444 [] Overfull \hbox (13.66899pt too wide) in paragraph at lines 7524--7528 [] [90] [91] Overfull \hbox (2.50272pt too wide) in paragraph at lines 7776--7776 []\T1/pcr/m/n/10 expression_threshold| Overfull \hbox (2.50272pt too wide) in paragraph at lines 7776--7776 []\T1/pcr/m/n/10 nr_expression_groups| [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] Underfull \hbox (badness 5970) in paragraph at lines 9096--9099 []\T1/ptm/m/n/10 based on the [105] [106] [107] [108] Overfull \hbox (266.03615pt too wide) in paragraph at lines 9559--9562 [] Underfull \hbox (badness 10000) in paragraph at lines 9559--9562 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 doLouvainCluster\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#dolou-vain-clus-ter>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 do-Ran-domWalk-Clus-ter\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <# do-ran-domwalk-clus-ter>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [109] Overfull \hbox (44.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 nn_network_to_use| Overfull \hbox (14.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 network_name| Overfull \hbox (8.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 python_path| Overfull \hbox (2.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 resolution| Overfull \hbox (2.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 weight_col| Overfull \hbox (26.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 partition_type| Overfull \hbox (32.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 init_membership| Overfull \hbox (14.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 n_iterations| Overfull \hbox (26.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 return_gobject| Overfull \hbox (8.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 seed_number| [110] Overfull \hbox (28.52188pt too wide) in paragraph at lines 9841--9841 []\T1/pcr/m/n/10 nn_network_to_use| Overfull \hbox (10.52188pt too wide) in paragraph at lines 9841--9841 []\T1/pcr/m/n/10 return_gobject| [111] [112] [113] [114] [115] [116] Overfull \hbox (82.97841pt too wide) in paragraph at lines 10391--10393 [] [117] [118] [119] Underfull \hbox (badness 10000) in paragraph at lines 10804--10806 []\T1/ptm/m/n/10 The sys-tem-atic steps [120] [121] [122] [123] [124] Overfull \hbox (2.31094pt too wide) in paragraph at lines 11422--11422 []\T1/pcr/m/n/10 min_expr_gini_score| Overfull \hbox (2.31094pt too wide) in paragraph at lines 11422--11422 []\T1/pcr/m/n/10 detection_threshold| [125] [126] Overfull \hbox (2.31094pt too wide) in paragraph at lines 11581--11581 []\T1/pcr/m/n/10 min_expr_gini_score| Overfull \hbox (2.31094pt too wide) in paragraph at lines 11581--11581 []\T1/pcr/m/n/10 detection_threshold| [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] Overfull \hbox (3.85144pt too wide) in alignment at lines 12817--12825 [] [] Overfull \hbox (3.85144pt too wide) in alignment at lines 12825--12836 [] [] Overfull \hbox (3.85144pt too wide) in alignment at lines 12836--12840 [] [] Overfull \hbox (3.85144pt too wide) in alignment at lines 12840--12842 [] [] Overfull \hbox (3.85144pt too wide) in alignment at lines 12842--12943 [] [] Overfull \hbox (3.85144pt too wide) in alignment at lines 12943--13004 [] [] [139] [140] [141] Underfull \hbox (badness 10000) in paragraph at lines 13272--13275 [] [142] Overfull \hbox (0.79196pt too wide) in paragraph at lines 13470--13470 []\T1/pcr/m/n/10 values_cluster_method| [143] [144] [145] [146] [147] Overfull \hbox (10.87033pt too wide) in paragraph at lines 13977--13977 []\T1/pcr/m/n/10 expression_values| Overfull \hbox (10.87033pt too wide) in paragraph at lines 13977--13977 []\T1/pcr/m/n/10 min_overlap_genes| Overfull \hbox (10.87033pt too wide) in paragraph at lines 13977--13977 []\T1/pcr/m/n/10 reverse_log_scale| Overfull \hbox (10.87033pt too wide) in paragraph at lines 13977--13977 []\T1/pcr/m/n/10 output_enrichment| [148] [149] Overfull \hbox (1.42032pt too wide) in paragraph at lines 14130--14130 []\T1/pcr/m/n/10 expression_values| Overfull \hbox (1.42032pt too wide) in paragraph at lines 14130--14130 []\T1/pcr/m/n/10 min_overlap_genes| Overfull \hbox (1.42032pt too wide) in paragraph at lines 14130--14130 []\T1/pcr/m/n/10 reverse_log_scale| Overfull \hbox (1.42032pt too wide) in paragraph at lines 14130--14130 []\T1/pcr/m/n/10 output_enrichment| Overfull \hbox (1.42032pt too wide) in paragraph at lines 14130--14130 []\T1/pcr/m/n/10 include_depletion| [150] [151] Underfull \hbox (badness 10000) in paragraph at lines 14288--14291 []\T1/ptm/m/n/10 Alternatively a [152] Overfull \hbox (4.65314pt too wide) in paragraph at lines 14413--14413 []\T1/pcr/m/n/10 expression_values| Overfull \hbox (4.65314pt too wide) in paragraph at lines 14413--14413 []\T1/pcr/m/n/10 reverse_log_scale| Overfull \hbox (4.65314pt too wide) in paragraph at lines 14413--14413 []\T1/pcr/m/n/10 output_enrichment| [153] [154] [155] [156] Underfull \hbox (badness 10000) in paragraph at lines 14875--14877 []\T1/ptm/m/n/10 and [][]$https : / / doi . org / 10 . 1186 / [157] Overfull \hbox (2.50272pt too wide) in paragraph at lines 15018--15018 []\T1/pcr/m/n/10 spatial_network_name| [158] Overfull \hbox (2.50272pt too wide) in paragraph at lines 15113--15113 []\T1/pcr/m/n/10 spatial_network_name| [159] Overfull \hbox (2.50272pt too wide) in paragraph at lines 15226--15226 []\T1/pcr/m/n/10 spatial_network_name| Overfull \hbox (64.62926pt too wide) in paragraph at lines 15233--15237 [] [160] Underfull \hbox (badness 10000) in paragraph at lines 15373--15373 []\T1/phv/m/n/10 Ar-gu- Overfull \hbox (10.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 spat_unit| Overfull \hbox (10.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 feat_type| Overfull \hbox (34.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 spat_loc_name| Overfull \hbox (16.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 dimensions| Overfull \hbox (52.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 maximum_distance| Overfull \hbox (10.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 minimum_k| Overfull \hbox (40.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 return_gobject| [161] [162] Overfull \hbox (8.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 feat_type| Overfull \hbox (8.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 spat_unit| Overfull \hbox (14.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 dimensions| Overfull \hbox (50.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 maximum_distance| Overfull \hbox (8.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 minimum_k| Overfull \hbox (8.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 show_plot| Overfull \hbox (20.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 return_plot| Overfull \hbox (8.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 save_plot| Overfull \hbox (14.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 save_param| Overfull \hbox (56.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 default_save_name| [163] [164] [165] Overfull \hbox (14.13692pt too wide) in paragraph at lines 15809--15809 []\T1/pcr/m/n/10 spat_loc_name| Overfull \hbox (26.13692pt too wide) in paragraph at lines 15809--15809 []\T1/pcr/m/n/10 delaunay_method| Overfull \hbox (86.13692pt too wide) in paragraph at lines 15809--15809 []\T1/pcr/m/n/10 maximum_distance_delaunay| Overfull \hbox (56.13692pt too wide) in paragraph at lines 15809--15809 []\T1/pcr/m/n/10 maximum_distance_knn| Overfull \hbox (20.13692pt too wide) in paragraph at lines 15809--15809 []\T1/pcr/m/n/10 return_gobject| Underfull \hbox (badness 10000) in paragraph at lines 15816--15819 []\T1/ptm/m/n/10 For De-lau-nay [166] [167] [168] [169] Overfull \hbox (3.17345pt too wide) in paragraph at lines 16333--16333 []\T1/pcr/m/n/10 expression_matrix| [170] [171] Overfull \hbox (14.28908pt too wide) in paragraph at lines 16555--16555 []\T1/pcr/m/n/10 expression_matrix| Overfull \hbox (8.28908pt too wide) in paragraph at lines 16555--16555 []\T1/pcr/m/n/10 spatial_networks| Overfull \hbox (2.28908pt too wide) in paragraph at lines 16555--16555 []\T1/pcr/m/n/10 percentage_rank| [172] Overfull \hbox (8.1722pt too wide) in paragraph at lines 16762--16762 []\T1/pcr/m/n/10 spatial_network_name| [173] [174] [175] Overfull \hbox (3.17345pt too wide) in paragraph at lines 17022--17022 []\T1/pcr/m/n/10 expression_values| Overfull \hbox (3.17345pt too wide) in paragraph at lines 17022--17022 []\T1/pcr/m/n/10 spatial_network_k| [176] Overfull \hbox (5.28992pt too wide) in paragraph at lines 17084--17086 [] [177] Overfull \hbox (33.70074pt too wide) in alignment at lines 17132--17140 [] [] Overfull \hbox (33.70074pt too wide) in alignment at lines 17140--17151 [] [] Overfull \hbox (33.70074pt too wide) in alignment at lines 17151--17155 [] [] Overfull \hbox (33.70074pt too wide) in alignment at lines 17155--17157 [] [] Overfull \hbox (33.70074pt too wide) in alignment at lines 17157--17258 [] [] Overfull \hbox (33.70074pt too wide) in alignment at lines 17258--17314 [] [] [178] [179] [180] [181] Overfull \hbox (20.76564pt too wide) in paragraph at lines 17700--17700 []\T1/pcr/m/n/10 expression_values| [182] Overfull \hbox (15.90158pt too wide) in paragraph at lines 17812--17812 []\T1/pcr/m/n/10 expression_values| [183] [184] [185] Overfull \hbox (1.98465pt too wide) in paragraph at lines 18157--18157 []\T1/pcr/m/n/10 spatial_network_name| [186] [187] Underfull \hbox (badness 10000) in paragraph at lines 18378--18380 []\T1/ptm/m/n/10 fully con- [188] 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Underfull \hbox (badness 10000) in paragraph at lines 18438--18438 []\T1/ptm/m/n/10 Ar-gu-ments passed on to \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 he atmSpa-tial-Cor-Feats\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#heatmspa-tial-cor-feat s>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ list(^^Pn^^Q, ^^Q ^^P, [189] [190] [191] Overfull \hbox (9.08342pt too wide) in paragraph at lines 18839--18839 []\T1/pcr/m/n/10 spatial_network_name| Overfull \hbox (9.08342pt too wide) in paragraph at lines 18839--18839 []\T1/pcr/m/n/10 dim_reduction_to_use| [192] [193] [194] [195] [196] [197] [198] Underfull \hbox (badness 10000) in paragraph at lines 19399--19399 []\T1/phv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 19399--19399 \T1/phv/m/n/10 gu- Overfull \hbox (7.23338pt too wide) in paragraph at lines 19399--19399 \T1/phv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 19399--19399 []\T1/pcr/m/n/10 .. 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Underfull \hbox (badness 5563) in paragraph at lines 23016--23016 []\T1/ptm/m/n/10 Ar-gu-ments passed on to \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 ce ll-Prox-im-i-tyS-pat-Plot2D\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#cell-prox-im-i-t ys-pat-plot2d>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ list(^^Pn^^Q, ^^Q ^^P, Overfull \vbox (3.0556pt too high) detected at line 23026 [245] [246] Overfull \hbox (10.58092pt too wide) in alignment at lines 23097--23105 [] [] Overfull \hbox (10.58092pt too wide) in alignment at lines 23105--23116 [] [] Overfull \hbox (10.58092pt too wide) in alignment at lines 23116--23120 [] [] Overfull \hbox (10.58092pt too wide) in alignment at lines 23120--23122 [] [] Overfull \hbox (10.58092pt too wide) in alignment at lines 23122--23223 [] [] Overfull \hbox (10.58092pt too wide) in alignment at lines 23223--23284 [] [] [247] [248] [249] [250] [251] [252] [253] [254] Underfull \hbox (badness 10000) in paragraph at lines 24153--24157 []\T1/ptm/m/n/10 are ex-pressed at [255] Underfull \hbox (badness 10000) in paragraph at lines 24325--24328 []\T1/ptm/m/n/10 are ex-pressed at [256] [257] Overfull \hbox (12.62749pt too wide) in paragraph at lines 24512--24512 []\T1/pcr/m/n/10 selected_cell_LR| Overfull \hbox (24.62749pt too wide) in paragraph at lines 24512--24512 []\T1/pcr/m/n/10 show_cell_LR_names| Overfull \hbox (18.62749pt too wide) in paragraph at lines 24512--24512 []\T1/pcr/m/n/10 default_save_name| [258] Overfull \hbox (4.17502pt too wide) in paragraph at lines 24637--24637 []\T1/pcr/m/n/10 default_save_name| [259] [260] [261] [262] Chapter 3. [263] [264] [265] [266] [267] [268] Underfull \vbox (badness 10000) detected at line 25550 Overfull \vbox (2.68169pt too high) detected at line 25550 [269] [270] Chapter 4. [271] [272] Chapter 5. [273] Overfull \vbox (684.45377pt too high) has occurred while \output is active [274 <./giotto_ip.png> <./giotto_ds.png> <./giotto_analysis.png> <./giotto_viz. png>] [275] [276] Chapter 6. [277] [278 <./1_whole_brain.png>] [279 <./2_whole_brain_clus4.png> <./3_whole_b rain_clus4_noOther.png>] [280 <./4_whole_brain_by_group_leiden_1.png> <./4_whol e_brain_by_group_leiden_2.png>] [281 <./5_whole_brain_HMRF.png> <./5_whole_brai n_by_group_HMRF_1.png>] [282 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_ brain.png>] [283 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>] [284] [285] [286 <./original_clusters_black.png>] [287 <./ppt_store_multiple_an alyses2.png>] [288 <./1_loess_hvg.png> <./1_group_hvg.png>] [289 <./1_hvg_table .png> <./2_loess_pca.png>] [290 <./2_group_pca.png> <./3_loess_umap.png>] [291 <./3_group_umap.png>] [292 <./4_spatial_network.png> <./4_large_network.pn g>] [293 <./4_distance_network.png>] [294 <./5_large_network_genes.png> <./5_la rge_distance_network_genes.png>] [295] [296] [297] [298 <./2_a_spatplot.png>] [299 <./2_b_spatplot_image.png>] [300 <./2_c_spatplot_image_adjusted_1.png>] [301 <./2_c_spatplot_image_adjusted_2.png>] [302 <./2_c_spatplot_image_adjusted _3.png>] [303 <./2_c_spatplot_image_adjusted_4.png>] [304 <./2_c_spatplot_image _adjusted_5.png>] [305 <./2_c_spatplot_image_adjusted_6.png>] [306 <./2_c_spatp lot_image_adjusted_7.png>] [307 <./2_c_spatplot_image_adjusted_8.png>] [308 <./ 2_c_spatplot_image_adjusted_9.png>] [309 <./2_c_spatplot_image_adjusted_10.png> ] [310 <./2_c_spatplot_image_adjusted_11.png> <./2_d_original_plot.png>] [311 <./3_a_background_colors.png>] [312 <./3_b_black_background.png>] [313 <./ 3_c_white_background.png>] [314 <./4_a_external_image_negated.png>] [315 <./4_b _external_image_charcoal.png>] [316 <./5_1_a_spatial_locations.png>] [317 <./5_ 1_b_nr_genes.png>] [318 <./5_1_c_nr_genes_black_bg.png>] [319 <./5_1_d_nr_genes _charc_bg.png>] [320 <./5_2_a_UMAP_reduction.png>] [321 <./5_3_a_UMAP_leiden.pn g>] [322 <./5_4_a_covis_leiden_black.png>] [323 <./5_4_b_covis_leiden_negated.p ng>] [324 <./5_4_c_covis_leiden_charc.png>] [325 <./5_5_a_spatgene_charc_vor.pn g>] [326 <./5_5_b_spatgene_charc_vor.png>] [327 <./5_6_a_subset_spatgene_charc. png>] [328 <./5_6_b_subset_spatgene_charc_vor.png>] [329 <./1_voronoi.png>] [330 <./2_voronoi_no_others.png>] [331 <./3_voronoi_no_others_black_border.png> ] [332 <./4_voronoi_spat_dim.png>] [333 <./5_voronoi_neighbors.png> <./6_origin al_points.png>] [334 <./7_voronoi_genes.png> <./8_voronoi_gene_black_bg.png>] [335] [336] Chapter 7. [337 <./visium_kidney_image_summary.png>] [338 <./visium_brain_image_summary.pn g>] [339 <./visium_prostate_summary.png> <./coming_soon_summary.png>] [340 <./c ortex_image_summary.png> <./osmFISH_SS_cortex_image_summary.png>] [341] [342] Chapter 8. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.27066 ...097/ADuTNKaQJdScAAAAAElFTkSuQmCC}.svg}} and a Docker image will b... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.27066 ...097/ADuTNKaQJdScAAAAAElFTkSuQmCC}.svg}} and a Docker image will b... [343] [344 <./GitHub_Logo.png>] [345] [346 <./01_environments.png>] [347 <./01_ vm.png>] [348 <./02_docker.png> <./03_upload.png>] [349 <./03_view.png>] [350 <./03_googlecloud.png> <./03_url.png>] [351 <./03_cloud.png>] Underfull \hbox (badness 10000) in paragraph at lines 27370--27379 \T1/ptm/m/n/10 Below is an ex-am-ple of run-ning [][]\T1/ptm/m/it/10 Binder.[][ ] \T1/ptm/m/n/10 note-book [][](a)-Creating-a-Giotto-Object[][]. Step 1 Underfull \hbox (badness 10000) in paragraph at lines 27370--27379 [] Overfull \hbox (8.50937pt too wide) in paragraph at lines 27370--27379 \T1/ptm/m/n/10 Step 2 [] Underfull \hbox (badness 10000) in paragraph at lines 27370--27379 \T1/ptm/m/n/10 Step 3 [] Step 4 [352 <./04_share.png>] [353 <./Binder_1.png> <./Binder_2.png>] [354 <./Binder_3 .png> <./Binder_4.png>] Chapter 9. [355] [356] [357] [358] Chapter 10. [359] [360] [361] [362] [363] [364] Chapter 11. [365 <./Giotto_to_suite.png>] [366] Chapter 12. [367 <./input_Compatibility.png> <./data_structure_Data_Structure.png>] [368 <./analysis.png>] Chapter 13. [369] [370] Chapter 14. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.27853 ...9d709e0c26b4fbf39bc5e8583/Giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.27853 ...9d709e0c26b4fbf39bc5e8583/Giotto}.svg}} [371] [372] Chapter 15. (./giottoteam-giotto.ind) [373] (./giottoteam-giotto.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on giottoteam-giotto.pdf (377 pages, 82167911 bytes). Transcript written on giottoteam-giotto.log. Latexmk: Index file 'giottoteam-giotto.idx' was written Latexmk: Log file says output to 'giottoteam-giotto.pdf' 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' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="giottoteam-giotto" "giotto.tex"' ------------ 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. 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[7] [8] [9 <./icons_configuration.png>] [10 <./icons_giotto.png> <./icons_proce ssing.png>] [11 <./icons_clustering.png>] [12 <./icons_images.png> <./icons_vis ualizations.png>] [13 <./icons_saving.png> <./icons_image_analysis.png>] [14 <./icons_cell_type.png> <./icons_deconvolution.png>] [15 <./icons_distribut ion.png> <./icons_interaction.png>] [16 <./icons_patterns.png> <./icons_subcell ular.png>] [17] [18] Chapter 2. [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 730--732 []\T1/ptm/m/n/10 See \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 in-stall-Giot-toEn-vi-r on-ment\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#in-stall-giot-toen-vi-ron- [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] Underfull \hbox (badness 10000) in paragraph at lines 1920--1920 []\T1/pcr/m/n/10 xmax_adj, xmin_adj, Underfull \hbox (badness 10000) in paragraph at lines 1920--1920 []\T1/pcr/m/n/10 xmin_set, xmax_set, [32] [33] Overfull \hbox (9.24567pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/10 largeImages| Overfull \hbox (21.24567pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/10 spat_loc_name| Overfull \hbox (15.24567pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/10 scale_factor| Overfull \hbox (3.24567pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/10 negative_y| [34] Underfull \hbox (badness 10000) in paragraph at lines 2082--2082 []\T1/phv/m/n/10 Ar-gu- Overfull \hbox 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, Underfull \hbox (badness 10000) in paragraph at lines 4320--4330 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ ptm/m/n/10 <#ge-t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS 1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_feature_info\TS1/ptm/m/it/10 ` \T1/ptm/m/n/ 10 <#get-fea-ture-info>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [58] Underfull \hbox (badness 10000) in paragraph at lines 4416--4426 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set-di m-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4416--4426 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ ptm/m/n/10 <#se-t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS 1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_feature_info\TS1/ptm/m/it/10 ` \T1/ptm/m/n/ 10 <#set-fea-ture-info>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [59] Underfull \hbox (badness 10000) in paragraph at lines 4501--4511 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [60] Underfull \hbox (badness 10000) in paragraph at lines 4591--4601 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4591--4601 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [61] Underfull \hbox (badness 10000) in paragraph at lines 4676--4686 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [62] Underfull \hbox (badness 10000) in paragraph at lines 4766--4776 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4766--4776 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4835--4845 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [63] Underfull \hbox (badness 10000) in paragraph at lines 4909--4919 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 4909--4919 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 7203) in paragraph at lines 4909--4919 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_feature_info\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-fea-ture-info>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_giottoImage\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set-giot-t oim-age>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_spatialGrid\TS1/ptm/m/it/10 ` [64] Underfull \hbox (badness 10000) in paragraph at lines 4973--4983 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [65] Underfull \hbox (badness 10000) in paragraph at lines 5047--5057 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 5047--5057 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 5131--5141 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 get_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#get-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 get_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#ge -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [66] Underfull \hbox (badness 10000) in paragraph at lines 5221--5231 []\T1/ptm/m/n/10 Other func-tions to set data in giotto ob-ject: \TS1/ptm/m/it/ 10 ``\T1/ptm/m/it/10 set_NearestNetwork\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#set- n-ear-est-net-work>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , Underfull \hbox (badness 10000) in paragraph at lines 5221--5231 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 set_dimReduction\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#set-dim-re-duc-tion>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 set_expression_values\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#se -t-ex-pres-sion-va-l-ues>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 10000) in paragraph at lines 6121--6121 []\T1/pcr/m/n/10 x_max, x_min, y_max, [76] Underfull \hbox (badness 10000) in paragraph at lines 6220--6220 []\T1/pcr/m/n/10 x_max, x_min, y_max, y_min, z_max, [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] Overfull \hbox (9.8002pt too wide) in paragraph at lines 7442--7444 [] Overfull \hbox (13.66899pt too wide) in paragraph at lines 7524--7528 [] [90] [91] Overfull \hbox (2.50272pt too wide) in paragraph at lines 7776--7776 []\T1/pcr/m/n/10 expression_threshold| Overfull \hbox (2.50272pt too wide) in paragraph at lines 7776--7776 []\T1/pcr/m/n/10 nr_expression_groups| [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] Underfull \hbox (badness 5970) in paragraph at lines 9096--9099 []\T1/ptm/m/n/10 based on the [105] [106] [107] [108] Overfull \hbox (266.03615pt too wide) in paragraph at lines 9559--9562 [] Underfull \hbox (badness 10000) in paragraph at lines 9559--9562 \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 doLouvainCluster\TS1/ptm/m/it/10 ` \T1/ptm/m /n/10 <#dolou-vain-clus-ter>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , \TS1/ptm/m/it/1 0 ``\T1/ptm/m/it/10 do-Ran-domWalk-Clus-ter\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <# do-ran-domwalk-clus-ter>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ , [109] Overfull \hbox (44.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 nn_network_to_use| Overfull \hbox (14.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 network_name| Overfull \hbox (8.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 python_path| Overfull \hbox (2.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 resolution| Overfull \hbox (2.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 weight_col| Overfull \hbox (26.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 partition_type| Overfull \hbox (32.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 init_membership| Overfull \hbox (14.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 n_iterations| Overfull \hbox (26.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 return_gobject| Overfull \hbox (8.17189pt too wide) in paragraph at lines 9687--9687 []\T1/pcr/m/n/10 seed_number| [110] Overfull \hbox (28.52188pt too wide) in paragraph at lines 9841--9841 []\T1/pcr/m/n/10 nn_network_to_use| Overfull \hbox (10.52188pt too wide) in paragraph at lines 9841--9841 []\T1/pcr/m/n/10 return_gobject| [111] [112] [113] [114] [115] [116] Overfull \hbox (82.97841pt too wide) in paragraph at lines 10391--10393 [] [117] [118] [119] Underfull \hbox (badness 10000) in paragraph at lines 10804--10806 []\T1/ptm/m/n/10 The sys-tem-atic steps [120] [121] [122] [123] [124] Overfull \hbox (2.31094pt too wide) in paragraph at lines 11422--11422 []\T1/pcr/m/n/10 min_expr_gini_score| Overfull \hbox (2.31094pt too wide) in paragraph at lines 11422--11422 []\T1/pcr/m/n/10 detection_threshold| [125] [126] Overfull \hbox (2.31094pt too wide) in paragraph at lines 11581--11581 []\T1/pcr/m/n/10 min_expr_gini_score| Overfull \hbox (2.31094pt too wide) in paragraph at lines 11581--11581 []\T1/pcr/m/n/10 detection_threshold| [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] Overfull \hbox (3.85144pt too wide) in alignment at lines 12817--12825 [] [] Overfull \hbox (3.85144pt too wide) in alignment at lines 12825--12836 [] [] Overfull \hbox (3.85144pt too wide) in alignment at lines 12836--12840 [] [] Overfull \hbox (3.85144pt too wide) in alignment at lines 12840--12842 [] [] Overfull \hbox (3.85144pt too wide) in alignment at lines 12842--12943 [] [] Overfull \hbox (3.85144pt too wide) in alignment at lines 12943--13004 [] [] [139] [140] [141] Underfull \hbox (badness 10000) in paragraph at lines 13272--13275 [] [142] Overfull \hbox (0.79196pt too wide) in paragraph at lines 13470--13470 []\T1/pcr/m/n/10 values_cluster_method| [143] [144] [145] [146] [147] Overfull \hbox (10.87033pt too wide) in paragraph at lines 13977--13977 []\T1/pcr/m/n/10 expression_values| Overfull \hbox (10.87033pt too wide) in paragraph at lines 13977--13977 []\T1/pcr/m/n/10 min_overlap_genes| Overfull \hbox (10.87033pt too wide) in paragraph at lines 13977--13977 []\T1/pcr/m/n/10 reverse_log_scale| Overfull \hbox (10.87033pt too wide) in paragraph at lines 13977--13977 []\T1/pcr/m/n/10 output_enrichment| [148] [149] Overfull \hbox (1.42032pt too wide) in paragraph at lines 14130--14130 []\T1/pcr/m/n/10 expression_values| Overfull \hbox (1.42032pt too wide) in paragraph at lines 14130--14130 []\T1/pcr/m/n/10 min_overlap_genes| Overfull \hbox (1.42032pt too wide) in paragraph at lines 14130--14130 []\T1/pcr/m/n/10 reverse_log_scale| Overfull \hbox (1.42032pt too wide) in paragraph at lines 14130--14130 []\T1/pcr/m/n/10 output_enrichment| Overfull \hbox (1.42032pt too wide) in paragraph at lines 14130--14130 []\T1/pcr/m/n/10 include_depletion| [150] [151] Underfull \hbox (badness 10000) in paragraph at lines 14288--14291 []\T1/ptm/m/n/10 Alternatively a [152] Overfull \hbox (4.65314pt too wide) in paragraph at lines 14413--14413 []\T1/pcr/m/n/10 expression_values| Overfull \hbox (4.65314pt too wide) in paragraph at lines 14413--14413 []\T1/pcr/m/n/10 reverse_log_scale| Overfull \hbox (4.65314pt too wide) in paragraph at lines 14413--14413 []\T1/pcr/m/n/10 output_enrichment| [153] [154] [155] [156] Underfull \hbox (badness 10000) in paragraph at lines 14875--14877 []\T1/ptm/m/n/10 and [][]$https : / / doi . org / 10 . 1186 / [157] Overfull \hbox (2.50272pt too wide) in paragraph at lines 15018--15018 []\T1/pcr/m/n/10 spatial_network_name| [158] Overfull \hbox (2.50272pt too wide) in paragraph at lines 15113--15113 []\T1/pcr/m/n/10 spatial_network_name| [159] Overfull \hbox (2.50272pt too wide) in paragraph at lines 15226--15226 []\T1/pcr/m/n/10 spatial_network_name| Overfull \hbox (64.62926pt too wide) in paragraph at lines 15233--15237 [] [160] Underfull \hbox (badness 10000) in paragraph at lines 15373--15373 []\T1/phv/m/n/10 Ar-gu- Overfull \hbox (10.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 spat_unit| Overfull \hbox (10.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 feat_type| Overfull \hbox (34.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 spat_loc_name| Overfull \hbox (16.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 dimensions| Overfull \hbox (52.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 maximum_distance| Overfull \hbox (10.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 minimum_k| Overfull \hbox (40.84094pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/10 return_gobject| [161] [162] Overfull \hbox (8.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 feat_type| Overfull \hbox (8.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 spat_unit| Overfull \hbox (14.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 dimensions| Overfull \hbox (50.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 maximum_distance| Overfull \hbox (8.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 minimum_k| Overfull \hbox (8.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 show_plot| Overfull \hbox (20.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 return_plot| Overfull \hbox (8.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 save_plot| Overfull \hbox (14.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 save_param| Overfull \hbox (56.4297pt too wide) in paragraph at lines 15521--15521 []\T1/pcr/m/n/10 default_save_name| [163] [164] [165] Overfull \hbox (14.13692pt too wide) in paragraph at lines 15809--15809 []\T1/pcr/m/n/10 spat_loc_name| Overfull \hbox (26.13692pt too wide) in paragraph at lines 15809--15809 []\T1/pcr/m/n/10 delaunay_method| Overfull \hbox (86.13692pt too wide) in paragraph at lines 15809--15809 []\T1/pcr/m/n/10 maximum_distance_delaunay| Overfull \hbox (56.13692pt too wide) in paragraph at lines 15809--15809 []\T1/pcr/m/n/10 maximum_distance_knn| Overfull \hbox (20.13692pt too wide) in paragraph at lines 15809--15809 []\T1/pcr/m/n/10 return_gobject| Underfull \hbox (badness 10000) in paragraph at lines 15816--15819 []\T1/ptm/m/n/10 For De-lau-nay [166] [167] [168] [169] Overfull \hbox (3.17345pt too wide) in paragraph at lines 16333--16333 []\T1/pcr/m/n/10 expression_matrix| [170] [171] Overfull \hbox (14.28908pt too wide) in paragraph at lines 16555--16555 []\T1/pcr/m/n/10 expression_matrix| Overfull \hbox (8.28908pt too wide) in paragraph at lines 16555--16555 []\T1/pcr/m/n/10 spatial_networks| Overfull \hbox (2.28908pt too wide) in paragraph at lines 16555--16555 []\T1/pcr/m/n/10 percentage_rank| [172] Overfull \hbox (8.1722pt too wide) in paragraph at lines 16762--16762 []\T1/pcr/m/n/10 spatial_network_name| [173] [174] [175] Overfull \hbox (3.17345pt too wide) in paragraph at lines 17022--17022 []\T1/pcr/m/n/10 expression_values| Overfull \hbox (3.17345pt too wide) in paragraph at lines 17022--17022 []\T1/pcr/m/n/10 spatial_network_k| [176] Overfull \hbox (5.28992pt too wide) in paragraph at lines 17084--17086 [] [177] Overfull \hbox (33.70074pt too wide) in alignment at lines 17132--17140 [] [] Overfull \hbox (33.70074pt too wide) in alignment at lines 17140--17151 [] [] Overfull \hbox (33.70074pt too wide) in alignment at lines 17151--17155 [] [] Overfull \hbox (33.70074pt too wide) in alignment at lines 17155--17157 [] [] Overfull \hbox (33.70074pt too wide) in alignment at lines 17157--17258 [] [] Overfull \hbox (33.70074pt too wide) in alignment at lines 17258--17314 [] [] [178] [179] [180] [181] Overfull \hbox (20.76564pt too wide) in paragraph at lines 17700--17700 []\T1/pcr/m/n/10 expression_values| [182] Overfull \hbox (15.90158pt too wide) in paragraph at lines 17812--17812 []\T1/pcr/m/n/10 expression_values| [183] [184] [185] Overfull \hbox (1.98465pt too wide) in paragraph at lines 18157--18157 []\T1/pcr/m/n/10 spatial_network_name| [186] [187] Underfull \hbox (badness 10000) in paragraph at lines 18378--18380 []\T1/ptm/m/n/10 fully con- [188] 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Underfull \hbox (badness 10000) in paragraph at lines 18438--18438 []\T1/ptm/m/n/10 Ar-gu-ments passed on to \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 he atmSpa-tial-Cor-Feats\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#heatmspa-tial-cor-feat s>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ list(^^Pn^^Q, ^^Q ^^P, [189] [190] [191] Overfull \hbox (9.08342pt too wide) in paragraph at lines 18839--18839 []\T1/pcr/m/n/10 spatial_network_name| Overfull \hbox (9.08342pt too wide) in paragraph at lines 18839--18839 []\T1/pcr/m/n/10 dim_reduction_to_use| [192] [193] [194] [195] [196] [197] [198] Underfull \hbox (badness 10000) in paragraph at lines 19399--19399 []\T1/phv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 19399--19399 \T1/phv/m/n/10 gu- Overfull \hbox (7.23338pt too wide) in paragraph at lines 19399--19399 \T1/phv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 19399--19399 []\T1/pcr/m/n/10 .. 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Underfull \hbox (badness 10000) in paragraph at lines 19761--19761 \T1/ptm/m/n/10 list(^^Pgiotto ob-ject^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^ Pgenes^^Q)), list(^^Pgenes to show^^Q)), ^^Pn^^Q, ^^Q ^^P, Underfull \hbox (badness 10000) in paragraph at lines 19827--19827 []\T1/phv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 19827--19827 \T1/phv/m/n/10 gu- Overfull \hbox (7.23338pt too wide) in paragraph at lines 19827--19827 \T1/phv/m/n/10 ment| Overfull \hbox (27.00366pt too wide) in paragraph at lines 19827--19827 []\T1/pcr/m/n/10 gobject| Underfull \hbox (badness 10000) in paragraph at lines 19827--19827 []\T1/pcr/m/n/10 .. 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Underfull \hbox (badness 10000) in paragraph at lines 20122--20122 \T1/ptm/m/n/10 list(^^Pgiotto ob-ject^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^ Pspat_unit^^Q)), list(^^Pspatial unit^^Q)), ^^Pn^^Q, ^^Q ^^P, Underfull \hbox (badness 5787) in paragraph at lines 20122--20122 \T1/ptm/m/n/10 list(list(list(^^Pfeat_type^^Q)), list(^^Pfeature type^^Q)), ^^P n^^Q, ^^Q ^^P, list(list(list(^^Pshow_image^^Q)), list(^^Pshow [214] Underfull \vbox (badness 10000) detected at line 20141 Overfull \vbox (49.52583pt too high) detected at line 20141 [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 20200--20200 []\T1/phv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20200--20200 \T1/phv/m/n/10 gu- Overfull \hbox (7.23338pt too wide) in paragraph at lines 20200--20200 \T1/phv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 20200--20200 []\T1/pcr/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 20200--20200 \T1/ptm/m/n/10 list(^^Pgiotto ob-ject^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^ Pspat_unit^^Q)), list(^^Pspatial unit^^Q)), ^^Pn^^Q, ^^Q ^^P, Underfull \hbox (badness 5787) in paragraph at lines 20200--20200 \T1/ptm/m/n/10 list(list(list(^^Pfeat_type^^Q)), list(^^Pfeature type^^Q)), ^^P n^^Q, ^^Q ^^P, list(list(list(^^Pshow_image^^Q)), list(^^Pshow Overfull \vbox (2.65561pt too high) detected at line 20219 [217] Underfull \vbox (badness 10000) detected at line 20219 Overfull \vbox (57.68169pt too high) detected at line 20219 [218] Underfull \hbox (badness 10000) in paragraph at lines 20234--20236 []\TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 spatDimCellPlot2D\TS1/ptm/m/it/10 ` \T1/pt m/m/n/10 <#spat-dim- [219] [220] [221] Underfull \hbox (badness 10000) in paragraph at lines 20593--20593 []\T1/phv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20593--20593 \T1/phv/m/n/10 gu- Overfull \hbox (19.06326pt too wide) 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Underfull \hbox (badness 5563) in paragraph at lines 23016--23016 []\T1/ptm/m/n/10 Ar-gu-ments passed on to \TS1/ptm/m/it/10 ``\T1/ptm/m/it/10 ce ll-Prox-im-i-tyS-pat-Plot2D\TS1/ptm/m/it/10 ` \T1/ptm/m/n/10 <#cell-prox-im-i-t ys-pat-plot2d>\TS1/ptm/m/n/10 `\T1/ptm/m/n/10 _ list(^^Pn^^Q, ^^Q ^^P, Overfull \vbox (3.0556pt too high) detected at line 23026 [245] [246] Overfull \hbox (10.58092pt too wide) in alignment at lines 23097--23105 [] [] Overfull \hbox (10.58092pt too wide) in alignment at lines 23105--23116 [] [] Overfull \hbox (10.58092pt too wide) in alignment at lines 23116--23120 [] [] Overfull \hbox (10.58092pt too wide) in alignment at lines 23120--23122 [] [] Overfull \hbox (10.58092pt too wide) in alignment at lines 23122--23223 [] [] Overfull \hbox (10.58092pt too wide) in alignment at lines 23223--23284 [] [] [247] [248] [249] [250] [251] [252] [253] [254] Underfull \hbox (badness 10000) in paragraph at lines 24153--24157 []\T1/ptm/m/n/10 are ex-pressed at [255] Underfull \hbox (badness 10000) in paragraph at lines 24325--24328 []\T1/ptm/m/n/10 are ex-pressed at [256] [257] Overfull \hbox (12.62749pt too wide) in paragraph at lines 24512--24512 []\T1/pcr/m/n/10 selected_cell_LR| Overfull \hbox (24.62749pt too wide) in paragraph at lines 24512--24512 []\T1/pcr/m/n/10 show_cell_LR_names| Overfull \hbox (18.62749pt too wide) in paragraph at lines 24512--24512 []\T1/pcr/m/n/10 default_save_name| [258] Overfull \hbox (4.17502pt too wide) in paragraph at lines 24637--24637 []\T1/pcr/m/n/10 default_save_name| [259] [260] [261] [262] Chapter 3. [263] [264] [265] [266] [267] [268] Underfull \vbox (badness 10000) detected at line 25550 Overfull \vbox (2.68169pt too high) detected at line 25550 [269] [270] Chapter 4. [271] [272] Chapter 5. [273] Overfull \vbox (684.45377pt too high) has occurred while \output is active [274 <./giotto_ip.png> <./giotto_ds.png> <./giotto_analysis.png> <./giotto_viz. png>] [275] [276] Chapter 6. [277] [278 <./1_whole_brain.png>] [279 <./2_whole_brain_clus4.png> <./3_whole_b rain_clus4_noOther.png>] [280 <./4_whole_brain_by_group_leiden_1.png> <./4_whol e_brain_by_group_leiden_2.png>] [281 <./5_whole_brain_HMRF.png> <./5_whole_brai n_by_group_HMRF_1.png>] [282 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_ brain.png>] [283 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>] [284] [285] [286 <./original_clusters_black.png>] [287 <./ppt_store_multiple_an alyses2.png>] [288 <./1_loess_hvg.png> <./1_group_hvg.png>] [289 <./1_hvg_table .png> <./2_loess_pca.png>] [290 <./2_group_pca.png> <./3_loess_umap.png>] [291 <./3_group_umap.png>] [292 <./4_spatial_network.png> <./4_large_network.pn g>] [293 <./4_distance_network.png>] [294 <./5_large_network_genes.png> <./5_la rge_distance_network_genes.png>] [295] [296] [297] [298 <./2_a_spatplot.png>] [299 <./2_b_spatplot_image.png>] [300 <./2_c_spatplot_image_adjusted_1.png>] [301 <./2_c_spatplot_image_adjusted_2.png>] [302 <./2_c_spatplot_image_adjusted _3.png>] [303 <./2_c_spatplot_image_adjusted_4.png>] [304 <./2_c_spatplot_image _adjusted_5.png>] [305 <./2_c_spatplot_image_adjusted_6.png>] [306 <./2_c_spatp lot_image_adjusted_7.png>] [307 <./2_c_spatplot_image_adjusted_8.png>] [308 <./ 2_c_spatplot_image_adjusted_9.png>] [309 <./2_c_spatplot_image_adjusted_10.png> ] [310 <./2_c_spatplot_image_adjusted_11.png> <./2_d_original_plot.png>] [311 <./3_a_background_colors.png>] [312 <./3_b_black_background.png>] [313 <./ 3_c_white_background.png>] [314 <./4_a_external_image_negated.png>] [315 <./4_b _external_image_charcoal.png>] [316 <./5_1_a_spatial_locations.png>] [317 <./5_ 1_b_nr_genes.png>] [318 <./5_1_c_nr_genes_black_bg.png>] [319 <./5_1_d_nr_genes _charc_bg.png>] [320 <./5_2_a_UMAP_reduction.png>] [321 <./5_3_a_UMAP_leiden.pn g>] [322 <./5_4_a_covis_leiden_black.png>] [323 <./5_4_b_covis_leiden_negated.p ng>] [324 <./5_4_c_covis_leiden_charc.png>] [325 <./5_5_a_spatgene_charc_vor.pn g>] [326 <./5_5_b_spatgene_charc_vor.png>] [327 <./5_6_a_subset_spatgene_charc. png>] [328 <./5_6_b_subset_spatgene_charc_vor.png>] [329 <./1_voronoi.png>] [330 <./2_voronoi_no_others.png>] [331 <./3_voronoi_no_others_black_border.png> ] [332 <./4_voronoi_spat_dim.png>] [333 <./5_voronoi_neighbors.png> <./6_origin al_points.png>] [334 <./7_voronoi_genes.png> <./8_voronoi_gene_black_bg.png>] [335] [336] Chapter 7. [337 <./visium_kidney_image_summary.png>] [338 <./visium_brain_image_summary.pn g>] [339 <./visium_prostate_summary.png> <./coming_soon_summary.png>] [340 <./c ortex_image_summary.png> <./osmFISH_SS_cortex_image_summary.png>] [341] [342] Chapter 8. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.27066 ...097/ADuTNKaQJdScAAAAAElFTkSuQmCC}.svg}} and a Docker image will b... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.27066 ...097/ADuTNKaQJdScAAAAAElFTkSuQmCC}.svg}} and a Docker image will b... [343] [344 <./GitHub_Logo.png>] [345] [346 <./01_environments.png>] [347 <./01_ vm.png>] [348 <./02_docker.png> <./03_upload.png>] [349 <./03_view.png>] [350 <./03_googlecloud.png> <./03_url.png>] [351 <./03_cloud.png>] Underfull \hbox (badness 10000) in paragraph at lines 27370--27379 \T1/ptm/m/n/10 Below is an ex-am-ple of run-ning [][]\T1/ptm/m/it/10 Binder.[][ ] \T1/ptm/m/n/10 note-book [][](a)-Creating-a-Giotto-Object[][]. Step 1 Underfull \hbox (badness 10000) in paragraph at lines 27370--27379 [] Overfull \hbox (8.50937pt too wide) in paragraph at lines 27370--27379 \T1/ptm/m/n/10 Step 2 [] Underfull \hbox (badness 10000) in paragraph at lines 27370--27379 \T1/ptm/m/n/10 Step 3 [] Step 4 [352 <./04_share.png>] [353 <./Binder_1.png> <./Binder_2.png>] [354 <./Binder_3 .png> <./Binder_4.png>] Chapter 9. [355] [356] [357] [358] Chapter 10. [359] [360] [361] [362] [363] [364] Chapter 11. [365 <./Giotto_to_suite.png>] [366] Chapter 12. [367 <./input_Compatibility.png> <./data_structure_Data_Structure.png>] [368 <./analysis.png>] Chapter 13. [369] [370] Chapter 14. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.27853 ...9d709e0c26b4fbf39bc5e8583/Giotto}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.27853 ...9d709e0c26b4fbf39bc5e8583/Giotto}.svg}} [371] [372] Chapter 15. (./giottoteam-giotto.ind) [373] (./giottoteam-giotto.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on giottoteam-giotto.pdf (377 pages, 82167911 bytes). Transcript written on giottoteam-giotto.log. Latexmk: Index file 'giottoteam-giotto.idx' was written Latexmk: Log file says output to '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: 2022-06-28T19:01:49.423811Z, end-time: 2022-06-28T19:01:49.521486Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/_build/latex/giottoteam-giotto.pdf /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/artifacts/suite/sphinx_pdf/giottoteam-giotto.pdf [rtd-command-info] start-time: 2022-06-28T19:01:49.790725Z, end-time: 2022-06-28T19:02:23.144200Z, duration: 33, 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 652 source files that are out of date updating environment: [new config] 652 added, 0 changed, 0 removed reading sources... 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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. 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/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. 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/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: 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