Read the Docs build information Build id: 997664 Project: giottoteam-giotto Version: master Commit: c2327557a1920a0c51b013ed62c9e8ddfe7e8dd7 Date: 2022-06-30T19:09:15.049034Z State: finished Success: True [rtd-command-info] start-time: 2022-06-30T19:09:44.575222Z, end-time: 2022-06-30T19:11:22.741237Z, duration: 98, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/sistia01/Giotto.git . Cloning into '.'... 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[rtd-command-info] start-time: 2022-06-30T19:11:23.033037Z, end-time: 2022-06-30T19:11:23.904402Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: switching to 'origin/master'. 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 c2327557 create docs [rtd-command-info] start-time: 2022-06-30T19:11:24.132908Z, end-time: 2022-06-30T19:11:24.219331Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-06-30T19:11:31.991209Z, end-time: 2022-06-30T19:11:36.603956Z, 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/master/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/master/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2022-06-30T19:11:36.793937Z, end-time: 2022-06-30T19:11:38.650179Z, 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/master/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 28.7 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: 2022-06-30T19:11:38.848833Z, end-time: 2022-06-30T19:11:47.293828Z, 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 31.2 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 159.7 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 183.4 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 207.5 MB/s eta 0:00:00 Collecting sphinx-rtd-theme 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pytz-2022.1-py2.py3-none-any.whl (503 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 503.5/503.5 kB 216.9 MB/s eta 0:00:00 Collecting zipp>=0.5 Downloading zipp-3.8.0-py3-none-any.whl (5.4 kB) Collecting typing-extensions>=3.6.4 Downloading typing_extensions-4.2.0-py3-none-any.whl (24 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 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 219.9 MB/s eta 0:00:00 Collecting charset-normalizer<3,>=2 Downloading charset_normalizer-2.1.0-py3-none-any.whl (39 kB) Collecting certifi>=2017.4.17 Downloading certifi-2022.6.15-py3-none-any.whl (160 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 160.2/160.2 kB 211.1 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 196.9 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 204.8 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=ed15418b028e64557bfff0c3df02a26f70cb5bbaa191cc30bf41c1940f8b8363 Stored in directory: /tmp/pip-ephem-wheel-cache-8qcadyhv/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=f26bcdab671be80f554922e0d0e631ad172675a2d519c4f5b3233d1de3ca29b3 Stored in directory: /tmp/pip-ephem-wheel-cache-8qcadyhv/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: snowballstemmer, pytz, mock, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, requests, packaging, Jinja2, importlib-metadata, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.6.15 charset-normalizer-2.1.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 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-2.28.1 snowballstemmer-2.2.0 sphinx-5.0.2 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.2.0 urllib3-1.26.9 zipp-3.8.0 [rtd-command-info] start-time: 2022-06-30T19:11:47.474365Z, end-time: 2022-06-30T19:12:00.402796Z, duration: 12, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting bluepy Downloading bluepy-1.3.0.tar.gz (217 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 217.9/217.9 kB 11.6 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 107.7 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 185.3 MB/s eta 0:00:00 Collecting readthedocs-sphinx-search==0.1.0 Downloading 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importlib-metadata>=3.6.0->domdf-python-tools>=2.9.0->sphinx-toolbox->-r docs/requirements.txt (line 8)) (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=554807 sha256=5f8abecf9fb4bd52a9ef781059f7f83a518887144551a883f0343c9c7abd3064 Stored in directory: /tmp/pip-ephem-wheel-cache-eexk_kwh/wheels/29/02/3d/a378a65b6771fb8359bf2c862f0ffe6f4bd6b0af88f4309c1c Successfully built bluepy Installing collected packages: webencodings, mypy-extensions, msgpack, lockfile, bluepy, typing-inspect, tabulate, soupsieve, six, ruamel.yaml.clib, readthedocs-sphinx-search, platformdirs, natsort, docutils, sphinx-jinja2-compat, sphinx, ruamel.yaml, 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 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: 2022-06-30T19:12:01.867543Z, end-time: 2022-06-30T19:12:01.953243Z, 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 extensions = [ 'sphinx.ext.autosectionlabel', 'sphinx.ext.autodoc', 'sphinx_rtd_theme', 'sphinx_design', 'sphinx_copybutton', 'sphinx_toolbox', 'sphinx_toolbox.shields', 'sphinx_toolbox.github', #'myst_parser' #myst_parser caused a fatal error #'sphinxcontrib.spelling' #spell checker fatal error ] # 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.*'] # -- 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" ########################################################################### # 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': "master", 'version_slug': "master", '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/master/pdf/"), ("html", "//giottoteam-giotto.readthedocs-hosted.com/_/downloads/en/master/htmlzip/"), ("epub", "//giottoteam-giotto.readthedocs-hosted.com/_/downloads/en/master/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': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', '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': 'c2327557', } # 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/997664/' 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: 2022-06-30T19:12:02.249820Z, end-time: 2022-06-30T19:12:32.665006Z, duration: 30, 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 232 source files that are out of date updating environment: [new config] 232 added, 0 changed, 0 removed reading sources... 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[ 25%] subsections/documentation_functions/combineCPG writing output... [ 25%] subsections/documentation_functions/combineCellProximityGenes writing output... [ 25%] subsections/documentation_functions/combineICG writing output... [ 26%] subsections/documentation_functions/combineInteractionChangedGenes writing output... [ 26%] subsections/documentation_functions/combineMetadata writing output... [ 27%] subsections/documentation_functions/createCrossSection writing output... [ 27%] subsections/documentation_functions/createGiottoImage writing output... [ 28%] subsections/documentation_functions/createGiottoInstructions writing output... [ 28%] subsections/documentation_functions/createGiottoObject writing output... [ 28%] subsections/documentation_functions/createGiottoVisiumObject writing output... [ 29%] subsections/documentation_functions/createMetagenes writing output... [ 29%] subsections/documentation_functions/createNearestNetwork writing output... 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[ 51%] subsections/documentation_functions/get10XMatrix_h5 writing output... [ 51%] subsections/documentation_functions/getClusterSimilarity writing output... [ 52%] subsections/documentation_functions/getDendrogramSplits writing output... [ 52%] subsections/documentation_functions/getGiottoImage writing output... [ 53%] subsections/documentation_functions/getSpatialDataset writing output... [ 53%] subsections/documentation_functions/heatmSpatialCorGenes writing output... [ 53%] subsections/documentation_functions/hyperGeometricEnrich writing output... [ 54%] subsections/documentation_functions/insertCrossSectionGenePlot3D writing output... [ 54%] subsections/documentation_functions/insertCrossSectionSpatPlot3D writing output... [ 55%] subsections/documentation_functions/installGiottoEnvironmentFunction writing output... [ 55%] subsections/documentation_functions/introduction writing output... [ 56%] subsections/documentation_functions/jackstrawPlot writing output... [ 56%] subsections/documentation_functions/loadHMRF writing output... [ 56%] subsections/documentation_functions/makeSignMatrixPAGE writing output... [ 57%] subsections/documentation_functions/makeSignMatrixRank writing output... [ 57%] subsections/documentation_functions/mergeClusters writing output... [ 58%] subsections/documentation_functions/normalizeGiotto writing output... [ 58%] subsections/documentation_functions/pDataDT writing output... [ 59%] subsections/documentation_functions/plotCCcomDotplot writing output... [ 59%] subsections/documentation_functions/plotCPG writing output... [ 59%] subsections/documentation_functions/plotCellProximityGenes writing output... [ 60%] subsections/documentation_functions/plotCombineCPG writing output... [ 60%] subsections/documentation_functions/plotCombineCellProximityGenes writing output... [ 61%] subsections/documentation_functions/plotCombineICG writing output... [ 61%] subsections/documentation_functions/plotCombineInteractionChangedGenes writing output... [ 62%] subsections/documentation_functions/plotGiottoImage writing output... [ 62%] subsections/documentation_functions/plotHeatmap writing output... [ 62%] subsections/documentation_functions/plotICG writing output... [ 63%] subsections/documentation_functions/plotInteractionChangedGenes writing output... [ 63%] subsections/documentation_functions/plotMetaDataCellsHeatmap writing output... [ 64%] subsections/documentation_functions/plotMetaDataHeatmap writing output... [ 64%] subsections/documentation_functions/plotPCA writing output... [ 65%] subsections/documentation_functions/plotPCA_3D writing output... [ 65%] subsections/documentation_functions/plotRankSpatvsExpr writing output... [ 65%] subsections/documentation_functions/plotRecovery writing output... [ 66%] subsections/documentation_functions/plotStatDelaunayNetwork writing output... [ 66%] subsections/documentation_functions/plotTSNE writing output... [ 67%] subsections/documentation_functions/plotTSNE_3D writing output... [ 67%] subsections/documentation_functions/plotUMAP writing output... [ 68%] subsections/documentation_functions/plotUMAP_3D writing output... [ 68%] subsections/documentation_functions/rankEnrich writing output... [ 68%] subsections/documentation_functions/rankSpatialCorGroups writing output... [ 69%] subsections/documentation_functions/readExprMatrix writing output... [ 69%] subsections/documentation_functions/readGiottoInstructions writing output... [ 70%] subsections/documentation_functions/removeCellAnnotation writing output... [ 70%] subsections/documentation_functions/removeGeneAnnotation writing output... [ 71%] subsections/documentation_functions/removeGiottoEnvironment writing output... [ 71%] subsections/documentation_functions/replaceGiottoInstructions writing output... [ 71%] subsections/documentation_functions/runDWLSDeconv writing output... [ 72%] subsections/documentation_functions/runHyperGeometricEnrich writing output... [ 72%] subsections/documentation_functions/runPAGEEnrich writing output... [ 73%] subsections/documentation_functions/runPCA writing output... [ 73%] subsections/documentation_functions/runPatternSimulation writing output... [ 74%] subsections/documentation_functions/runRankEnrich writing output... [ 74%] subsections/documentation_functions/runSpatialDeconv writing output... [ 75%] subsections/documentation_functions/runSpatialEnrich writing output... [ 75%] subsections/documentation_functions/runUMAP writing output... [ 75%] subsections/documentation_functions/runtSNE writing output... [ 76%] subsections/documentation_functions/screePlot writing output... [ 76%] subsections/documentation_functions/showClusterDendrogram writing output... [ 77%] subsections/documentation_functions/showClusterHeatmap writing output... 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[ 82%] subsections/documentation_functions/spatCellPlot2D writing output... [ 83%] subsections/documentation_functions/spatDimCellPlot writing output... [ 83%] subsections/documentation_functions/spatDimCellPlot2D writing output... [ 84%] subsections/documentation_functions/spatDimGenePlot writing output... [ 84%] subsections/documentation_functions/spatDimGenePlot3D writing output... [ 84%] subsections/documentation_functions/spatDimPlot writing output... [ 85%] subsections/documentation_functions/spatDimPlot3D writing output... [ 85%] subsections/documentation_functions/spatGenePlot writing output... [ 86%] subsections/documentation_functions/spatGenePlot3D writing output... [ 86%] subsections/documentation_functions/spatNetwDistributions writing output... [ 87%] subsections/documentation_functions/spatNetwDistributionsDistance writing output... [ 87%] subsections/documentation_functions/spatNetwDistributionsKneighbors writing output... [ 87%] subsections/documentation_functions/spatPlot writing output... [ 88%] subsections/documentation_functions/spatPlot2D writing output... [ 88%] subsections/documentation_functions/spatPlot3D writing output... [ 89%] subsections/documentation_functions/spatialAEH writing output... [ 89%] subsections/documentation_functions/spatialDE writing output... [ 90%] subsections/documentation_functions/stitchFieldCoordinates writing output... [ 90%] subsections/documentation_functions/stitchTileCoordinates writing output... [ 90%] subsections/documentation_functions/subClusterCells writing output... [ 91%] subsections/documentation_functions/subsetGiotto writing output... [ 91%] subsections/documentation_functions/subsetGiottoLocs writing output... [ 92%] subsections/documentation_functions/trendSceek writing output... [ 92%] subsections/documentation_functions/updateGiottoImage writing output... [ 93%] subsections/documentation_functions/viewHMRFresults writing output... [ 93%] subsections/documentation_functions/viewHMRFresults2D writing output... [ 93%] subsections/documentation_functions/viewHMRFresults3D writing output... [ 94%] subsections/documentation_functions/violinPlot writing output... [ 94%] subsections/documentation_functions/writeHMRFresults writing output... [ 95%] subsections/tipsandtricks/giottoclass writing output... [ 95%] subsections/tipsandtricks/howtosubsetgiottoobject writing output... [ 96%] subsections/tipsandtricks/howtovisualizeandsaveplots writing output... [ 96%] subsections/tipsandtricks/testandstoremultipleanayses writing output... [ 96%] subsections/tipsandtricks/visualizewithvoronoiplots writing output... [ 97%] subsections/tipsandtricks/waystovisualizespatialdata writing output... [ 97%] subsections/tipsandtricks/workingwithimages writing output... [ 98%] subsections/trygiotto/binder writing output... [ 98%] subsections/trygiotto/docker writing output... [ 99%] subsections/trygiotto/terra writing output... 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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}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb> Output written on giottoteam-giotto.pdf (709 pages, 350593424 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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Type H for immediate help. ... l.11202 ...�(1/2))/𝑑𝑒𝑙𝑡𝑎\end{split} [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 10000) in paragraph at lines 12363--12365 []|\T1/ptm/m/n/10 name for spa-tial net-work (de-fault = `de-lau- [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] Underfull \hbox (badness 5592) in paragraph at lines 15329--15331 []|\T1/ptm/m/n/10 betas to test for. three num-bers: start_beta, [171] [172] [173] [174] [175] [176] [177] [178] [179 <./dimPlot-1.png>] [180 <./dimPlot-2.png> <./dimPlot-3.png>] [181 <./dimPlot-4.png>] [182] [183 <./plotUMAP-1.png>] [184] [185] [186] [187 <./plotTSNE-1.png>] [188 <./plo tTSNE-2.png> <./plotTSNE-3.png>] [189 <./plotTSNE-4.png>] [190] [191 <./plotPCA -1.png>] [192 <./plotPCA-2.png> <./plotPCA-3.png>] [193 <./plotPCA-4.png>] [194] [195 <./dimGenePlot-1.png> <./dimGenePlot-2.png>] [196] [197] [198] [199] [200] [201 <./spatPlot-1.png> <./spatPlot-2.png>] [202 <./spatPlot-3.png> <./spatPlot-4.png>] [203] [204] [205] [206] [207] [208] [209] [210 <./spatGene Plot-1.png> <./spatGenePlot-2.png>] [211] [212] [213] [214] [215] [216 <./spatC ellPlot-1.png> <./spatCellPlot-2.png>] [217 <./spatCellPlot-3.png> <./spatCellP lot-4.png>] [218] [219] [220 <./spatDimPlot-1.png>] [221 <./spatDimPlot-2.png> <./spatDimPlot-3.png>] [222 <./spatDimPlot-4.png>] [223] [224] [225] [226] [227 <./spatDimGenePlot-1.png> <./spatDimGenePlot-2.png>] [228] [229] [230] [231 <./spatDimCellPlot-1.png> <./spatDimCellPlot-2.png>] [232 <./spatDimCellPl ot-3.png> <./spatDimCellPlot-4.png>] Underfull \vbox (badness 10000) detected at line 21726 Overfull \vbox (2.68169pt too high) detected at line 21726 [233] [234] [235] [236] [237 <./spatDimCellPlot2D-1.png> <./spatDimCellPlot2D-2 .png>] [238 <./spatDimCellPlot2D-3.png> <./spatDimCellPlot2D-4.png>] [239] [240] [241] [242 <./dimPlot2D-1.png> <./dimPlot2D-2.png>] [243 <./dimPlot2D-3.p ng> <./dimPlot2D-4.png>] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] Chapter 4. [303] [304] [305] [306] [307] [308] Underfull \vbox (badness 10000) detected at line 30239 Overfull \vbox (2.68169pt too high) detected at line 30239 [309] [310] Chapter 5. [311] [312 <./1_whole_brain.png>] [313 <./2_whole_brain_clus4.png> <./3_whole_b rain_clus4_noOther.png>] [314 <./4_whole_brain_by_group_leiden_1.png> <./4_whol e_brain_by_group_leiden_2.png>] [315 <./5_whole_brain_HMRF.png> <./5_whole_brai n_by_group_HMRF_1.png>] [316 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_ brain.png>] [317 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>] [318] [319] [320 <./original_clusters_black.png>] [321 <./ppt_store_multiple_an alyses2.png>] [322 <./1_loess_hvg.png> <./1_group_hvg.png>] [323 <./1_hvg_table .png> <./2_loess_pca.png>] [324 <./2_group_pca.png> <./3_loess_umap.png>] [325 <./3_group_umap.png>] [326 <./4_spatial_network.png> <./4_large_network.pn g>] [327 <./4_distance_network.png>] [328 <./5_large_network_genes.png> <./5_la rge_distance_network_genes.png>] [329] [330] [331] [332 <./2_a_spatplot1.png>] [333 <./2_b_spatplot_image.png>] [334 <./2_c_spatplot_image_adjusted_1.png>] [335 <./2_c_spatplot_image_adjusted_2.png>] [336 <./2_c_spatplot_image_adjusted _3.png>] [337 <./2_c_spatplot_image_adjusted_4.png>] [338 <./2_c_spatplot_image _adjusted_5.png>] [339 <./2_c_spatplot_image_adjusted_6.png>] [340 <./2_c_spatp lot_image_adjusted_7.png>] [341 <./2_c_spatplot_image_adjusted_8.png>] [342 <./ 2_c_spatplot_image_adjusted_9.png>] [343 <./2_c_spatplot_image_adjusted_10.png> ] [344 <./2_c_spatplot_image_adjusted_11.png> <./2_d_original_plot.png>] [345 <./3_a_background_colors.png>] [346 <./3_b_black_background.png>] [347 <./ 3_c_white_background.png>] [348 <./4_a_external_image_negated.png>] [349 <./4_b _external_image_charcoal.png>] [350 <./5_1_a_spatial_locations.png>] [351 <./5_ 1_b_nr_genes.png>] [352 <./5_1_c_nr_genes_black_bg.png>] [353 <./5_1_d_nr_genes _charc_bg.png>] [354 <./5_2_a_UMAP_reduction.png>] [355 <./5_3_a_UMAP_leiden.pn g>] [356 <./5_4_a_covis_leiden_black.png>] [357 <./5_4_b_covis_leiden_negated.p ng>] [358 <./5_4_c_covis_leiden_charc.png>] [359 <./5_5_a_spatgene_charc_vor.pn g>] [360 <./5_5_b_spatgene_charc_vor.png>] [361 <./5_6_a_subset_spatgene_charc. png>] [362 <./5_6_b_subset_spatgene_charc_vor.png>] [363 <./1_voronoi.png>] [364 <./2_voronoi_no_others.png>] [365 <./3_voronoi_no_others_black_border.png> ] [366 <./4_voronoi_spat_dim.png>] [367 <./5_voronoi_neighbors.png> <./6_origin al_points.png>] [368 <./7_voronoi_genes.png> <./8_voronoi_gene_black_bg.png>] [369] [370] Chapter 6. [371] [372] [373] [374 <./3.1_HVGplot.png> <./3.2_screePlot.png>] [375 <./3.3_j ackstrawPlot.png>] [376 <./3.4_PCA.png>] [377 <./3.5_tSNE.png>] [378 <./4.1_UMA P.png>] [379 <./4.2_showClusterHeatmap.png> <./4.3_showClusterDendrogram.png>] [380 <./5.1_violinPlot.png>] [381 <./5.2_plotMetaDataHeatmap.png>] [382 <./6.1_ spatDimPlot2D.png>] [383] [384 <./9.1_spatGenePlot2D.png>] [385 <./10.1_heatmSp atialCorGenes.png>] [386 <./10.2_spatCellPlot2D.png>] [387 <./12.1_cellProximit yBarplot.png>] [388 <./12.2_spatCellPlot2D.png>] [389 <./12.3_cellProximityHeat map.png>] [390 <./12.4_cellProximityNetwork.png>] [391 <./12.5_cellProximitySpa tPlot2D.png>] [392 <./12.6_spatPlot2D.png>] [393 <./13.1_plotCellProximityGenes .png>] [394 <./13.2_plotICG.png>] [395 <./14.1_plotCCcomHeatmap.png>] [396 <./1 4.2_plotCCcomDotplot.png>] [397 <./14.3_plotRankSpatvsExpr.png>] [398 <./14.4_p lotRecovery.png>] [399] [400] [401] [402] Overfull \vbox (1.02187pt too high) detected at line 32631 [403] [404] [405] [406] [407] [408 <./2_a_filtergenes.png> <./2_b_filtercells.p ng>] [409 <./2_c_filtercombos.png>] [410 <./3_a_screeplot1.png> <./3_b_PCA.png> ] [411] [412 <./3_d_UMAP_3D.png> <./3_e_TSNE.png>] [413 <./4_a_UMAP1.png>] [414 <./4_b_UMAP_3D.png> <./4_c_spatdimplot.png>] [415 <./4_e_clusterheatmap.pn g>] [416 <./4_f_clusterdendrogram.png>] [417 <./5_a_violinplot.png>] [418 <./5_ b_metaheatmap.png>] [419 <./6_a_spatdimplot.png>] [420 <./6_b_dimgeneplot.png> <./6_c_spatgeneplot.png>] [421 <./7_a_spatplot.png>] [422 <./8_a_plotStatDelaun ayNetwork.png>] [423 <./8_b_spatplot.png>] [424 <./8_c_spatplot.png>] [425 <./9 _a_spatgeneplot.png>] [426 <./9_b_spatgeneplot.png>] [427 <./10_a_heatmspatcor. png>] [428 <./10_b_rankcorgroup.png>] [429 <./10_c_spatcellplot.png>] [430 <./1 2_a_barplot1.png>] [431 <./12_b_heatmap.png>] [432 <./12_c_network.png>] [433 <./12_d_network.png>] [434 <./12_e_spatplot.png>] [435 <./12_e_cellproximi ty.png>] [436 <./13_a_insert.png> <./13_b_crossplot.png>] [437 <./13_c_cross.pn g>] [438 <./13_d_crossgeneplot.png> <./13_e_crossgene.png>] [439 <./mini_seqFIS H.png>] [440 <./mini_STARmap.png>] [441 <./mini_visium.png>] [442 <./cortex_svz _location_fields.png>] [443] [444] [445 <./2_a_spatplot.png>] [446 <./3_a_HVGpl ot2.png>] [447 <./3_b_screeplot2.png> <./3_c_PCA_reduction2.png>] [448 <./3_d_U MAP_reduction2.png>] [449 <./3_e_tSNE_reduction3.png>] [450 <./4_a_UMAP_leiden3 .png>] [451 <./4_b_UMAP_leiden_subcluster.png>] [452 <./4_c_heatmap.png>] [453 <./4_d_dendro.png>] [454 <./5_a_covis_leiden3.png>] [455 <./5_b_covis_leid en_selected.png>] Underfull \vbox (badness 10000) detected at line 33832 [456 <./6_a_violinplot_gini2.png>] [457 <./6_b_metaheatmap_gini2.png>] [458] [459 <./7_a_violinplot.png>] [460 <./7_b_covisualization.png>] [461 <./7_c_heat map.png>] [462 <./7_d_heatmap_selected.png>] [463 <./8_a_grid.png>] [464 <./9_a _spatial_network_delaunay.png> <./9_b_spatial_network_k3.png>] [465 <./9_c_spat ial_network_k10.png> <./9_d_spatial_network_dist.png>] [466 <./10_a_spatialgene s_km.png>] [467 <./10_b_spatialcoexpression_heatmap.png> <./10_c_spatialcoexpre ssion_rank.png>] [468 <./10_d_spatialcoexpression_metagenes.png>] [469 <./11_HM RF_2_k9_b.28.pdf>] [470 <./12_a_barplot_cell_cell_enrichment.png>] [471 <./12_b _heatmap_cell_cell_enrichment.png>] [472 <./12_c_network_cell_cell_enrichment.p ng>] [473 <./12_d_network_cell_cell_enrichment_self.pdf>] [474 <./12_e_cell_cel l_enrichment_selected.png>] [475 <./12_f_cell_cell_enrichment_sel_vs_not.png>] [476 <./13_a_CPG_dotplot.png>] [477 <./13_b_ICG_barplot.png>] Underfull \vbox (badness 3219) detected at line 34302 [478 <./14_a_communication_dotplot.png>] [479 <./14_b_expr_vs_spatial_expressio n_rank.png>] [480 <./14_c_spatial_recovery_expression_rank.png>] [481 <./14_d_e xpr_vs_spatial_activity.png>] [482 <./14_e_spatial_recovery_activity.png>] [483] [484 <./2_a_distribution_genes1.png>] [485 <./2_b_distribution_cells1.png >] [486 <./2_c_filter_combos.png>] [487 <./2_d_spatial_locations2D.png> <./2_e_ spatial_locations3D.png>] [488 <./3_a_screeplot.png>] [489 <./3_b_UMAP_reductio n.png>] [490 <./4_a_UMAP_leiden.png>] [491 <./5_b_leiden_2D.png>] [492 <./6_a_v iolinplot1.png>] [493 <./6_b_clusterheatmap_markers.png>] [494 <./7_a_clusterhe atmap_markers.png>] [495 <./7_b_clusterheatmap_markers_celltypes.png>] [496 <./ 7_c_umap_cell_types.png> <./7_d_spatPlot_cell_types_all.png>] [497 <./7_e_spatP lot2D_cell_types_all.png>] [498 <./7_f_spatPlot_cell_types_excit.png> <./7_g_sp atPlot2D_cell_types_excit.png>] [499 <./7_h_spatPlot_cell_types_inhib.png>] [500 <./7_i_spatPlot2D_cell_types_inhib.png> <./7_j_spatPlot_cell_types_ODandAs tro.png>] [501 <./7_k_spatPlot2D_cell_types_ODandAstro.png>] [502 <./7_l_spatPl ot_cell_types_other.png> <./7_m_spatPlot2D_cell_types_other.png>] [503] [504] [505 <./2_a_distribution_genes.png> <./2_b_distribution_cells.png>] [506 <./2_c_distribution_filters.png>] [507 <./2_d_spatial_locations.png> <./3_ a_hvg.png>] [508 <./3_b_signPCs.png> <./3_c_umap.png>] [509 <./4_leiden_0.2.png > <./5_a_covisualize_leiden_0.2.png>] [510 <./6_a_violinplot.png>] [511 <./6_b_ heatmap_leiden_0.2.png> <./7_a_general_cell_type.png>] [512 <./7_b_dim_plot_det ailed_cell_type.png> <./7_c_cluster_annotation_heatmap.png>] [513 <./8_cell_typ e_co_vis.png> <./9_a_Rorb_dim_plot.png>] Underfull \vbox (badness 1895) detected at line 35063 [514 <./9_b_Pcp4_dim_plot.png> <./9_c_Pcp4_spat_plot.png>] [515 <./9_d_Cux2_dim _plot.png> <./9_e_detailed_cell_types.png>] [516 <./9_f_Cux2_spat_plot.png> <./ 9_g_Ctgf_dim_plot.png>] [517 <./9_h_Ctgf_spat_plot.png> <./10_a_insert_cross_se ction_cell_types.png>] [518 <./10_b_insert_cross_section_Slc17a7.png> <./10_c_c ross_section_spat.png>] [519 <./10_d_cross_section_spat3d.png> <./10_e_Slc17a7_ cross_section_gene3d.png>] [520] [521 <./visium_technology.png> <./visium_brain _image_summary1.png>] Overfull \vbox (2.11395pt too high) detected at line 35272 [522 <./2_a_spatplot_image.png>] [523 <./2_b_spatplot_image_adjusted.png>] [524 <./2_c_in_tissue.png>] [525 <./2_d_spatial_locations1.png>] [526 <./2_e_nr _genes.png>] [527 <./3_a_HVGplot.png>] [528 <./3_b_screeplot.png> <./3_c_PCA_re duction.png>] [529 <./3_d_UMAP_reduction.png>] [530 <./3_e_tSNE_reduction.png>] [531 <./4_a_UMAP_leiden1.png>] [532 <./5_a_covis_leiden.png>] [533 <./5_b_nr_ge nes.png>] [534 <./5_c_DEG_subset.png>] Underfull \vbox (badness 10000) detected at line 35457 [535 <./6_a_violinplot_gini.png>] [536 <./6_b_metaheatmap_gini.png> <./6_c_gini _umap.png>] [537] [538 <./6_d_violinplot_scran.png>] [539 <./6_e_metaheatmap_sc ran.png> <./6_f_scran_umap.png>] [540] [541 <./7_a_metaheatmap2.png>] [542 <./7 _b_spatcellplot.png>] [543 <./7_c_spatcellplot.png>] [544 <./7_d_spatDimCellPlo t.png>] [545 <./8_grid.png>] [546 <./9_a_knn_network.png>] [547 <./10_a_spatial _genes_km.png>] [548 <./10_b_spatial_genes_rank.png>] [549 <./10_c_heatmap.png> ] [550 <./10_d_spatPlot2D_HMRF.png>] [551] [552 <./mouse_kidney_highres.png>] [553 <./2_a_spatplot_image1.png>] [554 <./2_b_spatplot_image_adjusted1.png>] [555 <./2_c_in_tissue1.png>] [556 <./2_d_spatial_locations2.png>] [557 <./2_e_n r_genes1.png>] [558 <./3_a_HVGplot1.png>] [559 <./3_b_screeplot1.png> <./3_c_PC A_reduction1.png>] [560 <./3_d_UMAP_reduction1.png>] [561 <./3_e_tSNE_reduction 1.png>] [562 <./4_a_UMAP_leiden2.png>] [563 <./5_a_covis_leiden1.png>] [564 <./ 5_b_nr_genes1.png>] Underfull \vbox (badness 10000) detected at line 36031 [565 <./6_a_violinplot_gini1.png>] [566 <./6_b_metaheatmap_gini1.png> <./6_c_gi ni_umap1.png>] [567] [568 <./6_d_violinplot_scran1.png>] [569 <./6_e_metaheatma p_scran1.png> <./6_f_scran_umap1.png>] [570 <./8_grid1.png>] [571 <./9_a_delaun ay_network.png>] [572 <./9_b_delaunay_network.png>] [573 <./10_a_spatial_genes_ km1.png>] [574 <./10_b_spatial_genes_rank1.png>] [575 <./10_d_Napsa_correlated_ genes.png>] [576 <./10_e_heatmap_correlated_genes.png> <./10_f_rank_correlated_ groups.png>] [577 <./10_g_spat_enrichment_score_plots.png> <./10_h_spat_enrichm ent_score_plots_genes.png>] [578] [579] [580] [581] [582 <./2_a_spatPlot1.png>] [583 <./2_b_spatPlot.png>] [584 <./3_a_spatPlot.png> <./3_b_PCA1.png>] [585 <./ 3_c_UMAP1.png>] [586 <./4_a_UMAP2.png>] [587 <./4_b_spatplot.png>] [588 <./5_a_ spatdimplot1.png>] [589 <./6_a_metaheatmap1.png>] [590 <./6_b_violinplot.png>] [591 <./6_c_metaheatmap.png>] [592 <./6_d_violinplot.png>] [593 <./7_a_metaheat map1.png>] [594 <./7_b_umap.png>] [595 <./7_c_spatplot1.png>] [596 <./8_a_umap. png>] [597 <./8_b_spatplot1.png>] [598 <./8_c_spatdimplot.png>] [599 <./8_d_uma p.png>] [600 <./8_e_spatPlot.png>] [601 <./8_f_spatdimgeneplot.png>] [602] [603 <./osmfish_image_demo.png>] [604] [605 <./2_a_original_clusters.png> <./2_ b_original_regions.png>] [606 <./2_c_clusterID.png>] [607 <./2_d_total_expr_lim its.png>] [608 <./3_a_screeplot2.png> <./3_b_PCA_reduction.png>] [609 <./3_c_UM AP_reduction.png>] [610 <./3_d_UMAP_reduction_expression.png>] [611 <./3_e_tSNE _reduction2.png>] [612 <./4_a_UMAP_hclust.png>] [613 <./4_b_UMAP_kmeans.png>] [614 <./4_c_UMAP_leiden.png>] [615 <./4_d_UMAP_leiden_merged.png>] [616 <./4_e_ heatmap.png> <./4_f_dendro.png>] [617 <./5_a_covis_leiden2.png>] [618 <./5_b_co vis_leiden_m.png>] [619 <./5_c_covis_leiden_merged_selected.png>] [620 <./5_d_t otal_expr.png>] [621 <./6_a_violinplot2.png>] [622 <./6_b_metaheatmap.png>] [623 <./6_e_metaheatmap_all_genes.png>] [624 <./6_f_metaheatmap_all_genes_names .png>] [625 <./7_a_annotation_leiden_merged_detailed.png>] [626 <./7_b_annotati on_leiden_merged_coarse.png>] [627 <./7_c_clusterHeatmap_det_cell_types.png>] [628 <./7_d_heatamp_det_cell_types.png>] [629 <./7_e_metaheatmap.png>] [630 <./ 8_grid_det_cell_types.png>] [631 <./9_spatial_network_k10.png> <./10_a_spatial_ genes_km2.png>] [632 <./11_a_barplot_cell_cell_enrichment.png>] [633 <./11_b_he atmap_cell_cell_enrichment.png>] [634 <./11_c_network_cell_cell_enrichment.png> ] [635 <./11_d_cell_cell_enrichment_selected.png>] [636] [637 <./2_a_spatPlot.p ng>] [638 <./2_b_spatPlot_column.png>] [639 <./2_c_spatPlot_row.png>] [640 <./2 _d_spatPlot_hist.png>] [641 <./2_e_spatPlot_hist2.png>] [642] [643 <./3_a_signP CA.png> <./3_b_PCAplot.png>] [644 <./3_c_UMAP.png>] [645 <./4_a_UMAP.png>] [646 <./4_b_UMAP.png>] [647 <./4_c_spatplot.png>] [648 <./4_d_spatPlot.png>] [649 <./5_a_spatdimplot.png>] [650 <./5_b_spatdimplot.png>] [651 <./5_c_spatdim plot.png>] [652 <./6_a_metaheatmap.png>] [653 <./6_b_violinplot_gini.png>] [654 <./7_a_metaheatmap.png>] [655 <./7_b_metaheatmap.png>] [656 <./7_c_spatplo t.png>] [657 <./7_d_spatplot.png>] [658 <./7_e_spatplot.png>] [659 <./7_f_spatp lot.png> <./7_g_spatplot_1.png>] Overfull \vbox (0.91441pt too high) detected at line 37738 [660 <./7_g_spatplot_2.png>] [661 <./7_h_spatdimplot.png>] [662 <./7_i_spatplot .png>] [663 <./7_j_umap.png>] [664 <./8_a_spatplot.png>] [665 <./12_a_barplot.p ng>] [666 <./12_b_network.png>] [667 <./12_c_proxspatplot.png>] [668 <./xx_a_me taheatmap.png>] [669 <./xx_b_spatplot.png>] [670 <./xx_c_spatgeneplot.png>] [671 <./xx_d_umap.png>] [672 <./xx_e_dimGeneplot.png>] [673 <./xx_f_spatplot.pn g>] [674 <./xx_g_spatGeneplot.png>] [675 <./xx_h_umap.png>] [676 <./xx_i_dimGen eplot.png> <./human_cyCIF_PDAC_image_summary.png>] [677 <./merFISH_hypoth_image _summary.png> <./CODEX_spleen_image_summary.png>] [678 <./visium_brain_image_su mmary.png> <./visium_kidney_image_summary.png>] [679 <./osmFISH_SS_cortex_image _summary.png> <./mouse_SS_cortex_and_subventricular.png>] [680] Chapter 7. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.37973 ...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.37973 ...097/ADuTNKaQJdScAAAAAElFTkSuQmCC}.svg}} and a Docker image will b... [681] [682 <./GitHub_Logo.png>] [683] [684 <./01_environments.png>] [685 <./01_ vm.png>] [686 <./02_docker.png> <./03_upload.png>] [687 <./03_view.png>] [688 <./03_googlecloud.png> <./03_url.png>] [689 <./03_cloud.png>] Underfull \hbox (badness 10000) in paragraph at lines 38277--38286 \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[][]. 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Type H for immediate help. ... l.38725 ...phen{}orientation (100 μm and 400  μm). \sphinxstylestrong{F... ! Package inputenc Error: Unicode char μ (U+3BC) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.38725 ...en{}orientation (100 μm and 400 μ m). \sphinxstylestrong{Fig... [704 <./Index_Fig_B.png> <./Index_Fig_C.png> <./Index_Fig_D.png>] (./giottoteam-giotto.ind) [705] (./giottoteam-giotto.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb> Output written on giottoteam-giotto.pdf (709 pages, 350611943 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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Type H for immediate help. ... l.11202 ...�(1/2))/𝑑𝑒𝑙𝑡𝑎\end{split} [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 10000) in paragraph at lines 12363--12365 []|\T1/ptm/m/n/10 name for spa-tial net-work (de-fault = `de-lau- [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] Underfull \hbox (badness 5592) in paragraph at lines 15329--15331 []|\T1/ptm/m/n/10 betas to test for. three num-bers: start_beta, [171] [172] [173] [174] [175] [176] [177] [178] [179 <./dimPlot-1.png>] [180 <./dimPlot-2.png> <./dimPlot-3.png>] [181 <./dimPlot-4.png>] [182] [183 <./plotUMAP-1.png>] [184] [185] [186] [187 <./plotTSNE-1.png>] [188 <./plo tTSNE-2.png> <./plotTSNE-3.png>] [189 <./plotTSNE-4.png>] [190] [191 <./plotPCA -1.png>] [192 <./plotPCA-2.png> <./plotPCA-3.png>] [193 <./plotPCA-4.png>] [194] [195 <./dimGenePlot-1.png> <./dimGenePlot-2.png>] [196] [197] [198] [199] [200] [201 <./spatPlot-1.png> <./spatPlot-2.png>] [202 <./spatPlot-3.png> <./spatPlot-4.png>] [203] [204] [205] [206] [207] [208] [209] [210 <./spatGene Plot-1.png> <./spatGenePlot-2.png>] [211] [212] [213] [214] [215] [216 <./spatC ellPlot-1.png> <./spatCellPlot-2.png>] [217 <./spatCellPlot-3.png> <./spatCellP lot-4.png>] [218] [219] [220 <./spatDimPlot-1.png>] [221 <./spatDimPlot-2.png> <./spatDimPlot-3.png>] [222 <./spatDimPlot-4.png>] [223] [224] [225] [226] [227 <./spatDimGenePlot-1.png> <./spatDimGenePlot-2.png>] [228] [229] [230] [231 <./spatDimCellPlot-1.png> <./spatDimCellPlot-2.png>] [232 <./spatDimCellPl ot-3.png> <./spatDimCellPlot-4.png>] Underfull \vbox (badness 10000) detected at line 21726 Overfull \vbox (2.68169pt too high) detected at line 21726 [233] [234] [235] [236] [237 <./spatDimCellPlot2D-1.png> <./spatDimCellPlot2D-2 .png>] [238 <./spatDimCellPlot2D-3.png> <./spatDimCellPlot2D-4.png>] [239] [240] [241] [242 <./dimPlot2D-1.png> <./dimPlot2D-2.png>] [243 <./dimPlot2D-3.p ng> <./dimPlot2D-4.png>] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] Chapter 4. [303] [304] [305] [306] [307] [308] Underfull \vbox (badness 10000) detected at line 30239 Overfull \vbox (2.68169pt too high) detected at line 30239 [309] [310] Chapter 5. [311] [312 <./1_whole_brain.png>] [313 <./2_whole_brain_clus4.png> <./3_whole_b rain_clus4_noOther.png>] [314 <./4_whole_brain_by_group_leiden_1.png> <./4_whol e_brain_by_group_leiden_2.png>] [315 <./5_whole_brain_HMRF.png> <./5_whole_brai n_by_group_HMRF_1.png>] [316 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_ brain.png>] [317 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>] [318] [319] [320 <./original_clusters_black.png>] [321 <./ppt_store_multiple_an alyses2.png>] [322 <./1_loess_hvg.png> <./1_group_hvg.png>] [323 <./1_hvg_table .png> <./2_loess_pca.png>] [324 <./2_group_pca.png> <./3_loess_umap.png>] [325 <./3_group_umap.png>] [326 <./4_spatial_network.png> <./4_large_network.pn g>] [327 <./4_distance_network.png>] [328 <./5_large_network_genes.png> <./5_la rge_distance_network_genes.png>] [329] [330] [331] [332 <./2_a_spatplot1.png>] [333 <./2_b_spatplot_image.png>] [334 <./2_c_spatplot_image_adjusted_1.png>] [335 <./2_c_spatplot_image_adjusted_2.png>] [336 <./2_c_spatplot_image_adjusted _3.png>] [337 <./2_c_spatplot_image_adjusted_4.png>] [338 <./2_c_spatplot_image _adjusted_5.png>] [339 <./2_c_spatplot_image_adjusted_6.png>] [340 <./2_c_spatp lot_image_adjusted_7.png>] [341 <./2_c_spatplot_image_adjusted_8.png>] [342 <./ 2_c_spatplot_image_adjusted_9.png>] [343 <./2_c_spatplot_image_adjusted_10.png> ] [344 <./2_c_spatplot_image_adjusted_11.png> <./2_d_original_plot.png>] [345 <./3_a_background_colors.png>] [346 <./3_b_black_background.png>] [347 <./ 3_c_white_background.png>] [348 <./4_a_external_image_negated.png>] [349 <./4_b _external_image_charcoal.png>] [350 <./5_1_a_spatial_locations.png>] [351 <./5_ 1_b_nr_genes.png>] [352 <./5_1_c_nr_genes_black_bg.png>] [353 <./5_1_d_nr_genes _charc_bg.png>] [354 <./5_2_a_UMAP_reduction.png>] [355 <./5_3_a_UMAP_leiden.pn g>] [356 <./5_4_a_covis_leiden_black.png>] [357 <./5_4_b_covis_leiden_negated.p ng>] [358 <./5_4_c_covis_leiden_charc.png>] [359 <./5_5_a_spatgene_charc_vor.pn g>] [360 <./5_5_b_spatgene_charc_vor.png>] [361 <./5_6_a_subset_spatgene_charc. png>] [362 <./5_6_b_subset_spatgene_charc_vor.png>] [363 <./1_voronoi.png>] [364 <./2_voronoi_no_others.png>] [365 <./3_voronoi_no_others_black_border.png> ] [366 <./4_voronoi_spat_dim.png>] [367 <./5_voronoi_neighbors.png> <./6_origin al_points.png>] [368 <./7_voronoi_genes.png> <./8_voronoi_gene_black_bg.png>] [369] [370] Chapter 6. [371] [372] [373] [374 <./3.1_HVGplot.png> <./3.2_screePlot.png>] [375 <./3.3_j ackstrawPlot.png>] [376 <./3.4_PCA.png>] [377 <./3.5_tSNE.png>] [378 <./4.1_UMA P.png>] [379 <./4.2_showClusterHeatmap.png> <./4.3_showClusterDendrogram.png>] [380 <./5.1_violinPlot.png>] [381 <./5.2_plotMetaDataHeatmap.png>] [382 <./6.1_ spatDimPlot2D.png>] [383] [384 <./9.1_spatGenePlot2D.png>] [385 <./10.1_heatmSp atialCorGenes.png>] [386 <./10.2_spatCellPlot2D.png>] [387 <./12.1_cellProximit yBarplot.png>] [388 <./12.2_spatCellPlot2D.png>] [389 <./12.3_cellProximityHeat map.png>] [390 <./12.4_cellProximityNetwork.png>] [391 <./12.5_cellProximitySpa tPlot2D.png>] [392 <./12.6_spatPlot2D.png>] [393 <./13.1_plotCellProximityGenes .png>] [394 <./13.2_plotICG.png>] [395 <./14.1_plotCCcomHeatmap.png>] [396 <./1 4.2_plotCCcomDotplot.png>] [397 <./14.3_plotRankSpatvsExpr.png>] [398 <./14.4_p lotRecovery.png>] [399] [400] [401] [402] Overfull \vbox (1.02187pt too high) detected at line 32631 [403] [404] [405] [406] [407] [408 <./2_a_filtergenes.png> <./2_b_filtercells.p ng>] [409 <./2_c_filtercombos.png>] [410 <./3_a_screeplot1.png> <./3_b_PCA.png> ] [411] [412 <./3_d_UMAP_3D.png> <./3_e_TSNE.png>] [413 <./4_a_UMAP1.png>] [414 <./4_b_UMAP_3D.png> <./4_c_spatdimplot.png>] [415 <./4_e_clusterheatmap.pn g>] [416 <./4_f_clusterdendrogram.png>] [417 <./5_a_violinplot.png>] [418 <./5_ b_metaheatmap.png>] [419 <./6_a_spatdimplot.png>] [420 <./6_b_dimgeneplot.png> <./6_c_spatgeneplot.png>] [421 <./7_a_spatplot.png>] [422 <./8_a_plotStatDelaun ayNetwork.png>] [423 <./8_b_spatplot.png>] [424 <./8_c_spatplot.png>] [425 <./9 _a_spatgeneplot.png>] [426 <./9_b_spatgeneplot.png>] [427 <./10_a_heatmspatcor. png>] [428 <./10_b_rankcorgroup.png>] [429 <./10_c_spatcellplot.png>] [430 <./1 2_a_barplot1.png>] [431 <./12_b_heatmap.png>] [432 <./12_c_network.png>] [433 <./12_d_network.png>] [434 <./12_e_spatplot.png>] [435 <./12_e_cellproximi ty.png>] [436 <./13_a_insert.png> <./13_b_crossplot.png>] [437 <./13_c_cross.pn g>] [438 <./13_d_crossgeneplot.png> <./13_e_crossgene.png>] [439 <./mini_seqFIS H.png>] [440 <./mini_STARmap.png>] [441 <./mini_visium.png>] [442 <./cortex_svz _location_fields.png>] [443] [444] [445 <./2_a_spatplot.png>] [446 <./3_a_HVGpl ot2.png>] [447 <./3_b_screeplot2.png> <./3_c_PCA_reduction2.png>] [448 <./3_d_U MAP_reduction2.png>] [449 <./3_e_tSNE_reduction3.png>] [450 <./4_a_UMAP_leiden3 .png>] [451 <./4_b_UMAP_leiden_subcluster.png>] [452 <./4_c_heatmap.png>] [453 <./4_d_dendro.png>] [454 <./5_a_covis_leiden3.png>] [455 <./5_b_covis_leid en_selected.png>] Underfull \vbox (badness 10000) detected at line 33832 [456 <./6_a_violinplot_gini2.png>] [457 <./6_b_metaheatmap_gini2.png>] [458] [459 <./7_a_violinplot.png>] [460 <./7_b_covisualization.png>] [461 <./7_c_heat map.png>] [462 <./7_d_heatmap_selected.png>] [463 <./8_a_grid.png>] [464 <./9_a _spatial_network_delaunay.png> <./9_b_spatial_network_k3.png>] [465 <./9_c_spat ial_network_k10.png> <./9_d_spatial_network_dist.png>] [466 <./10_a_spatialgene s_km.png>] [467 <./10_b_spatialcoexpression_heatmap.png> <./10_c_spatialcoexpre ssion_rank.png>] [468 <./10_d_spatialcoexpression_metagenes.png>] [469 <./11_HM RF_2_k9_b.28.pdf>] [470 <./12_a_barplot_cell_cell_enrichment.png>] [471 <./12_b _heatmap_cell_cell_enrichment.png>] [472 <./12_c_network_cell_cell_enrichment.p ng>] [473 <./12_d_network_cell_cell_enrichment_self.pdf>] [474 <./12_e_cell_cel l_enrichment_selected.png>] [475 <./12_f_cell_cell_enrichment_sel_vs_not.png>] [476 <./13_a_CPG_dotplot.png>] [477 <./13_b_ICG_barplot.png>] Underfull \vbox (badness 3219) detected at line 34302 [478 <./14_a_communication_dotplot.png>] [479 <./14_b_expr_vs_spatial_expressio n_rank.png>] [480 <./14_c_spatial_recovery_expression_rank.png>] [481 <./14_d_e xpr_vs_spatial_activity.png>] [482 <./14_e_spatial_recovery_activity.png>] [483] [484 <./2_a_distribution_genes1.png>] [485 <./2_b_distribution_cells1.png >] [486 <./2_c_filter_combos.png>] [487 <./2_d_spatial_locations2D.png> <./2_e_ spatial_locations3D.png>] [488 <./3_a_screeplot.png>] [489 <./3_b_UMAP_reductio n.png>] [490 <./4_a_UMAP_leiden.png>] [491 <./5_b_leiden_2D.png>] [492 <./6_a_v iolinplot1.png>] [493 <./6_b_clusterheatmap_markers.png>] [494 <./7_a_clusterhe atmap_markers.png>] [495 <./7_b_clusterheatmap_markers_celltypes.png>] [496 <./ 7_c_umap_cell_types.png> <./7_d_spatPlot_cell_types_all.png>] [497 <./7_e_spatP lot2D_cell_types_all.png>] [498 <./7_f_spatPlot_cell_types_excit.png> <./7_g_sp atPlot2D_cell_types_excit.png>] [499 <./7_h_spatPlot_cell_types_inhib.png>] [500 <./7_i_spatPlot2D_cell_types_inhib.png> <./7_j_spatPlot_cell_types_ODandAs tro.png>] [501 <./7_k_spatPlot2D_cell_types_ODandAstro.png>] [502 <./7_l_spatPl ot_cell_types_other.png> <./7_m_spatPlot2D_cell_types_other.png>] [503] [504] [505 <./2_a_distribution_genes.png> <./2_b_distribution_cells.png>] [506 <./2_c_distribution_filters.png>] [507 <./2_d_spatial_locations.png> <./3_ a_hvg.png>] [508 <./3_b_signPCs.png> <./3_c_umap.png>] [509 <./4_leiden_0.2.png > <./5_a_covisualize_leiden_0.2.png>] [510 <./6_a_violinplot.png>] [511 <./6_b_ heatmap_leiden_0.2.png> <./7_a_general_cell_type.png>] [512 <./7_b_dim_plot_det ailed_cell_type.png> <./7_c_cluster_annotation_heatmap.png>] [513 <./8_cell_typ e_co_vis.png> <./9_a_Rorb_dim_plot.png>] Underfull \vbox (badness 1895) detected at line 35063 [514 <./9_b_Pcp4_dim_plot.png> <./9_c_Pcp4_spat_plot.png>] [515 <./9_d_Cux2_dim _plot.png> <./9_e_detailed_cell_types.png>] [516 <./9_f_Cux2_spat_plot.png> <./ 9_g_Ctgf_dim_plot.png>] [517 <./9_h_Ctgf_spat_plot.png> <./10_a_insert_cross_se ction_cell_types.png>] [518 <./10_b_insert_cross_section_Slc17a7.png> <./10_c_c ross_section_spat.png>] [519 <./10_d_cross_section_spat3d.png> <./10_e_Slc17a7_ cross_section_gene3d.png>] [520] [521 <./visium_technology.png> <./visium_brain _image_summary1.png>] Overfull \vbox (2.11395pt too high) detected at line 35272 [522 <./2_a_spatplot_image.png>] [523 <./2_b_spatplot_image_adjusted.png>] [524 <./2_c_in_tissue.png>] [525 <./2_d_spatial_locations1.png>] [526 <./2_e_nr _genes.png>] [527 <./3_a_HVGplot.png>] [528 <./3_b_screeplot.png> <./3_c_PCA_re duction.png>] [529 <./3_d_UMAP_reduction.png>] [530 <./3_e_tSNE_reduction.png>] [531 <./4_a_UMAP_leiden1.png>] [532 <./5_a_covis_leiden.png>] [533 <./5_b_nr_ge nes.png>] [534 <./5_c_DEG_subset.png>] Underfull \vbox (badness 10000) detected at line 35457 [535 <./6_a_violinplot_gini.png>] [536 <./6_b_metaheatmap_gini.png> <./6_c_gini _umap.png>] [537] [538 <./6_d_violinplot_scran.png>] [539 <./6_e_metaheatmap_sc ran.png> <./6_f_scran_umap.png>] [540] [541 <./7_a_metaheatmap2.png>] [542 <./7 _b_spatcellplot.png>] [543 <./7_c_spatcellplot.png>] [544 <./7_d_spatDimCellPlo t.png>] [545 <./8_grid.png>] [546 <./9_a_knn_network.png>] [547 <./10_a_spatial _genes_km.png>] [548 <./10_b_spatial_genes_rank.png>] [549 <./10_c_heatmap.png> ] [550 <./10_d_spatPlot2D_HMRF.png>] [551] [552 <./mouse_kidney_highres.png>] [553 <./2_a_spatplot_image1.png>] [554 <./2_b_spatplot_image_adjusted1.png>] [555 <./2_c_in_tissue1.png>] [556 <./2_d_spatial_locations2.png>] [557 <./2_e_n r_genes1.png>] [558 <./3_a_HVGplot1.png>] [559 <./3_b_screeplot1.png> <./3_c_PC A_reduction1.png>] [560 <./3_d_UMAP_reduction1.png>] [561 <./3_e_tSNE_reduction 1.png>] [562 <./4_a_UMAP_leiden2.png>] [563 <./5_a_covis_leiden1.png>] [564 <./ 5_b_nr_genes1.png>] Underfull \vbox (badness 10000) detected at line 36031 [565 <./6_a_violinplot_gini1.png>] [566 <./6_b_metaheatmap_gini1.png> <./6_c_gi ni_umap1.png>] [567] [568 <./6_d_violinplot_scran1.png>] [569 <./6_e_metaheatma p_scran1.png> <./6_f_scran_umap1.png>] [570 <./8_grid1.png>] [571 <./9_a_delaun ay_network.png>] [572 <./9_b_delaunay_network.png>] [573 <./10_a_spatial_genes_ km1.png>] [574 <./10_b_spatial_genes_rank1.png>] [575 <./10_d_Napsa_correlated_ genes.png>] [576 <./10_e_heatmap_correlated_genes.png> <./10_f_rank_correlated_ groups.png>] [577 <./10_g_spat_enrichment_score_plots.png> <./10_h_spat_enrichm ent_score_plots_genes.png>] [578] [579] [580] [581] [582 <./2_a_spatPlot1.png>] [583 <./2_b_spatPlot.png>] [584 <./3_a_spatPlot.png> <./3_b_PCA1.png>] [585 <./ 3_c_UMAP1.png>] [586 <./4_a_UMAP2.png>] [587 <./4_b_spatplot.png>] [588 <./5_a_ spatdimplot1.png>] [589 <./6_a_metaheatmap1.png>] [590 <./6_b_violinplot.png>] [591 <./6_c_metaheatmap.png>] [592 <./6_d_violinplot.png>] [593 <./7_a_metaheat map1.png>] [594 <./7_b_umap.png>] [595 <./7_c_spatplot1.png>] [596 <./8_a_umap. png>] [597 <./8_b_spatplot1.png>] [598 <./8_c_spatdimplot.png>] [599 <./8_d_uma p.png>] [600 <./8_e_spatPlot.png>] [601 <./8_f_spatdimgeneplot.png>] [602] [603 <./osmfish_image_demo.png>] [604] [605 <./2_a_original_clusters.png> <./2_ b_original_regions.png>] [606 <./2_c_clusterID.png>] [607 <./2_d_total_expr_lim its.png>] [608 <./3_a_screeplot2.png> <./3_b_PCA_reduction.png>] [609 <./3_c_UM AP_reduction.png>] [610 <./3_d_UMAP_reduction_expression.png>] [611 <./3_e_tSNE _reduction2.png>] [612 <./4_a_UMAP_hclust.png>] [613 <./4_b_UMAP_kmeans.png>] [614 <./4_c_UMAP_leiden.png>] [615 <./4_d_UMAP_leiden_merged.png>] [616 <./4_e_ heatmap.png> <./4_f_dendro.png>] [617 <./5_a_covis_leiden2.png>] [618 <./5_b_co vis_leiden_m.png>] [619 <./5_c_covis_leiden_merged_selected.png>] [620 <./5_d_t otal_expr.png>] [621 <./6_a_violinplot2.png>] [622 <./6_b_metaheatmap.png>] [623 <./6_e_metaheatmap_all_genes.png>] [624 <./6_f_metaheatmap_all_genes_names .png>] [625 <./7_a_annotation_leiden_merged_detailed.png>] [626 <./7_b_annotati on_leiden_merged_coarse.png>] [627 <./7_c_clusterHeatmap_det_cell_types.png>] [628 <./7_d_heatamp_det_cell_types.png>] [629 <./7_e_metaheatmap.png>] [630 <./ 8_grid_det_cell_types.png>] [631 <./9_spatial_network_k10.png> <./10_a_spatial_ genes_km2.png>] [632 <./11_a_barplot_cell_cell_enrichment.png>] [633 <./11_b_he atmap_cell_cell_enrichment.png>] [634 <./11_c_network_cell_cell_enrichment.png> ] [635 <./11_d_cell_cell_enrichment_selected.png>] [636] [637 <./2_a_spatPlot.p ng>] [638 <./2_b_spatPlot_column.png>] [639 <./2_c_spatPlot_row.png>] [640 <./2 _d_spatPlot_hist.png>] [641 <./2_e_spatPlot_hist2.png>] [642] [643 <./3_a_signP CA.png> <./3_b_PCAplot.png>] [644 <./3_c_UMAP.png>] [645 <./4_a_UMAP.png>] [646 <./4_b_UMAP.png>] [647 <./4_c_spatplot.png>] [648 <./4_d_spatPlot.png>] [649 <./5_a_spatdimplot.png>] [650 <./5_b_spatdimplot.png>] [651 <./5_c_spatdim plot.png>] [652 <./6_a_metaheatmap.png>] [653 <./6_b_violinplot_gini.png>] [654 <./7_a_metaheatmap.png>] [655 <./7_b_metaheatmap.png>] [656 <./7_c_spatplo t.png>] [657 <./7_d_spatplot.png>] [658 <./7_e_spatplot.png>] [659 <./7_f_spatp lot.png> <./7_g_spatplot_1.png>] Overfull \vbox (0.91441pt too high) detected at line 37738 [660 <./7_g_spatplot_2.png>] [661 <./7_h_spatdimplot.png>] [662 <./7_i_spatplot .png>] [663 <./7_j_umap.png>] [664 <./8_a_spatplot.png>] [665 <./12_a_barplot.p ng>] [666 <./12_b_network.png>] [667 <./12_c_proxspatplot.png>] [668 <./xx_a_me taheatmap.png>] [669 <./xx_b_spatplot.png>] [670 <./xx_c_spatgeneplot.png>] [671 <./xx_d_umap.png>] [672 <./xx_e_dimGeneplot.png>] [673 <./xx_f_spatplot.pn g>] [674 <./xx_g_spatGeneplot.png>] [675 <./xx_h_umap.png>] [676 <./xx_i_dimGen eplot.png> <./human_cyCIF_PDAC_image_summary.png>] [677 <./merFISH_hypoth_image _summary.png> <./CODEX_spleen_image_summary.png>] [678 <./visium_brain_image_su mmary.png> <./visium_kidney_image_summary.png>] [679 <./osmFISH_SS_cortex_image _summary.png> <./mouse_SS_cortex_and_subventricular.png>] [680] Chapter 7. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.37973 ...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.37973 ...097/ADuTNKaQJdScAAAAAElFTkSuQmCC}.svg}} and a Docker image will b... [681] [682 <./GitHub_Logo.png>] [683] [684 <./01_environments.png>] [685 <./01_ vm.png>] [686 <./02_docker.png> <./03_upload.png>] [687 <./03_view.png>] [688 <./03_googlecloud.png> <./03_url.png>] [689 <./03_cloud.png>] Underfull \hbox (badness 10000) in paragraph at lines 38277--38286 \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[][]. 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Underfull \hbox (badness 10000) in paragraph at lines 38714--38723 \T1/ptm/m/n/10 Fig-ure 2A [][][][][] Fig- Underfull \hbox (badness 10000) in paragraph at lines 38714--38723 \T1/ptm/m/n/10 ure 2B [][][][][] Fig- Underfull \hbox (badness 10000) in paragraph at lines 38714--38723 \T1/ptm/m/n/10 ure 2C [][][][][] Fig-ure 2D [703 <./Index_Fig_A.png>] ! Package inputenc Error: Unicode char   (U+2009) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.38724 ...om the same 3D sample (distance unit  = 1 μm). ! Package inputenc Error: Unicode char   (U+2009) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.38724 ...he same 3D sample (distance unit =  1 μm). ! Package inputenc Error: Unicode char   (U+2009) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.38724 ...ame 3D sample (distance unit = 1  μm). ! Package inputenc Error: Unicode char μ (U+3BC) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.38724 ...e 3D sample (distance unit = 1 μ m). ! Package inputenc Error: Unicode char   (U+2009) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.38725 ...the z\sphinxhyphen{}orientation (100  μm and 400 μm). \sphin... ! Package inputenc Error: Unicode char μ (U+3BC) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.38725 ...e z\sphinxhyphen{}orientation (100 μ m and 400 μm). \sphinxs... ! Package inputenc Error: Unicode char   (U+2009) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.38725 ...phen{}orientation (100 μm and 400  μm). \sphinxstylestrong{F... ! Package inputenc Error: Unicode char μ (U+3BC) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.38725 ...en{}orientation (100 μm and 400 μ m). \sphinxstylestrong{Fig... [704 <./Index_Fig_B.png> <./Index_Fig_C.png> <./Index_Fig_D.png>] (./giottoteam-giotto.ind) [705] (./giottoteam-giotto.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb> Output written on giottoteam-giotto.pdf (709 pages, 350611943 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: 2022-06-30T19:26:59.512593Z, end-time: 2022-06-30T19:26:59.607427Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/_build/latex/giottoteam-giotto.pdf /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/artifacts/master/sphinx_pdf/giottoteam-giotto.pdf [rtd-command-info] start-time: 2022-06-30T19:26:59.806152Z, end-time: 2022-06-30T19:27:36.483139Z, duration: 36, 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 232 source files that are out of date updating environment: [new config] 232 added, 0 changed, 0 removed reading sources... 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