Read the Docs build information Build id: 1014371 Project: giottoteam-giotto Version: master Commit: f509847a0bb2da6ad8f0df9ed17fae011921b863 Date: 2022-07-14T19:39:38.517334Z State: finished Success: True [rtd-command-info] start-time: 2022-07-14T19:39:40.469570Z, end-time: 2022-07-14T19:41:39.771349Z, duration: 119, 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: 2022-07-14T19:41:40.122337Z, end-time: 2022-07-14T19:41:41.000550Z, 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 f509847a updates to website [rtd-command-info] start-time: 2022-07-14T19:41:41.242014Z, end-time: 2022-07-14T19:41:41.368149Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-07-14T19:41:48.677863Z, end-time: 2022-07-14T19:41:53.210457Z, 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: 2022-07-14T19:41:53.402829Z, end-time: 2022-07-14T19:41:55.188714Z, 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 26.2 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 63.2.0 Uninstalling setuptools-63.2.0: Successfully uninstalled setuptools-63.2.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-07-14T19:41:55.375809Z, end-time: 2022-07-14T19:42:03.603642Z, 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 26.0 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 150.2 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 188.0 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 225.3 MB/s eta 0:00:00 Collecting sphinx-rtd-theme 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certifi>=2017.4.17 Downloading certifi-2022.6.15-py3-none-any.whl (160 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 160.2/160.2 kB 222.0 MB/s eta 0:00:00 Collecting pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 217.3 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=15f7cbc9d4997a07701d99e947bbcdbba6b0e3ac39d09341aeafdc44623877fb Stored in directory: /tmp/pip-ephem-wheel-cache-efz0o38c/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=509b4ad5edd9466e3014e3a98c0f406e61106042f5c5d95731d12b725d7195f6 Stored in directory: /tmp/pip-ephem-wheel-cache-efz0o38c/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: snowballstemmer, pytz, mock, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, requests, packaging, Jinja2, importlib-metadata, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.6.15 charset-normalizer-2.1.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.4.1 importlib-metadata-4.12.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.8 recommonmark-0.5.0 requests-2.28.1 snowballstemmer-2.2.0 sphinx-5.0.2 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.3.0 urllib3-1.26.10 zipp-3.8.1 [rtd-command-info] start-time: 2022-07-14T19:42:03.789839Z, end-time: 2022-07-14T19:42:14.514357Z, duration: 10, 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 12.8 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting sphinx==4.5.0 Downloading Sphinx-4.5.0-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 134.7 MB/s eta 0:00:00 Collecting 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packaging->sphinx==4.5.0->-r docs/requirements.txt (line 4)) (3.0.9) 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=554802 sha256=c0f9ece709395829cb17705ebefbb18f6706697f3faf7a5355ba4a9d8bb48de0 Stored in directory: /tmp/pip-ephem-wheel-cache-xzbatxn2/wheels/29/02/3d/a378a65b6771fb8359bf2c862f0ffe6f4bd6b0af88f4309c1c Successfully built bluepy Installing collected packages: webencodings, mypy-extensions, msgpack, mistune, lockfile, bluepy, typing-inspect, tabulate, soupsieve, six, ruamel.yaml.clib, readthedocs-sphinx-search, platformdirs, natsort, docutils, sphinx-jinja2-compat, sphinx, ruamel.yaml, m2r2, html5lib, domdf-python-tools, cssutils, cachecontrol, beautifulsoup4, sphinx-tabs, sphinx_rtd_theme, sphinx-prompt, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, dict2css, autodocsumm, apeye, sphinx-toolbox Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 5.0.2 Uninstalling Sphinx-5.0.2: Successfully uninstalled Sphinx-5.0.2 Attempting uninstall: sphinx_rtd_theme Found existing installation: sphinx-rtd-theme 1.0.0 Uninstalling sphinx-rtd-theme-1.0.0: Successfully uninstalled sphinx-rtd-theme-1.0.0 Successfully installed apeye-1.2.0 autodocsumm-0.2.8 beautifulsoup4-4.11.1 bluepy-1.3.0 cachecontrol-0.12.11 cssutils-2.5.0 dict2css-0.3.0 docutils-0.16 domdf-python-tools-3.3.0 html5lib-1.1 lockfile-0.12.2 m2r2-0.3.2 mistune-0.8.4 msgpack-1.0.4 mypy-extensions-0.4.3 natsort-8.1.0 platformdirs-2.5.2 readthedocs-sphinx-search-0.1.0 ruamel.yaml-0.17.21 ruamel.yaml.clib-0.2.6 six-1.16.0 soupsieve-2.3.2.post1 sphinx-4.5.0 sphinx-autodoc-typehints-1.18.3 sphinx-copybutton-0.5.0 sphinx-design-0.2.0 sphinx-jinja2-compat-0.1.2 sphinx-prompt-1.5.0 sphinx-tabs-3.2.0 sphinx-toolbox-3.1.2 sphinx_rtd_theme-0.5.2 tabulate-0.8.10 typing-inspect-0.7.1 webencodings-0.5.1 [rtd-command-info] start-time: 2022-07-14T19:42:15.961500Z, end-time: 2022-07-14T19:42:16.024505Z, 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 #sys.path.insert(0, os.path.abspath('..')) import sphinx_rtd_theme master_doc = '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.*'] # -- 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': [ ("master", "/en/master/"), ("suite", "/en/suite/"), ], '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/master/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/source/', 'api_host': 'https://readthedocs.com', 'github_user': 'sistia01', 'proxied_api_host': '/_', 'github_repo': 'Giotto', 'github_version': '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': 'f509847a', } # 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/1014371/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2022-07-14T19:42:16.397409Z, end-time: 2022-07-14T19:43:08.309598Z, duration: 51, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v4.5.0 loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 659 source files that are out of date updating environment: [new config] 659 added, 0 changed, 0 removed reading sources... 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LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on giottoteam-giotto.pdf (719 pages, 350700621 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' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="giottoteam-giotto" "giotto.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./giotto.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1425--1428 []|\T1/qtm/m/n/10 list of in-struc-tions or out-put re-sult from [21] Underfull \hbox (badness 10000) in paragraph at lines 1626--1629 []|\T1/qtm/m/n/10 list of in-struc-tions or out-put re-sult from [22] Underfull \hbox (badness 10000) in paragraph at lines 1661--1663 []\T1/txtt/m/n/10 expr_data\T1/qtm/m/n/10 : raw will take ex-pres-sion data fro m \T1/txtt/m/n/10 raw_feature_bc_matrix \T1/qtm/m/n/10 and fil-ter from [23] [24] [25] [26] [27 <./subsetGiottoLocs-1.png> <./subsetGiottoLocs-2.png>] [28 <./subsetGiottoLocs-3.png> <./subsetGiottoLocs-4.png>] [29] [30] [31] [32] [33] [34] [35] [36] [37] Underfull \hbox (badness 10000) in paragraph at lines 2968--2970 []\T1/qtm/m/n/10 An ex-am-ple for the \T1/txtt/m/n/10 gene_clusters \T1/qtm/m/n /10 could be like this: \T1/txtt/m/n/10 cluster_vector = c(1, 1, 2, 2)\T1/qtm/m /n/10 ; [38] [39 <./createMetagenes-1.png> <./createMetagenes-2.png>] [40] [41] [42 <./filterDistributions-1.png>] [43 <./filterDistributions-2.png> <./filterD istributions-3.png>] [44] [45] [46 <./filterCombinations-1.png>] [47 <./filterC ombinations-2.png>] [48] [49] [50] [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 4235--4238 []|\T1/qtm/m/n/10 merge meta-data based on \T1/txtt/m/n/10 cell_ID \T1/qtm/m/n/ 10 col-umn in [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71 <./calculateHVG-1.png>] [72 <./calculateHVG-2.png> <./calculateHV G-3.png>] [73] [74] [75] [76 <./screePlot-1.png>] [77 <./screePlot-2.png>] [78] [79] [80 <./runPCA-1.png>] [81 <./runPCA-2.png>] [82] [83 <./runUMAP-1.png > <./runUMAP-2.png>] [84] [85 <./runtSNE-1.png> <./runtSNE-2.png>] [86] [87] [88] [89] [90] Underfull \hbox (badness 10000) in paragraph at lines 8631--8633 [][][]$\T1/qtm/m/n/10 doLeidenCluster$[][], [][]$doLouvainCluster _ community$[ ][], [][]$doLouvainCluster _ multinet$[][], [][]$doLouvainCluster$[][], [91] [92] [93] [94] [95 <./doKmeans-1.png>] [96 <./doKmeans-2.png>] [97] [98 <./doHclust-1.png> <./doHclust-2.png>] [99] [100] [101] [102] [103] [104] [105] Underfull \vbox (badness 10000) detected at line 10400 Underfull \vbox (badness 10000) detected at line 10400 [106] [107 <./mergeClusters-1.png>] [108 <./mergeClusters-2.png>] [109] [110] [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 10000) in paragraph at lines 11605--11608 []\T1/qtm/m/n/10 clus-ter_column = `lei- [117] [118] [119] [120] [121] [122 <./showClusterHeatmap-1.png>] [123 <./showCl usterHeatmap-2.png>] [124] [125 <./showClusterDendrogram-1.png> <./showClusterD endrogram-2.png>] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] ! 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Package inputenc Error: Unicode char ∗ (U+2217) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.14031 ...�(1/2))/𝑑𝑒𝑙𝑡𝑎\end{split} ! Package inputenc Error: Unicode char 𝑚 (U+1D45A) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.14031 ...�(1/2))/𝑑𝑒𝑙𝑡𝑎\end{split} ! Package inputenc Error: Unicode char 𝑑 (U+1D451) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.14031 ...�(1/2))/𝑑𝑒𝑙𝑡𝑎\end{split} ! Package inputenc Error: Unicode char 𝑒 (U+1D452) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.14031 ...�(1/2))/𝑑𝑒𝑙𝑡𝑎\end{split} ! Package inputenc Error: Unicode char 𝑙 (U+1D459) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.14031 ...�(1/2))/𝑑𝑒𝑙𝑡𝑎\end{split} ! Package inputenc Error: Unicode char 𝑡 (U+1D461) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.14031 ...�(1/2))/𝑑𝑒𝑙𝑡𝑎\end{split} ! Package inputenc Error: Unicode char 𝑎 (U+1D44E) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.14031 ...�(1/2))/𝑑𝑒𝑙𝑡𝑎\end{split} [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 5133) in paragraph at lines 15020--15023 []|\T1/qtm/m/n/10 Cal-cu-late Gene Sig-na-ture En-rich-ment Score With Underfull \hbox (badness 5133) in paragraph at lines 15055--15058 []|\T1/qtm/m/n/10 Cal-cu-late Gene Sig-na-ture En-rich-ment Score With [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] Overfull \vbox (0.63725pt too high) detected at line 16606 [156] Underfull \hbox (badness 5133) in paragraph at lines 16669--16672 []|\T1/qtm/m/n/10 kmeans al-go-rithm to use (kmeans, kmeans_arma, [157] Overfull \vbox (0.9757pt too high) detected at line 16934 [158] Underfull \hbox (badness 5133) in paragraph at lines 16990--16993 []|\T1/qtm/m/n/10 kmeans al-go-rithm to use (kmeans, kmeans_arma, [159] [160] Underfull \hbox (badness 5133) in paragraph at lines 17301--17304 []|\T1/qtm/m/n/10 kmeans al-go-rithm to use (kmeans, kmeans_arma, [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 10000) in paragraph at lines 19355--19358 []|\T1/qtm/m/n/10 be-tas to test for. three num-bers: start_beta, [176] Overfull \vbox (10.47963pt too high) detected at line 19546 [177] [178] [179] [180] [181] [182] [183] [184] [185 <./dimPlot-1.png> <./dimPl ot-2.png>] [186 <./dimPlot-3.png> <./dimPlot-4.png>] [187] [188] [189 <./plotUM AP-1.png>] [190] [191] [192] [193 <./plotTSNE-1.png> <./plotTSNE-2.png>] [194 <./plotTSNE-3.png> <./plotTSNE-4.png>] [195] [196 <./plotPCA-1.png>] [197 <./plotPCA-2.png> <./plotPCA-3.png>] [198 <./plotPCA-4.png>] [199] [200 <./dimGenePlot-1.png> <./dimGenePlot-2.png>] [201] Overfull \vbox (0.8174pt too high) detected at line 22820 [202] [203] [204] [205] [206 <./spatPlot-1.png> <./spatPlot-2.png>] [207 <./spa tPlot-3.png> <./spatPlot-4.png>] Underfull \vbox (badness 10000) detected at line 23483 Underfull \vbox (badness 10000) detected at line 23483 [208] [209] [210] [211] [212] [213] [214] [215 <./spatGenePlot-1.png> <./spatGe nePlot-2.png>] [216] [217] [218] [219] [220] [221 <./spatCellPlot-1.png> <./spa tCellPlot-2.png>] [222 <./spatCellPlot-3.png> <./spatCellPlot-4.png>] [223] [224] [225 <./spatDimPlot-1.png>] [226 <./spatDimPlot-2.png> <./spatDimPlot-3.p ng>] [227 <./spatDimPlot-4.png>] [228] [229] [230] [231] [232 <./spatDimGenePlo t-1.png> <./spatDimGenePlot-2.png>] [233] [234] Overfull \vbox (2.3165pt too high) detected at line 27638 [235] [236 <./spatDimCellPlot-1.png> <./spatDimCellPlot-2.png>] [237 <./spatDim CellPlot-3.png> <./spatDimCellPlot-4.png>] Overfull \vbox (2.37871pt too high) detected at line 27753 [238] [239] [240] [241] [242 <./spatDimCellPlot2D-1.png>] [243 <./spatDimCellPl ot2D-2.png> <./spatDimCellPlot2D-3.png>] [244 <./spatDimCellPlot2D-4.png>] [245] [246] [247 <./dimPlot2D-1.png>] [248 <./dimPlot2D-2.png> <./dimPlot2D-3.p ng>] [249 <./dimPlot2D-4.png>] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] Overfull \vbox (0.9757pt too high) detected at line 30839 [260] [261] [262] Underfull \hbox (badness 7468) in paragraph at lines 31367--31370 []|\T1/qtm/m/n/10 equa-tion re-quired by method ^^Pequa-tion^^Q.equations [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Overfull \vbox (1.07416pt too high) detected at line 32995 [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] Underfull \hbox (badness 7685) in paragraph at lines 35024--35027 []|\T1/qhv/m/n/10 Ar-gu-ments passed on to [][]com-bineIn-ter-ac-tion- [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Chapter 4. [309] [310] [311] [312] [313] [314] [315] [316] Chapter 5. [317] [318 <./1_whole_brain.png>] [319 <./2_whole_brain_clus4.png> <./3_whole_b rain_clus4_noOther.png>] [320 <./4_whole_brain_by_group_leiden_1.png> <./4_whol e_brain_by_group_leiden_2.png>] [321 <./5_whole_brain_HMRF.png> <./5_whole_brai n_by_group_HMRF_1.png>] [322 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_ brain.png>] [323 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>] [324] [325] [326] [327 <./original_clusters_black.png>] Overfull \vbox (3.38263pt too high) detected at line 39223 [328 <./ppt_store_multiple_analyses2.png> <./1_loess_hvg.png>] [329 <./1_group_ hvg.png> <./1_hvg_table.png>] [330 <./2_loess_pca.png> <./2_group_pca.png>] [331 <./3_loess_umap.png>] [332 <./3_group_umap.png>] [333 <./4_spatial_network .png> <./4_large_network.png>] [334 <./4_distance_network.png>] [335 <./5_large _network_genes.png> <./5_large_distance_network_genes.png>] [336] [337] [338] [339 <./2_a_spatplot1.png>] [340 <./2_b_spatplot_image.png>] [341 <./2_c_ spatplot_image_adjusted_1.png>] [342 <./2_c_spatplot_image_adjusted_2.png>] [343 <./2_c_spatplot_image_adjusted_3.png>] [344 <./2_c_spatplot_image_adjusted _4.png>] [345 <./2_c_spatplot_image_adjusted_5.png>] [346 <./2_c_spatplot_image _adjusted_6.png>] [347 <./2_c_spatplot_image_adjusted_7.png>] [348 <./2_c_spatp lot_image_adjusted_8.png>] [349 <./2_c_spatplot_image_adjusted_9.png>] [350 <./ 2_c_spatplot_image_adjusted_10.png>] [351 <./2_c_spatplot_image_adjusted_11.png > <./2_d_original_plot.png>] [352 <./3_a_background_colors.png>] [353 <./3_b_bl ack_background.png>] [354 <./3_c_white_background.png>] [355 <./4_a_external_im age_negated.png>] [356 <./4_b_external_image_charcoal.png>] [357 <./5_1_a_spati al_locations.png>] [358 <./5_1_b_nr_genes.png>] [359 <./5_1_c_nr_genes_black_bg .png>] [360 <./5_1_d_nr_genes_charc_bg.png>] [361 <./5_2_a_UMAP_reduction.png>] [362 <./5_3_a_UMAP_leiden.png>] [363 <./5_4_a_covis_leiden_black.png>] [364 <./ 5_4_b_covis_leiden_negated.png>] [365 <./5_4_c_covis_leiden_charc.png>] [366 <./5_5_a_spatgene_charc_vor.png>] [367 <./5_5_b_spatgene_charc_vor.png>] [368 <./5_6_a_subset_spatgene_charc.png>] [369 <./5_6_b_subset_spatgene_charc_v or.png>] [370 <./1_voronoi.png>] [371 <./2_voronoi_no_others.png>] [372 <./3_vo ronoi_no_others_black_border.png>] [373 <./4_voronoi_spat_dim.png>] [374 <./5_v oronoi_neighbors.png> <./6_original_points.png>] [375 <./7_voronoi_genes.png> < ./8_voronoi_gene_black_bg.png>] [376] Chapter 6. [377] [378] [379] [380 <./3.1_HVGplot.png> <./3.2_screePlot.png>] [381 <./3.3_j ackstrawPlot.png>] [382 <./3.4_PCA.png>] [383 <./3.5_tSNE.png>] [384 <./4.1_UMA P.png>] [385 <./4.2_showClusterHeatmap.png> <./4.3_showClusterDendrogram.png>] [386 <./5.1_violinPlot.png>] [387 <./5.2_plotMetaDataHeatmap.png>] [388 <./6.1_ spatDimPlot2D.png>] [389] [390 <./9.1_spatGenePlot2D.png>] [391 <./10.1_heatmSp atialCorGenes.png>] Overfull \vbox (2.14355pt too high) detected at line 40742 [392 <./10.2_spatCellPlot2D.png>] [393 <./12.1_cellProximityBarplot.png>] [394 <./12.2_spatCellPlot2D.png>] [395 <./12.3_cellProximityHeatmap.png>] [396 <./12.4_cellProximityNetwork.png>] [397 <./12.5_cellProximitySpatPlot2D.pn g>] [398 <./12.6_spatPlot2D.png>] [399 <./13.1_plotCellProximityGenes.png>] Overfull \vbox (2.14355pt too high) detected at line 40924 [400 <./13.2_plotICG.png>] [401 <./14.1_plotCCcomHeatmap.png>] [402 <./14.2_plo tCCcomDotplot.png>] [403 <./14.3_plotRankSpatvsExpr.png>] [404 <./14.4_plotReco very.png>] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414 <./2_a_fi ltergenes.png>] [415 <./2_b_filtercells.png>] [416 <./2_c_filtercombos.png>] [417 <./3_a_screeplot1.png> <./3_b_PCA.png>] [418] [419 <./3_d_UMAP_3D.png> <./ 3_e_TSNE.png>] [420 <./4_a_UMAP1.png>] [421 <./4_b_UMAP_3D.png> <./4_c_spatdimp lot.png>] [422 <./4_e_clusterheatmap.png>] [423 <./4_f_clusterdendrogram.png>] [424 <./5_a_violinplot.png>] [425 <./5_b_metaheatmap.png>] [426 <./6_a_spatdimp lot.png>] [427 <./6_b_dimgeneplot.png> <./6_c_spatgeneplot.png>] [428 <./7_a_sp atplot.png>] [429 <./8_a_plotStatDelaunayNetwork.png>] [430 <./8_b_spatplot.png >] [431 <./8_c_spatplot.png>] [432 <./9_a_spatgeneplot.png>] [433 <./9_b_spatge neplot.png>] [434 <./10_a_heatmspatcor.png>] [435 <./10_b_rankcorgroup.png>] Overfull \vbox (2.14355pt too high) detected at line 42066 [436 <./10_c_spatcellplot.png>] [437 <./12_a_barplot1.png>] [438 <./12_b_heatma p.png>] [439 <./12_c_network.png>] [440 <./12_d_network.png>] [441 <./12_e_spat plot.png>] [442 <./12_e_cellproximity.png>] Underfull \vbox (badness 1158) detected at line 42199 [443 <./13_a_insert.png> <./13_b_crossplot.png>] [444 <./13_c_cross.png>] [445 <./13_d_crossgeneplot.png> <./13_e_crossgene.png>] [446] [447 <./mini_seqF ISH.png>] [448 <./mini_STARmap.png>] [449 <./mini_visium.png>] [450 <./cortex_s vz_location_fields.png>] [451] [452] [453 <./2_a_spatplot.png>] [454 <./3_a_HVG plot2.png>] [455 <./3_b_screeplot2.png> <./3_c_PCA_reduction2.png>] [456 <./3_d _UMAP_reduction2.png>] [457 <./3_e_tSNE_reduction3.png>] [458 <./4_a_UMAP_leide n3.png>] [459 <./4_b_UMAP_leiden_subcluster.png>] [460 <./4_c_heatmap.png>] [461 <./4_d_dendro.png>] [462 <./5_a_covis_leiden3.png>] [463 <./5_b_covis_leid en_selected.png>] Underfull \vbox (badness 10000) detected at line 42633 [464 <./6_a_violinplot_gini2.png>] Underfull \vbox (badness 1320) detected at line 42674 [465 <./6_b_metaheatmap_gini2.png>] [466] [467 <./7_a_violinplot.png>] [468 <./ 7_b_covisualization.png>] [469 <./7_c_heatmap.png>] [470 <./7_d_heatmap_selecte d.png>] [471 <./8_a_grid.png>] [472 <./9_a_spatial_network_delaunay.png> <./9_b _spatial_network_k3.png>] [473 <./9_c_spatial_network_k10.png> <./9_d_spatial_n etwork_dist.png>] [474 <./10_a_spatialgenes_km.png>] Underfull \vbox (badness 10000) detected at line 42859 [475 <./10_b_spatialcoexpression_heatmap.png> <./10_c_spatialcoexpression_rank. png>] [476 <./10_d_spatialcoexpression_metagenes.png>] [477 <./11_HMRF_2_k9_b.2 8.pdf>] [478 <./12_a_barplot_cell_cell_enrichment.png>] [479 <./12_b_heatmap_ce ll_cell_enrichment.png>] [480 <./12_c_network_cell_cell_enrichment.png>] [481 <./12_d_network_cell_cell_enrichment_self.pdf>] [482 <./12_e_cell_cell_enr ichment_selected.png>] [483 <./12_f_cell_cell_enrichment_sel_vs_not.png>] [484 <./13_a_CPG_dotplot.png>] Overfull \vbox (2.14355pt too high) detected at line 43084 [485 <./13_b_ICG_barplot.png>] Underfull \vbox (badness 1194) detected at line 43103 [486 <./14_a_communication_dotplot.png>] [487 <./14_b_expr_vs_spatial_expressio n_rank.png>] [488 <./14_c_spatial_recovery_expression_rank.png>] [489 <./14_d_e xpr_vs_spatial_activity.png>] [490 <./14_e_spatial_recovery_activity.png>] [491] [492] [493 <./2_a_distribution_genes1.png> <./2_b_distribution_cells1.png >] [494 <./2_c_filter_combos.png>] [495 <./2_d_spatial_locations2D.png> <./2_e_ spatial_locations3D.png>] [496 <./3_a_screeplot.png>] [497 <./3_b_UMAP_reductio n.png>] [498 <./4_a_UMAP_leiden.png>] [499 <./5_b_leiden_2D.png>] [500 <./6_a_v iolinplot1.png>] [501 <./6_b_clusterheatmap_markers.png>] [502 <./7_a_clusterhe atmap_markers.png>] [503 <./7_b_clusterheatmap_markers_celltypes.png>] [504 <./ 7_c_umap_cell_types.png> <./7_d_spatPlot_cell_types_all.png>] [505 <./7_e_spatP lot2D_cell_types_all.png>] [506 <./7_f_spatPlot_cell_types_excit.png> <./7_g_sp atPlot2D_cell_types_excit.png>] [507 <./7_h_spatPlot_cell_types_inhib.png>] [508 <./7_i_spatPlot2D_cell_types_inhib.png>] [509 <./7_j_spatPlot_cell_types_O DandAstro.png> <./7_k_spatPlot2D_cell_types_ODandAstro.png>] [510 <./7_l_spatPl ot_cell_types_other.png>] [511 <./7_m_spatPlot2D_cell_types_other.png>] [512] [513 <./2_a_distribution_genes.png>] [514 <./2_b_distribution_cells.png>] [515 <./2_c_distribution_filters.png>] [516 <./2_d_spatial_locations.png> <./3_ a_hvg.png>] [517 <./3_b_signPCs.png> <./3_c_umap.png>] [518 <./4_leiden_0.2.png >] [519 <./5_a_covisualize_leiden_0.2.png>] [520 <./6_a_violinplot.png> <./6_b_ heatmap_leiden_0.2.png>] [521 <./7_a_general_cell_type.png>] [522 <./7_b_dim_pl ot_detailed_cell_type.png> <./7_c_cluster_annotation_heatmap.png>] [523 <./8_ce ll_type_co_vis.png> <./9_a_Rorb_dim_plot.png>] [524 <./9_b_Pcp4_dim_plot.png> < ./9_c_Pcp4_spat_plot.png>] [525 <./9_d_Cux2_dim_plot.png> <./9_e_detailed_cell_ types.png>] [526 <./9_f_Cux2_spat_plot.png> <./9_g_Ctgf_dim_plot.png>] [527 <./ 9_h_Ctgf_spat_plot.png> <./10_a_insert_cross_section_cell_types.png>] [528 <./1 0_b_insert_cross_section_Slc17a7.png> <./10_c_cross_section_spat.png>] [529 <./ 10_d_cross_section_spat3d.png> <./10_e_Slc17a7_cross_section_gene3d.png>] [530] [531 <./visium_technology.png> <./visium_brain_image_summary1.png>] [532 <./2_a_spatplot_image.png>] [533 <./2_b_spatplot_image_adjusted.png>] [534 <./2_c_in_tissue.png>] [535 <./2_d_spatial_locations1.png>] [536 <./2_e_nr _genes.png>] [537 <./3_a_HVGplot.png>] [538 <./3_b_screeplot.png> <./3_c_PCA_re duction.png>] [539 <./3_d_UMAP_reduction.png>] [540 <./3_e_tSNE_reduction.png>] [541 <./4_a_UMAP_leiden1.png>] [542 <./5_a_covis_leiden.png>] [543 <./5_b_nr_ge nes.png>] [544 <./5_c_DEG_subset.png>] Underfull \vbox (badness 10000) detected at line 44284 [545 <./6_a_violinplot_gini.png>] [546 <./6_b_metaheatmap_gini.png> <./6_c_gini _umap.png>] [547] [548 <./6_d_violinplot_scran.png>] [549 <./6_e_metaheatmap_sc ran.png> <./6_f_scran_umap.png>] Overfull \vbox (3.018pt too high) detected at line 44405 [550] [551 <./7_a_metaheatmap2.png>] [552 <./7_b_spatcellplot.png>] [553 <./7_c _spatcellplot.png>] [554 <./7_d_spatDimCellPlot.png>] [555 <./8_grid.png>] [556 <./9_a_knn_network.png>] [557 <./10_a_spatial_genes_km.png>] [558 <./10_b_ spatial_genes_rank.png>] [559 <./10_c_heatmap.png>] [560 <./10_d_spatPlot2D_HMR F.png>] [561] [562 <./mouse_kidney_highres.png>] [563 <./2_a_spatplot_image1.pn g>] [564 <./2_b_spatplot_image_adjusted1.png>] [565 <./2_c_in_tissue1.png>] [566 <./2_d_spatial_locations2.png>] [567 <./2_e_nr_genes1.png>] [568 <./3_a_HV Gplot1.png>] [569 <./3_b_screeplot1.png> <./3_c_PCA_reduction1.png>] [570 <./3_ d_UMAP_reduction1.png>] [571 <./3_e_tSNE_reduction1.png>] [572 <./4_a_UMAP_leid en2.png>] [573 <./5_a_covis_leiden1.png>] [574 <./5_b_nr_genes1.png>] Underfull \vbox (badness 10000) detected at line 44873 [575 <./6_a_violinplot_gini1.png>] [576 <./6_b_metaheatmap_gini1.png> <./6_c_gi ni_umap1.png>] [577] [578 <./6_d_violinplot_scran1.png>] [579 <./6_e_metaheatma p_scran1.png> 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<./8_b_spatplot1.png>] [609 <./8_c_spatdimplot.png>] [610 <./8_d_umap.png>] [611 <./8_e_spatPlot.png>] [612 <./8_f_spatdimgeneplot.png>] [613] [614 <./osmfish_image_demo.png>] [615] [616 <./2_a_original_clusters.png> <./2_b_original_regions.png>] [617 <./ 2_c_clusterID.png>] [618 <./2_d_total_expr_limits.png>] [619 <./3_a_screeplot2. png> <./3_b_PCA_reduction.png>] [620 <./3_c_UMAP_reduction.png>] [621 <./3_d_UM AP_reduction_expression.png>] [622 <./3_e_tSNE_reduction2.png>] [623 <./4_a_UMA P_hclust.png>] [624 <./4_b_UMAP_kmeans.png>] [625 <./4_c_UMAP_leiden.png>] [626 <./4_d_UMAP_leiden_merged.png>] [627 <./4_e_heatmap.png> <./4_f_dendro.png >] [628 <./5_a_covis_leiden2.png>] [629 <./5_b_covis_leiden_m.png>] [630 <./5_c _covis_leiden_merged_selected.png>] [631 <./5_d_total_expr.png>] [632 <./6_a_vi olinplot2.png>] [633 <./6_b_metaheatmap.png>] [634 <./6_e_metaheatmap_all_genes .png>] [635 <./6_f_metaheatmap_all_genes_names.png>] [636 <./7_a_annotation_lei den_merged_detailed.png>] [637 <./7_b_annotation_leiden_merged_coarse.png>] [638 <./7_c_clusterHeatmap_det_cell_types.png>] [639 <./7_d_heatamp_det_cell_ty pes.png>] [640 <./7_e_metaheatmap.png>] [641 <./8_grid_det_cell_types.png>] [642 <./9_spatial_network_k10.png> <./10_a_spatial_genes_km2.png>] [643 <./11_a _barplot_cell_cell_enrichment.png>] [644 <./11_b_heatmap_cell_cell_enrichment.p ng>] [645 <./11_c_network_cell_cell_enrichment.png>] [646 <./11_d_cell_cell_enr ichment_selected.png>] [647] [648 <./2_a_spatPlot.png>] [649 <./2_b_spatPlot_co lumn.png>] [650 <./2_c_spatPlot_row.png>] [651 <./2_d_spatPlot_hist.png>] [652 <./2_e_spatPlot_hist2.png>] [653] [654 <./3_a_signPCA.png> <./3_b_PCAplot. png>] [655 <./3_c_UMAP.png>] [656 <./4_a_UMAP.png>] [657 <./4_b_UMAP.png>] [658 <./4_c_spatplot.png>] [659 <./4_d_spatPlot.png>] [660 <./5_a_spatdimplot.p ng>] [661 <./5_b_spatdimplot.png>] [662 <./5_c_spatdimplot.png>] [663 <./6_a_me taheatmap.png>] [664 <./6_b_violinplot_gini.png>] [665 <./7_a_metaheatmap.png>] [666 <./7_b_metaheatmap.png>] [667 <./7_c_spatplot.png>] [668 <./7_d_spatplot.p ng>] [669 <./7_e_spatplot.png>] [670 <./7_f_spatplot.png> <./7_g_spatplot_1.png >] [671 <./7_g_spatplot_2.png>] [672 <./7_h_spatdimplot.png>] [673 <./7_i_spatp lot.png>] [674 <./7_j_umap.png>] [675 <./8_a_spatplot.png>] [676 <./12_a_barplo t.png>] [677 <./12_b_network.png>] [678 <./12_c_proxspatplot.png>] [679 <./xx_a _metaheatmap.png>] [680 <./xx_b_spatplot.png>] [681 <./xx_c_spatgeneplot.png>] [682 <./xx_d_umap.png>] [683 <./xx_e_dimGeneplot.png>] [684 <./xx_f_spatplot.pn g>] [685 <./xx_g_spatGeneplot.png>] [686 <./xx_h_umap.png>] [687 <./xx_i_dimGen eplot.png> <./human_cyCIF_PDAC_image_summary.png>] [688 <./merFISH_hypoth_image _summary.png> <./CODEX_spleen_image_summary.png>] [689 <./visium_brain_image_su mmary.png> <./visium_kidney_image_summary.png>] [690 <./osmFISH_SS_cortex_image _summary.png> <./mouse_SS_cortex_and_subventricular.png>] Chapter 7. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.47002 ...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.47002 ...097/ADuTNKaQJdScAAAAAElFTkSuQmCC}.svg}} and a Docker image will b... [691] [692 <./GitHub_Logo.png>] [693] [694 <./01_environments.png>] [695 <./01_ vm.png>] [696 <./02_docker.png> <./03_upload.png>] [697 <./03_view.png>] [698 <./03_googlecloud.png> <./03_url.png>] [699 <./03_cloud.png>] Overfull \hbox (11.18954pt too wide) in paragraph at lines 47388--47392 []\T1/qtm/m/n/10 Step 1 [] [700 <./04_share.png>] Overfull \hbox (11.18954pt too wide) in paragraph at lines 47406--47410 []\T1/qtm/m/n/10 Step 2 [] [701 <./Binder_1.png> <./Binder_2.png> <./Binder_3.png>] [702 <./Binder_4.png>] Chapter 8. [703] Underfull \hbox (badness 10000) in paragraph at lines 47554--47556 []\T1/qtm/m/it/10 ^^PThis worked for me in Mac OS Catalina as well! I used the gfor-tran 8.2 Mo-jave in-stal-la-tion [704] [705] [706] Chapter 9. [707] [708] [709] [710] [711] [712] Chapter 10. [713 <./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.48016 ...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.48016 ...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.48016 ...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.48016 ...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.48017 ...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.48017 ...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.48017 ...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.48017 ...en{}orientation (100 μm and 400 μ m). \sphinxstylestrong{Fig... [714 <./Index_Fig_B.png> <./Index_Fig_C.png> <./Index_Fig_D.png>] (./giottoteam-giotto.ind) [715] (./giottoteam-giotto.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on giottoteam-giotto.pdf (719 pages, 350782836 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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[17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1425--1428 []|\T1/qtm/m/n/10 list of in-struc-tions or out-put re-sult from [21] Underfull \hbox (badness 10000) in paragraph at lines 1626--1629 []|\T1/qtm/m/n/10 list of in-struc-tions or out-put re-sult from [22] Underfull \hbox (badness 10000) in paragraph at lines 1661--1663 []\T1/txtt/m/n/10 expr_data\T1/qtm/m/n/10 : raw will take ex-pres-sion data fro m \T1/txtt/m/n/10 raw_feature_bc_matrix \T1/qtm/m/n/10 and fil-ter from [23] [24] [25] [26] [27 <./subsetGiottoLocs-1.png> <./subsetGiottoLocs-2.png>] [28 <./subsetGiottoLocs-3.png> <./subsetGiottoLocs-4.png>] [29] [30] [31] [32] [33] [34] [35] [36] [37] Underfull \hbox (badness 10000) in paragraph at lines 2968--2970 []\T1/qtm/m/n/10 An ex-am-ple for the \T1/txtt/m/n/10 gene_clusters \T1/qtm/m/n /10 could be like this: \T1/txtt/m/n/10 cluster_vector = c(1, 1, 2, 2)\T1/qtm/m /n/10 ; [38] [39 <./createMetagenes-1.png> <./createMetagenes-2.png>] [40] [41] [42 <./filterDistributions-1.png>] [43 <./filterDistributions-2.png> <./filterD istributions-3.png>] [44] [45] [46 <./filterCombinations-1.png>] [47 <./filterC ombinations-2.png>] [48] [49] [50] [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 4235--4238 []|\T1/qtm/m/n/10 merge meta-data based on \T1/txtt/m/n/10 cell_ID \T1/qtm/m/n/ 10 col-umn in [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71 <./calculateHVG-1.png>] [72 <./calculateHVG-2.png> <./calculateHV G-3.png>] [73] [74] [75] [76 <./screePlot-1.png>] [77 <./screePlot-2.png>] [78] [79] [80 <./runPCA-1.png>] [81 <./runPCA-2.png>] [82] [83 <./runUMAP-1.png > <./runUMAP-2.png>] [84] [85 <./runtSNE-1.png> <./runtSNE-2.png>] [86] [87] [88] [89] [90] Underfull \hbox (badness 10000) in paragraph at lines 8631--8633 [][][]$\T1/qtm/m/n/10 doLeidenCluster$[][], [][]$doLouvainCluster _ community$[ ][], [][]$doLouvainCluster _ multinet$[][], [][]$doLouvainCluster$[][], [91] [92] [93] [94] [95 <./doKmeans-1.png>] [96 <./doKmeans-2.png>] [97] [98 <./doHclust-1.png> <./doHclust-2.png>] [99] [100] [101] [102] [103] [104] [105] Underfull \vbox (badness 10000) detected at line 10400 Underfull \vbox (badness 10000) detected at line 10400 [106] [107 <./mergeClusters-1.png>] [108 <./mergeClusters-2.png>] [109] [110] [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 10000) in paragraph at lines 11605--11608 []\T1/qtm/m/n/10 clus-ter_column = `lei- [117] [118] [119] [120] [121] [122 <./showClusterHeatmap-1.png>] [123 <./showCl usterHeatmap-2.png>] [124] [125 <./showClusterDendrogram-1.png> <./showClusterD endrogram-2.png>] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] ! 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Type H for immediate help. ... l.14031 ...�(1/2))/𝑑𝑒𝑙𝑡𝑎\end{split} [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 5133) in paragraph at lines 15020--15023 []|\T1/qtm/m/n/10 Cal-cu-late Gene Sig-na-ture En-rich-ment Score With Underfull \hbox (badness 5133) in paragraph at lines 15055--15058 []|\T1/qtm/m/n/10 Cal-cu-late Gene Sig-na-ture En-rich-ment Score With [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] Overfull \vbox (0.63725pt too high) detected at line 16606 [156] Underfull \hbox (badness 5133) in paragraph at lines 16669--16672 []|\T1/qtm/m/n/10 kmeans al-go-rithm to use (kmeans, kmeans_arma, [157] Overfull \vbox (0.9757pt too high) detected at line 16934 [158] Underfull \hbox (badness 5133) in paragraph at lines 16990--16993 []|\T1/qtm/m/n/10 kmeans al-go-rithm to use (kmeans, kmeans_arma, [159] [160] Underfull \hbox (badness 5133) in paragraph at lines 17301--17304 []|\T1/qtm/m/n/10 kmeans al-go-rithm to use (kmeans, kmeans_arma, [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 10000) in paragraph at lines 19355--19358 []|\T1/qtm/m/n/10 be-tas to test for. three num-bers: start_beta, [176] Overfull \vbox (10.47963pt too high) detected at line 19546 [177] [178] [179] [180] [181] [182] [183] [184] [185 <./dimPlot-1.png> <./dimPl ot-2.png>] [186 <./dimPlot-3.png> <./dimPlot-4.png>] [187] [188] [189 <./plotUM AP-1.png>] [190] [191] [192] [193 <./plotTSNE-1.png> <./plotTSNE-2.png>] [194 <./plotTSNE-3.png> <./plotTSNE-4.png>] [195] [196 <./plotPCA-1.png>] [197 <./plotPCA-2.png> <./plotPCA-3.png>] [198 <./plotPCA-4.png>] [199] [200 <./dimGenePlot-1.png> <./dimGenePlot-2.png>] [201] Overfull \vbox (0.8174pt too high) detected at line 22820 [202] [203] [204] [205] [206 <./spatPlot-1.png> <./spatPlot-2.png>] [207 <./spa tPlot-3.png> <./spatPlot-4.png>] Underfull \vbox (badness 10000) detected at line 23483 Underfull \vbox (badness 10000) detected at line 23483 [208] [209] [210] [211] [212] [213] [214] [215 <./spatGenePlot-1.png> <./spatGe nePlot-2.png>] [216] [217] [218] [219] [220] [221 <./spatCellPlot-1.png> <./spa tCellPlot-2.png>] [222 <./spatCellPlot-3.png> <./spatCellPlot-4.png>] [223] [224] [225 <./spatDimPlot-1.png>] [226 <./spatDimPlot-2.png> <./spatDimPlot-3.p ng>] [227 <./spatDimPlot-4.png>] [228] [229] [230] [231] [232 <./spatDimGenePlo t-1.png> <./spatDimGenePlot-2.png>] [233] [234] Overfull \vbox (2.3165pt too high) detected at line 27638 [235] [236 <./spatDimCellPlot-1.png> <./spatDimCellPlot-2.png>] [237 <./spatDim CellPlot-3.png> <./spatDimCellPlot-4.png>] Overfull \vbox (2.37871pt too high) detected at line 27753 [238] [239] [240] [241] [242 <./spatDimCellPlot2D-1.png>] [243 <./spatDimCellPl ot2D-2.png> <./spatDimCellPlot2D-3.png>] [244 <./spatDimCellPlot2D-4.png>] [245] [246] [247 <./dimPlot2D-1.png>] [248 <./dimPlot2D-2.png> <./dimPlot2D-3.p ng>] [249 <./dimPlot2D-4.png>] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] Overfull \vbox (0.9757pt too high) detected at line 30839 [260] [261] [262] Underfull \hbox (badness 7468) in paragraph at lines 31367--31370 []|\T1/qtm/m/n/10 equa-tion re-quired by method ^^Pequa-tion^^Q.equations [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Overfull \vbox (1.07416pt too high) detected at line 32995 [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] Underfull \hbox (badness 7685) in paragraph at lines 35024--35027 []|\T1/qhv/m/n/10 Ar-gu-ments passed on to [][]com-bineIn-ter-ac-tion- [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Chapter 4. [309] [310] [311] [312] [313] [314] [315] [316] Chapter 5. [317] [318 <./1_whole_brain.png>] [319 <./2_whole_brain_clus4.png> <./3_whole_b rain_clus4_noOther.png>] [320 <./4_whole_brain_by_group_leiden_1.png> <./4_whol e_brain_by_group_leiden_2.png>] [321 <./5_whole_brain_HMRF.png> <./5_whole_brai n_by_group_HMRF_1.png>] [322 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_ brain.png>] [323 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>] [324] [325] [326] [327 <./original_clusters_black.png>] Overfull \vbox (3.38263pt too high) detected at line 39223 [328 <./ppt_store_multiple_analyses2.png> <./1_loess_hvg.png>] [329 <./1_group_ hvg.png> <./1_hvg_table.png>] [330 <./2_loess_pca.png> <./2_group_pca.png>] [331 <./3_loess_umap.png>] [332 <./3_group_umap.png>] [333 <./4_spatial_network .png> <./4_large_network.png>] [334 <./4_distance_network.png>] [335 <./5_large _network_genes.png> <./5_large_distance_network_genes.png>] [336] [337] [338] [339 <./2_a_spatplot1.png>] [340 <./2_b_spatplot_image.png>] [341 <./2_c_ spatplot_image_adjusted_1.png>] [342 <./2_c_spatplot_image_adjusted_2.png>] [343 <./2_c_spatplot_image_adjusted_3.png>] [344 <./2_c_spatplot_image_adjusted _4.png>] [345 <./2_c_spatplot_image_adjusted_5.png>] [346 <./2_c_spatplot_image _adjusted_6.png>] [347 <./2_c_spatplot_image_adjusted_7.png>] [348 <./2_c_spatp lot_image_adjusted_8.png>] [349 <./2_c_spatplot_image_adjusted_9.png>] [350 <./ 2_c_spatplot_image_adjusted_10.png>] [351 <./2_c_spatplot_image_adjusted_11.png > <./2_d_original_plot.png>] [352 <./3_a_background_colors.png>] [353 <./3_b_bl ack_background.png>] [354 <./3_c_white_background.png>] [355 <./4_a_external_im age_negated.png>] [356 <./4_b_external_image_charcoal.png>] [357 <./5_1_a_spati al_locations.png>] [358 <./5_1_b_nr_genes.png>] [359 <./5_1_c_nr_genes_black_bg .png>] [360 <./5_1_d_nr_genes_charc_bg.png>] [361 <./5_2_a_UMAP_reduction.png>] [362 <./5_3_a_UMAP_leiden.png>] [363 <./5_4_a_covis_leiden_black.png>] [364 <./ 5_4_b_covis_leiden_negated.png>] [365 <./5_4_c_covis_leiden_charc.png>] [366 <./5_5_a_spatgene_charc_vor.png>] [367 <./5_5_b_spatgene_charc_vor.png>] [368 <./5_6_a_subset_spatgene_charc.png>] [369 <./5_6_b_subset_spatgene_charc_v or.png>] [370 <./1_voronoi.png>] [371 <./2_voronoi_no_others.png>] [372 <./3_vo ronoi_no_others_black_border.png>] [373 <./4_voronoi_spat_dim.png>] [374 <./5_v oronoi_neighbors.png> <./6_original_points.png>] [375 <./7_voronoi_genes.png> < ./8_voronoi_gene_black_bg.png>] [376] Chapter 6. [377] [378] [379] [380 <./3.1_HVGplot.png> <./3.2_screePlot.png>] [381 <./3.3_j ackstrawPlot.png>] [382 <./3.4_PCA.png>] [383 <./3.5_tSNE.png>] [384 <./4.1_UMA P.png>] [385 <./4.2_showClusterHeatmap.png> <./4.3_showClusterDendrogram.png>] [386 <./5.1_violinPlot.png>] [387 <./5.2_plotMetaDataHeatmap.png>] [388 <./6.1_ spatDimPlot2D.png>] [389] [390 <./9.1_spatGenePlot2D.png>] [391 <./10.1_heatmSp atialCorGenes.png>] Overfull \vbox (2.14355pt too high) detected at line 40742 [392 <./10.2_spatCellPlot2D.png>] [393 <./12.1_cellProximityBarplot.png>] [394 <./12.2_spatCellPlot2D.png>] [395 <./12.3_cellProximityHeatmap.png>] [396 <./12.4_cellProximityNetwork.png>] [397 <./12.5_cellProximitySpatPlot2D.pn g>] [398 <./12.6_spatPlot2D.png>] [399 <./13.1_plotCellProximityGenes.png>] Overfull \vbox (2.14355pt too high) detected at line 40924 [400 <./13.2_plotICG.png>] [401 <./14.1_plotCCcomHeatmap.png>] [402 <./14.2_plo tCCcomDotplot.png>] [403 <./14.3_plotRankSpatvsExpr.png>] [404 <./14.4_plotReco very.png>] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414 <./2_a_fi ltergenes.png>] [415 <./2_b_filtercells.png>] [416 <./2_c_filtercombos.png>] [417 <./3_a_screeplot1.png> <./3_b_PCA.png>] [418] [419 <./3_d_UMAP_3D.png> <./ 3_e_TSNE.png>] [420 <./4_a_UMAP1.png>] [421 <./4_b_UMAP_3D.png> <./4_c_spatdimp lot.png>] [422 <./4_e_clusterheatmap.png>] [423 <./4_f_clusterdendrogram.png>] [424 <./5_a_violinplot.png>] [425 <./5_b_metaheatmap.png>] [426 <./6_a_spatdimp lot.png>] [427 <./6_b_dimgeneplot.png> <./6_c_spatgeneplot.png>] [428 <./7_a_sp atplot.png>] [429 <./8_a_plotStatDelaunayNetwork.png>] [430 <./8_b_spatplot.png >] [431 <./8_c_spatplot.png>] [432 <./9_a_spatgeneplot.png>] [433 <./9_b_spatge neplot.png>] [434 <./10_a_heatmspatcor.png>] [435 <./10_b_rankcorgroup.png>] Overfull \vbox (2.14355pt too high) detected at line 42066 [436 <./10_c_spatcellplot.png>] [437 <./12_a_barplot1.png>] [438 <./12_b_heatma p.png>] [439 <./12_c_network.png>] [440 <./12_d_network.png>] [441 <./12_e_spat plot.png>] [442 <./12_e_cellproximity.png>] Underfull \vbox (badness 1158) detected at line 42199 [443 <./13_a_insert.png> <./13_b_crossplot.png>] [444 <./13_c_cross.png>] [445 <./13_d_crossgeneplot.png> <./13_e_crossgene.png>] [446] [447 <./mini_seqF ISH.png>] [448 <./mini_STARmap.png>] [449 <./mini_visium.png>] [450 <./cortex_s vz_location_fields.png>] [451] [452] [453 <./2_a_spatplot.png>] [454 <./3_a_HVG plot2.png>] [455 <./3_b_screeplot2.png> <./3_c_PCA_reduction2.png>] [456 <./3_d _UMAP_reduction2.png>] [457 <./3_e_tSNE_reduction3.png>] [458 <./4_a_UMAP_leide n3.png>] [459 <./4_b_UMAP_leiden_subcluster.png>] [460 <./4_c_heatmap.png>] [461 <./4_d_dendro.png>] [462 <./5_a_covis_leiden3.png>] [463 <./5_b_covis_leid en_selected.png>] Underfull \vbox (badness 10000) detected at line 42633 [464 <./6_a_violinplot_gini2.png>] Underfull \vbox (badness 1320) detected at line 42674 [465 <./6_b_metaheatmap_gini2.png>] [466] [467 <./7_a_violinplot.png>] [468 <./ 7_b_covisualization.png>] [469 <./7_c_heatmap.png>] [470 <./7_d_heatmap_selecte d.png>] [471 <./8_a_grid.png>] [472 <./9_a_spatial_network_delaunay.png> <./9_b _spatial_network_k3.png>] [473 <./9_c_spatial_network_k10.png> <./9_d_spatial_n etwork_dist.png>] [474 <./10_a_spatialgenes_km.png>] Underfull \vbox (badness 10000) detected at line 42859 [475 <./10_b_spatialcoexpression_heatmap.png> <./10_c_spatialcoexpression_rank. png>] [476 <./10_d_spatialcoexpression_metagenes.png>] [477 <./11_HMRF_2_k9_b.2 8.pdf>] [478 <./12_a_barplot_cell_cell_enrichment.png>] [479 <./12_b_heatmap_ce ll_cell_enrichment.png>] [480 <./12_c_network_cell_cell_enrichment.png>] [481 <./12_d_network_cell_cell_enrichment_self.pdf>] [482 <./12_e_cell_cell_enr ichment_selected.png>] [483 <./12_f_cell_cell_enrichment_sel_vs_not.png>] [484 <./13_a_CPG_dotplot.png>] Overfull \vbox (2.14355pt too high) detected at line 43084 [485 <./13_b_ICG_barplot.png>] Underfull \vbox (badness 1194) detected at line 43103 [486 <./14_a_communication_dotplot.png>] [487 <./14_b_expr_vs_spatial_expressio n_rank.png>] [488 <./14_c_spatial_recovery_expression_rank.png>] [489 <./14_d_e xpr_vs_spatial_activity.png>] [490 <./14_e_spatial_recovery_activity.png>] [491] [492] [493 <./2_a_distribution_genes1.png> <./2_b_distribution_cells1.png >] [494 <./2_c_filter_combos.png>] [495 <./2_d_spatial_locations2D.png> <./2_e_ spatial_locations3D.png>] [496 <./3_a_screeplot.png>] [497 <./3_b_UMAP_reductio n.png>] [498 <./4_a_UMAP_leiden.png>] [499 <./5_b_leiden_2D.png>] [500 <./6_a_v iolinplot1.png>] [501 <./6_b_clusterheatmap_markers.png>] [502 <./7_a_clusterhe atmap_markers.png>] [503 <./7_b_clusterheatmap_markers_celltypes.png>] [504 <./ 7_c_umap_cell_types.png> <./7_d_spatPlot_cell_types_all.png>] [505 <./7_e_spatP lot2D_cell_types_all.png>] [506 <./7_f_spatPlot_cell_types_excit.png> <./7_g_sp atPlot2D_cell_types_excit.png>] [507 <./7_h_spatPlot_cell_types_inhib.png>] [508 <./7_i_spatPlot2D_cell_types_inhib.png>] [509 <./7_j_spatPlot_cell_types_O DandAstro.png> <./7_k_spatPlot2D_cell_types_ODandAstro.png>] [510 <./7_l_spatPl ot_cell_types_other.png>] [511 <./7_m_spatPlot2D_cell_types_other.png>] [512] [513 <./2_a_distribution_genes.png>] [514 <./2_b_distribution_cells.png>] [515 <./2_c_distribution_filters.png>] [516 <./2_d_spatial_locations.png> <./3_ a_hvg.png>] [517 <./3_b_signPCs.png> <./3_c_umap.png>] [518 <./4_leiden_0.2.png >] [519 <./5_a_covisualize_leiden_0.2.png>] [520 <./6_a_violinplot.png> <./6_b_ heatmap_leiden_0.2.png>] [521 <./7_a_general_cell_type.png>] [522 <./7_b_dim_pl ot_detailed_cell_type.png> <./7_c_cluster_annotation_heatmap.png>] [523 <./8_ce ll_type_co_vis.png> <./9_a_Rorb_dim_plot.png>] [524 <./9_b_Pcp4_dim_plot.png> < ./9_c_Pcp4_spat_plot.png>] [525 <./9_d_Cux2_dim_plot.png> <./9_e_detailed_cell_ types.png>] [526 <./9_f_Cux2_spat_plot.png> <./9_g_Ctgf_dim_plot.png>] [527 <./ 9_h_Ctgf_spat_plot.png> <./10_a_insert_cross_section_cell_types.png>] [528 <./1 0_b_insert_cross_section_Slc17a7.png> <./10_c_cross_section_spat.png>] [529 <./ 10_d_cross_section_spat3d.png> <./10_e_Slc17a7_cross_section_gene3d.png>] [530] [531 <./visium_technology.png> <./visium_brain_image_summary1.png>] [532 <./2_a_spatplot_image.png>] [533 <./2_b_spatplot_image_adjusted.png>] [534 <./2_c_in_tissue.png>] [535 <./2_d_spatial_locations1.png>] [536 <./2_e_nr _genes.png>] [537 <./3_a_HVGplot.png>] [538 <./3_b_screeplot.png> <./3_c_PCA_re duction.png>] [539 <./3_d_UMAP_reduction.png>] [540 <./3_e_tSNE_reduction.png>] [541 <./4_a_UMAP_leiden1.png>] [542 <./5_a_covis_leiden.png>] [543 <./5_b_nr_ge nes.png>] [544 <./5_c_DEG_subset.png>] Underfull \vbox (badness 10000) detected at line 44284 [545 <./6_a_violinplot_gini.png>] [546 <./6_b_metaheatmap_gini.png> <./6_c_gini _umap.png>] [547] [548 <./6_d_violinplot_scran.png>] [549 <./6_e_metaheatmap_sc ran.png> <./6_f_scran_umap.png>] Overfull \vbox (3.018pt too high) detected at line 44405 [550] [551 <./7_a_metaheatmap2.png>] [552 <./7_b_spatcellplot.png>] [553 <./7_c _spatcellplot.png>] [554 <./7_d_spatDimCellPlot.png>] [555 <./8_grid.png>] [556 <./9_a_knn_network.png>] [557 <./10_a_spatial_genes_km.png>] [558 <./10_b_ spatial_genes_rank.png>] [559 <./10_c_heatmap.png>] [560 <./10_d_spatPlot2D_HMR F.png>] [561] [562 <./mouse_kidney_highres.png>] [563 <./2_a_spatplot_image1.pn g>] [564 <./2_b_spatplot_image_adjusted1.png>] [565 <./2_c_in_tissue1.png>] [566 <./2_d_spatial_locations2.png>] [567 <./2_e_nr_genes1.png>] [568 <./3_a_HV Gplot1.png>] [569 <./3_b_screeplot1.png> <./3_c_PCA_reduction1.png>] [570 <./3_ d_UMAP_reduction1.png>] [571 <./3_e_tSNE_reduction1.png>] [572 <./4_a_UMAP_leid en2.png>] [573 <./5_a_covis_leiden1.png>] [574 <./5_b_nr_genes1.png>] Underfull \vbox (badness 10000) detected at line 44873 [575 <./6_a_violinplot_gini1.png>] [576 <./6_b_metaheatmap_gini1.png> <./6_c_gi ni_umap1.png>] [577] [578 <./6_d_violinplot_scran1.png>] [579 <./6_e_metaheatma p_scran1.png> <./6_f_scran_umap1.png>] [580 <./8_grid1.png>] [581 <./9_a_delaun ay_network.png>] [582 <./9_b_delaunay_network.png>] [583 <./10_a_spatial_genes_ km1.png>] [584 <./10_b_spatial_genes_rank1.png>] [585 <./10_d_Napsa_correlated_ genes.png>] Underfull \vbox (badness 10000) detected at line 45069 [586 <./10_e_heatmap_correlated_genes.png> <./10_f_rank_correlated_groups.png>] [587 <./10_g_spat_enrichment_score_plots.png> <./10_h_spat_enrichment_score_plo ts_genes.png>] [588] [589] [590] Overfull \vbox (6.31403pt too high) detected at line 45324 [591] [592] [593 <./2_a_spatPlot1.png>] [594 <./2_b_spatPlot.png>] [595 <./3_a_ spatPlot.png> <./3_b_PCA1.png>] [596 <./3_c_UMAP1.png>] [597 <./4_a_UMAP2.png>] [598 <./4_b_spatplot.png>] [599 <./5_a_spatdimplot1.png>] [600 <./6_a_metaheatm ap1.png>] [601 <./6_b_violinplot.png>] [602 <./6_c_metaheatmap.png>] [603 <./6_ d_violinplot.png>] [604 <./7_a_metaheatmap1.png>] [605 <./7_b_umap.png>] [606 <./7_c_spatplot1.png>] [607 <./8_a_umap.png>] [608 <./8_b_spatplot1.png>] [609 <./8_c_spatdimplot.png>] [610 <./8_d_umap.png>] [611 <./8_e_spatPlot.png>] [612 <./8_f_spatdimgeneplot.png>] [613] [614 <./osmfish_image_demo.png>] [615] [616 <./2_a_original_clusters.png> <./2_b_original_regions.png>] [617 <./ 2_c_clusterID.png>] [618 <./2_d_total_expr_limits.png>] [619 <./3_a_screeplot2. png> <./3_b_PCA_reduction.png>] [620 <./3_c_UMAP_reduction.png>] [621 <./3_d_UM AP_reduction_expression.png>] [622 <./3_e_tSNE_reduction2.png>] [623 <./4_a_UMA P_hclust.png>] [624 <./4_b_UMAP_kmeans.png>] [625 <./4_c_UMAP_leiden.png>] [626 <./4_d_UMAP_leiden_merged.png>] [627 <./4_e_heatmap.png> <./4_f_dendro.png >] [628 <./5_a_covis_leiden2.png>] [629 <./5_b_covis_leiden_m.png>] [630 <./5_c _covis_leiden_merged_selected.png>] [631 <./5_d_total_expr.png>] [632 <./6_a_vi olinplot2.png>] [633 <./6_b_metaheatmap.png>] [634 <./6_e_metaheatmap_all_genes .png>] [635 <./6_f_metaheatmap_all_genes_names.png>] [636 <./7_a_annotation_lei den_merged_detailed.png>] [637 <./7_b_annotation_leiden_merged_coarse.png>] [638 <./7_c_clusterHeatmap_det_cell_types.png>] [639 <./7_d_heatamp_det_cell_ty pes.png>] [640 <./7_e_metaheatmap.png>] [641 <./8_grid_det_cell_types.png>] [642 <./9_spatial_network_k10.png> <./10_a_spatial_genes_km2.png>] [643 <./11_a _barplot_cell_cell_enrichment.png>] [644 <./11_b_heatmap_cell_cell_enrichment.p ng>] [645 <./11_c_network_cell_cell_enrichment.png>] [646 <./11_d_cell_cell_enr ichment_selected.png>] [647] [648 <./2_a_spatPlot.png>] [649 <./2_b_spatPlot_co lumn.png>] [650 <./2_c_spatPlot_row.png>] [651 <./2_d_spatPlot_hist.png>] [652 <./2_e_spatPlot_hist2.png>] [653] [654 <./3_a_signPCA.png> <./3_b_PCAplot. png>] [655 <./3_c_UMAP.png>] [656 <./4_a_UMAP.png>] [657 <./4_b_UMAP.png>] [658 <./4_c_spatplot.png>] [659 <./4_d_spatPlot.png>] [660 <./5_a_spatdimplot.p ng>] [661 <./5_b_spatdimplot.png>] [662 <./5_c_spatdimplot.png>] [663 <./6_a_me taheatmap.png>] [664 <./6_b_violinplot_gini.png>] [665 <./7_a_metaheatmap.png>] [666 <./7_b_metaheatmap.png>] [667 <./7_c_spatplot.png>] [668 <./7_d_spatplot.p ng>] [669 <./7_e_spatplot.png>] [670 <./7_f_spatplot.png> <./7_g_spatplot_1.png >] [671 <./7_g_spatplot_2.png>] [672 <./7_h_spatdimplot.png>] [673 <./7_i_spatp lot.png>] [674 <./7_j_umap.png>] [675 <./8_a_spatplot.png>] [676 <./12_a_barplo t.png>] [677 <./12_b_network.png>] [678 <./12_c_proxspatplot.png>] [679 <./xx_a _metaheatmap.png>] [680 <./xx_b_spatplot.png>] [681 <./xx_c_spatgeneplot.png>] [682 <./xx_d_umap.png>] [683 <./xx_e_dimGeneplot.png>] [684 <./xx_f_spatplot.pn g>] [685 <./xx_g_spatGeneplot.png>] [686 <./xx_h_umap.png>] [687 <./xx_i_dimGen eplot.png> <./human_cyCIF_PDAC_image_summary.png>] [688 <./merFISH_hypoth_image _summary.png> <./CODEX_spleen_image_summary.png>] [689 <./visium_brain_image_su mmary.png> <./visium_kidney_image_summary.png>] [690 <./osmFISH_SS_cortex_image _summary.png> <./mouse_SS_cortex_and_subventricular.png>] Chapter 7. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.47002 ...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.47002 ...097/ADuTNKaQJdScAAAAAElFTkSuQmCC}.svg}} and a Docker image will b... [691] [692 <./GitHub_Logo.png>] [693] [694 <./01_environments.png>] [695 <./01_ vm.png>] [696 <./02_docker.png> <./03_upload.png>] [697 <./03_view.png>] [698 <./03_googlecloud.png> <./03_url.png>] [699 <./03_cloud.png>] Overfull \hbox (11.18954pt too wide) in paragraph at lines 47388--47392 []\T1/qtm/m/n/10 Step 1 [] [700 <./04_share.png>] Overfull \hbox (11.18954pt too wide) in paragraph at lines 47406--47410 []\T1/qtm/m/n/10 Step 2 [] [701 <./Binder_1.png> <./Binder_2.png> <./Binder_3.png>] [702 <./Binder_4.png>] Chapter 8. [703] Underfull \hbox (badness 10000) in paragraph at lines 47554--47556 []\T1/qtm/m/it/10 ^^PThis worked for me in Mac OS Catalina as well! I used the gfor-tran 8.2 Mo-jave in-stal-la-tion [704] [705] [706] Chapter 9. [707] [708] [709] [710] [711] [712] Chapter 10. [713 <./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.48016 ...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.48016 ...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.48016 ...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.48016 ...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.48017 ...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.48017 ...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.48017 ...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.48017 ...en{}orientation (100 μm and 400 μ m). \sphinxstylestrong{Fig... [714 <./Index_Fig_B.png> <./Index_Fig_C.png> <./Index_Fig_D.png>] (./giottoteam-giotto.ind) [715] (./giottoteam-giotto.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on giottoteam-giotto.pdf (719 pages, 350782836 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: 2022-07-14T19:57:42.614098Z, end-time: 2022-07-14T19:57:42.702524Z, 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: 2022-07-14T19:57:42.905416Z, end-time: 2022-07-14T19:58:34.376973Z, duration: 51, exit-code: 0 python -m sphinx -T -E -b epub -d _build/doctrees -D language=en . _build/epub Running Sphinx v4.5.0 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 659 source files that are out of date updating environment: [new config] 659 added, 0 changed, 0 removed reading sources... 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[ 10%] subsections/documentation_functions/createSpatialDelaunayNetwork reading sources... [ 10%] subsections/documentation_functions/createSpatialEnrich reading sources... [ 10%] subsections/documentation_functions/createSpatialGrid reading sources... [ 11%] subsections/documentation_functions/createSpatialKNNnetwork reading sources... [ 11%] subsections/documentation_functions/createSpatialNetwork reading sources... [ 11%] subsections/documentation_functions/crossSectionGenePlot reading sources... [ 11%] subsections/documentation_functions/crossSectionGenePlot3D reading sources... [ 11%] subsections/documentation_functions/crossSectionPlot reading sources... [ 11%] subsections/documentation_functions/crossSectionPlot3D reading sources... [ 11%] subsections/documentation_functions/detectSpatialCorGenes reading sources... [ 12%] subsections/documentation_functions/dimCellPlot reading sources... [ 12%] subsections/documentation_functions/dimGenePlot reading sources... [ 12%] subsections/documentation_functions/dimGenePlot3D reading sources... [ 12%] subsections/documentation_functions/dimPlot reading sources... [ 12%] subsections/documentation_functions/dimPlot2D reading sources... [ 12%] subsections/documentation_functions/dimPlot3D reading sources... [ 13%] subsections/documentation_functions/doHMRF reading sources... [ 13%] subsections/documentation_functions/doHclust reading sources... [ 13%] subsections/documentation_functions/doKmeans reading sources... [ 13%] subsections/documentation_functions/doLeidenCluster reading sources... [ 13%] subsections/documentation_functions/doLeidenSubCluster reading sources... [ 13%] subsections/documentation_functions/doLouvainCluster reading sources... [ 13%] subsections/documentation_functions/doLouvainSubCluster reading sources... [ 14%] subsections/documentation_functions/estimateImageBg reading sources... [ 14%] subsections/documentation_functions/exportGiottoViewer reading sources... [ 14%] subsections/documentation_functions/exprCellCellcom reading sources... [ 14%] subsections/documentation_functions/extractNearestNetwork reading sources... [ 14%] subsections/documentation_functions/fDataDT reading sources... [ 14%] subsections/documentation_functions/filterCPG reading sources... [ 15%] subsections/documentation_functions/filterCellProximityGenes reading sources... [ 15%] subsections/documentation_functions/filterCombinations reading sources... [ 15%] subsections/documentation_functions/filterDistributions reading sources... [ 15%] subsections/documentation_functions/filterGiotto reading sources... [ 15%] subsections/documentation_functions/filterICG reading sources... [ 15%] subsections/documentation_functions/filterInteractionChangedGenes reading sources... [ 15%] subsections/documentation_functions/findCPG reading sources... [ 16%] subsections/documentation_functions/findCellProximityGenes reading sources... [ 16%] subsections/documentation_functions/findGiniMarkers reading sources... [ 16%] subsections/documentation_functions/findGiniMarkers_one_vs_all reading sources... [ 16%] subsections/documentation_functions/findICG reading sources... [ 16%] subsections/documentation_functions/findInteractionChangedGenes reading sources... [ 16%] subsections/documentation_functions/findMarkers reading sources... [ 16%] subsections/documentation_functions/findMarkers_one_vs_all reading sources... [ 17%] subsections/documentation_functions/findMastMarkers reading sources... [ 17%] subsections/documentation_functions/findMastMarkers_one_vs_all reading sources... [ 17%] subsections/documentation_functions/findNetworkNeighbors reading sources... [ 17%] subsections/documentation_functions/findScranMarkers reading sources... [ 17%] subsections/documentation_functions/findScranMarkers_one_vs_all reading sources... [ 17%] subsections/documentation_functions/get10XMatrix reading sources... [ 18%] subsections/documentation_functions/get10XMatrix_h5 reading sources... [ 18%] subsections/documentation_functions/getClusterSimilarity reading sources... [ 18%] subsections/documentation_functions/getDendrogramSplits reading sources... [ 18%] subsections/documentation_functions/getGiottoImage reading sources... [ 18%] subsections/documentation_functions/getSpatialDataset reading sources... [ 18%] subsections/documentation_functions/heatmSpatialCorGenes reading sources... [ 18%] subsections/documentation_functions/hyperGeometricEnrich reading sources... [ 19%] subsections/documentation_functions/insertCrossSectionGenePlot3D reading sources... [ 19%] subsections/documentation_functions/insertCrossSectionSpatPlot3D reading sources... [ 19%] subsections/documentation_functions/installGiottoEnvironmentFunction reading sources... [ 19%] subsections/documentation_functions/introduction reading sources... [ 19%] subsections/documentation_functions/jackstrawPlot reading sources... [ 19%] subsections/documentation_functions/loadHMRF reading sources... [ 20%] subsections/documentation_functions/makeSignMatrixPAGE reading sources... [ 20%] subsections/documentation_functions/makeSignMatrixRank reading sources... [ 20%] subsections/documentation_functions/mergeClusters reading sources... [ 20%] subsections/documentation_functions/normalizeGiotto reading sources... [ 20%] subsections/documentation_functions/pDataDT reading sources... [ 20%] subsections/documentation_functions/plotCCcomDotplot reading sources... [ 20%] subsections/documentation_functions/plotCPG reading sources... [ 21%] subsections/documentation_functions/plotCellProximityGenes reading sources... [ 21%] subsections/documentation_functions/plotCombineCPG reading sources... [ 21%] subsections/documentation_functions/plotCombineCellProximityGenes reading sources... [ 21%] subsections/documentation_functions/plotCombineICG reading sources... [ 21%] subsections/documentation_functions/plotCombineInteractionChangedGenes reading sources... [ 21%] subsections/documentation_functions/plotGiottoImage reading sources... [ 22%] subsections/documentation_functions/plotHeatmap reading sources... [ 22%] subsections/documentation_functions/plotICG reading sources... [ 22%] subsections/documentation_functions/plotInteractionChangedGenes reading sources... [ 22%] subsections/documentation_functions/plotMetaDataCellsHeatmap reading sources... [ 22%] subsections/documentation_functions/plotMetaDataHeatmap reading sources... [ 22%] subsections/documentation_functions/plotPCA reading sources... [ 22%] subsections/documentation_functions/plotPCA_3D reading sources... [ 23%] subsections/documentation_functions/plotRankSpatvsExpr reading sources... [ 23%] subsections/documentation_functions/plotRecovery reading sources... [ 23%] subsections/documentation_functions/plotStatDelaunayNetwork reading sources... 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[ 28%] subsections/documentation_functions/spatCellPlot reading sources... [ 29%] subsections/documentation_functions/spatCellPlot2D reading sources... [ 29%] subsections/documentation_functions/spatDimCellPlot reading sources... [ 29%] subsections/documentation_functions/spatDimCellPlot2D reading sources... [ 29%] subsections/documentation_functions/spatDimGenePlot reading sources... [ 29%] subsections/documentation_functions/spatDimGenePlot3D reading sources... [ 29%] subsections/documentation_functions/spatDimPlot reading sources... [ 30%] subsections/documentation_functions/spatDimPlot3D reading sources... [ 30%] subsections/documentation_functions/spatGenePlot reading sources... [ 30%] subsections/documentation_functions/spatGenePlot3D reading sources... [ 30%] subsections/documentation_functions/spatNetwDistributions reading sources... [ 30%] subsections/documentation_functions/spatNetwDistributionsDistance reading sources... 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[ 39%] subsections/md_rst/cellProximityBarplot reading sources... [ 39%] subsections/md_rst/cellProximityEnrichment reading sources... [ 39%] subsections/md_rst/cellProximityHeatmap reading sources... [ 39%] subsections/md_rst/cellProximityNetwork reading sources... [ 39%] subsections/md_rst/cellProximitySpatPlot reading sources... [ 40%] subsections/md_rst/cellProximitySpatPlot2D reading sources... [ 40%] subsections/md_rst/cellProximitySpatPlot3D reading sources... [ 40%] subsections/md_rst/cellProximityVisPlot reading sources... [ 40%] subsections/md_rst/cellProximityVisPlot_2D_ggplot reading sources... [ 40%] subsections/md_rst/cellProximityVisPlot_2D_plotly reading sources... [ 40%] subsections/md_rst/cellProximityVisPlot_3D_plotly reading sources... [ 40%] subsections/md_rst/changeGiottoInstructions reading sources... [ 41%] subsections/md_rst/changeImageBg reading sources... [ 41%] subsections/md_rst/checkAndFixSpatialGenes reading sources... 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[ 61%] subsections/md_rst/findMarkers reading sources... [ 61%] subsections/md_rst/findMarkers_one_vs_all reading sources... [ 62%] subsections/md_rst/findMastMarkers reading sources... [ 62%] subsections/md_rst/findMastMarkers_one_vs_all reading sources... [ 62%] subsections/md_rst/findNetworkNeighbors reading sources... [ 62%] subsections/md_rst/findScranMarkers reading sources... [ 62%] subsections/md_rst/findScranMarkers_one_vs_all reading sources... [ 62%] subsections/md_rst/find_dampening_constant reading sources... [ 62%] subsections/md_rst/find_grid_2D reading sources... [ 63%] subsections/md_rst/find_grid_3D reading sources... [ 63%] subsections/md_rst/find_grid_x reading sources... [ 63%] subsections/md_rst/find_grid_y reading sources... [ 63%] subsections/md_rst/find_grid_z reading sources... [ 63%] subsections/md_rst/find_x_y_ranges reading sources... [ 63%] subsections/md_rst/flex_lapply reading sources... [ 64%] subsections/md_rst/general_save_function reading sources... 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[ 98%] subsections/tipsandtricks/giottoclass writing output... [ 98%] subsections/tipsandtricks/howtosubsetgiottoobject writing output... [ 98%] subsections/tipsandtricks/howtovisualizeandsaveplots writing output... [ 98%] subsections/tipsandtricks/testandstoremultipleanayses writing output... [ 98%] subsections/tipsandtricks/visualizewithvoronoiplots writing output... [ 99%] subsections/tipsandtricks/waystovisualizespatialdata writing output... [ 99%] subsections/tipsandtricks/workingwithimages writing output... [ 99%] subsections/trygiotto/binder writing output... [ 99%] subsections/trygiotto/docker writing output... [ 99%] subsections/trygiotto/terra writing output... [ 99%] tipsandtricks writing output... [100%] trygiotto /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/tipsandtricks.rst:22: WARNING: 'any' reference target not found: terrainformation>`(see :ref:`Try Giotto