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[rtd-command-info] start-time: 2022-09-08T18:36:49.760336Z, end-time: 2022-09-08T18:36:50.024121Z, 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 c77f94e3 updated card-carousel [rtd-command-info] start-time: 2022-09-08T18:36:50.235578Z, end-time: 2022-09-08T18:36:50.320702Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-09-08T18:37:07.329762Z, end-time: 2022-09-08T18:37:11.873502Z, 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: 2022-09-08T18:37:12.186180Z, end-time: 2022-09-08T18:37:14.030205Z, 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 (22.2.2) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 26.6 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 65.3.0 Uninstalling setuptools-65.3.0: Successfully uninstalled setuptools-65.3.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-09-08T18:37:14.246498Z, end-time: 2022-09-08T18:37:21.585411Z, duration: 7, exit-code: 0 python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2 Collecting pillow Downloading Pillow-9.2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 61.2 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 241.6 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.9.1 Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 182.6 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-5.1.1-py3-none-any.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 206.2 MB/s eta 0:00:00 Collecting 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typing_extensions-4.3.0-py3-none-any.whl (25 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 197.6 MB/s eta 0:00:00 Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.12-py2.py3-none-any.whl (140 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.4/140.4 kB 219.6 MB/s eta 0:00:00 Collecting charset-normalizer<3,>=2 Downloading charset_normalizer-2.1.1-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 223.4 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 214.2 MB/s eta 0:00:00 Building wheels for collected packages: mock 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=472d42f917b8eed580271b32166ff7d8ab525ebbbf336f8966b57cb48c738fc9 Stored in directory: /tmp/pip-ephem-wheel-cache-q1dpv88f/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, requests, packaging, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.13.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.6.15 charset-normalizer-2.1.1 commonmark-0.9.1 docutils-0.17.1 idna-3.3 imagesize-1.4.1 importlib-metadata-4.12.0 mock-1.0.1 packaging-21.3 pillow-9.2.0 pyparsing-3.0.9 pytz-2022.2.1 readthedocs-sphinx-ext-2.1.8 recommonmark-0.5.0 requests-2.28.1 snowballstemmer-2.2.0 sphinx-5.1.1 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 urllib3-1.26.12 zipp-3.8.1 [rtd-command-info] start-time: 2022-09-08T18:37:21.770186Z, end-time: 2022-09-08T18:37:42.045290Z, duration: 20, 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 15.7 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) 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sphinx_tabs-3.3.0-py3-none-any.whl (10 kB) Downloading sphinx_tabs-3.2.0-py3-none-any.whl (9.8 kB) Collecting mypy-extensions>=0.3.0 Downloading mypy_extensions-0.4.3-py2.py3-none-any.whl (4.5 kB) Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/master/lib/python3.7/site-packages (from 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=554824 sha256=2902ce79a44b32362f64da4d99cd16d32c842470510d50d6f9a705b36f099169 Stored in directory: /tmp/pip-ephem-wheel-cache-qwczqbag/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 5.1.1 Uninstalling Sphinx-5.1.1: Successfully uninstalled Sphinx-5.1.1 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-0.2.9 beautifulsoup4-4.11.1 bluepy-1.3.0 cachecontrol-0.12.11 cssutils-2.6.0 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-8.2.0 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-1.19.1 sphinx-copybutton-0.5.0 sphinx-design-0.3.0 sphinx-jinja2-compat-0.2.0 sphinx-prompt-1.5.0 sphinx-tabs-3.2.0 sphinx-toolbox-3.2.0 sphinx_rtd_theme-0.5.2 tabulate-0.8.10 typing-inspect-0.8.0 webencodings-0.5.1 [rtd-command-info] start-time: 2022-09-08T18:37:43.944960Z, end-time: 2022-09-08T18:37:44.014018Z, 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': 'c77f94e3', } # 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/1088374/' 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: 2022-09-08T18:37:44.318529Z, end-time: 2022-09-08T18:38:27.268365Z, duration: 42, 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 462 source files that are out of date updating environment: [new config] 462 added, 0 changed, 0 removed reading sources... 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[100%] trygiotto /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:95: WARNING: unknown document: installGiottoEnvironmentFunction /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:97: WARNING: unknown document: removeGiottoEnvironment /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:99: WARNING: unknown document: checkGiottoEnvironment /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:230: WARNING: unknown document: /subsections/md_rst/get10XMatrix /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:232: WARNING: unknown document: /subsections/md_rst/get10XMatrix_h5 /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:409: WARNING: unknown document: /subsections/md_rst/findMarkersFunction /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/gettingstarted.rst:224: WARNING: undefined label: creategiottoinstructions /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 `(see :ref:`Try Giotto `(see :ref:`Try Giotto chunk 1. 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[237] [238] [239] [240] [241] Overfull \hbox (5.90836pt too wide) in paragraph at lines 27512--27512 []\T1/txtt/m/n/10 edge_weight_range_depletion| Overfull \hbox (11.15834pt too wide) in paragraph at lines 27512--27512 []\T1/txtt/m/n/10 edge_weight_range_enrichment| Overfull \hbox (0.65837pt too wide) in paragraph at lines 27512--27512 []\T1/txtt/m/n/10 only_show_enrichment_edges| [242] Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 27582--27582 \T1/qhv/m/n/10 ment| Overfull \hbox (21.75356pt too wide) in paragraph at lines 27582--27582 []\T1/txtt/m/n/10 gobject| Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 []\T1/txtt/m/n/10 .. 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[289] [290 <./1_whole_brain.png>] [291 <./2_whole_brain_clus4.png> <./3_whole_b rain_clus4_noOther.png>] [292 <./4_whole_brain_by_group_leiden_1.png> <./4_whol e_brain_by_group_leiden_2.png>] [293 <./5_whole_brain_HMRF.png> <./5_whole_brai n_by_group_HMRF_1.png>] [294 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_ brain.png>] [295 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>] [296] [297] [298] [299 <./original_clusters_black.png>] Overfull \vbox (3.38263pt too high) detected at line 33290 [300 <./ppt_store_multiple_analyses2.png> <./1_loess_hvg.png>] [301 <./1_group_ hvg.png> <./1_hvg_table.png>] [302 <./2_loess_pca.png> <./2_group_pca.png>] [303 <./3_loess_umap.png>] [304 <./3_group_umap.png>] [305 <./4_spatial_network .png> <./4_large_network.png>] [306 <./4_distance_network.png>] [307 <./5_large _network_genes.png> <./5_large_distance_network_genes.png>] [308] [309] [310] [311 <./2_a_spatplot1.png>] [312 <./2_b_spatplot_image.png>] [313 <./2_c_ spatplot_image_adjusted_1.png>] [314 <./2_c_spatplot_image_adjusted_2.png>] [315 <./2_c_spatplot_image_adjusted_3.png>] [316 <./2_c_spatplot_image_adjusted _4.png>] [317 <./2_c_spatplot_image_adjusted_5.png>] [318 <./2_c_spatplot_image _adjusted_6.png>] [319 <./2_c_spatplot_image_adjusted_7.png>] [320 <./2_c_spatp lot_image_adjusted_8.png>] [321 <./2_c_spatplot_image_adjusted_9.png>] [322 <./ 2_c_spatplot_image_adjusted_10.png>] [323 <./2_c_spatplot_image_adjusted_11.png > <./2_d_original_plot.png>] [324 <./3_a_background_colors.png>] [325 <./3_b_bl ack_background.png>] [326 <./3_c_white_background.png>] [327 <./4_a_external_im age_negated.png>] [328 <./4_b_external_image_charcoal.png>] [329 <./5_1_a_spati al_locations.png>] [330 <./5_1_b_nr_genes.png>] [331 <./5_1_c_nr_genes_black_bg .png>] [332 <./5_1_d_nr_genes_charc_bg.png>] [333 <./5_2_a_UMAP_reduction.png>] [334 <./5_3_a_UMAP_leiden.png>] [335 <./5_4_a_covis_leiden_black.png>] [336 <./ 5_4_b_covis_leiden_negated.png>] [337 <./5_4_c_covis_leiden_charc.png>] [338 <./5_5_a_spatgene_charc_vor.png>] [339 <./5_5_b_spatgene_charc_vor.png>] [340 <./5_6_a_subset_spatgene_charc.png>] [341 <./5_6_b_subset_spatgene_charc_v or.png>] [342 <./1_voronoi.png>] [343 <./2_voronoi_no_others.png>] [344 <./3_vo ronoi_no_others_black_border.png>] [345 <./4_voronoi_spat_dim.png>] [346 <./5_v oronoi_neighbors.png> <./6_original_points.png>] [347 <./7_voronoi_genes.png> < ./8_voronoi_gene_black_bg.png>] LaTeX Warning: Hyper reference `subsections/trygiotto/docker:dockerinformation' on page 348 undefined on input line 34292. 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LaTeX Warning: Hyper reference `subsections/tipsandtricks/testandstoremultiplea nayses:test-and-store' on page 679 undefined on input line 41641. LaTeX Warning: Hyper reference `subsections/tipsandtricks/visualizewithvoronoip lots:voronoi-plots' on page 679 undefined on input line 41645. LaTeX Warning: Hyper reference `subsections/tipsandtricks/giottoclass:giotto-cl ass' on page 679 undefined on input line 41649. LaTeX Warning: Hyper reference `subsections/tipsandtricks/workingwithimages:wor king-with-giotto-images' on page 679 undefined on input line 41653. [679] [680] Chapter 9. [681] [682] [683] [684] [685] [686] Chapter 10. [687 <./Index_Fig_A.png>] [688 <./Index_Fig_B.png> <./Index_Fig_C.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.42017 ...om the same 3D sample (distance unit  = 1 μm). ! 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. 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 (693 pages, 348519519 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' ------------ Latexmk: applying rule 'makeindex giottoteam-giotto.idx'... ------------ Running 'makeindex -s python.ist -o "giottoteam-giotto.ind" "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.181 ...8b9d709e0c26b4fbf39bc5e8583/Giotto}.svg}} [4] [5] [6] Chapter 2. [7] [8] Overfull \vbox (27.0568pt too high) has occurred while \output is active [9 <./GiottoInstallationWorkflow.png>] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [10] [11] [12] [13] [14] [15] [16] Chapter 3. 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Underfull \hbox (badness 6284) in paragraph at lines 14331--14331 \T1/qtm/m/n/10 ^^Q ^^P, list(list(list(^^Plogbase^^Q)), list(^^Plog base to use if re-verse_log_scale = TRUE^^Q)), ^^Pn^^Q, ^^Q ^^P, [128] Overfull \hbox (1.52061pt too wide) in paragraph at lines 14464--14464 []\T1/txtt/m/n/10 expression_values| Overfull \hbox (1.52061pt too wide) in paragraph at lines 14464--14464 []\T1/txtt/m/n/10 reverse_log_scale| Overfull \hbox (1.52061pt too wide) in paragraph at lines 14464--14464 []\T1/txtt/m/n/10 output_enrichment| [129] Underfull \hbox (badness 10000) in paragraph at lines 14527--14527 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 14527--14527 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 14527--14527 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 14527--14527 []\T1/txtt/m/n/10 .. [130] [131] [132] Underfull \hbox (badness 5133) in paragraph at lines 14819--14822 []|\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 14854--14857 []|\T1/qtm/m/n/10 Cal-cu-late Gene Sig-na-ture En-rich-ment Score With [133] [134] [135] Overfull \hbox (63.84494pt too wide) in paragraph at lines 15269--15274 [] [136] Underfull \hbox (badness 10000) in paragraph at lines 15425--15425 []\T1/qhv/m/n/10 Ar-gu- Overfull \hbox (14.1738pt too wide) in paragraph at lines 15425--15425 []\T1/txtt/m/n/10 dimensions| Overfull \hbox (45.6737pt too wide) in paragraph at lines 15425--15425 []\T1/txtt/m/n/10 maximum_distance| Overfull \hbox (8.92381pt too wide) in paragraph at lines 15425--15425 []\T1/txtt/m/n/10 minimum_k| Overfull \hbox (35.17374pt too wide) in paragraph at lines 15425--15425 []\T1/txtt/m/n/10 return_gobject| [137] Underfull \hbox (badness 10000) in paragraph at lines 15599--15599 []\T1/qhv/m/n/10 Ar-gu- Overfull \hbox (12.00728pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 dimensions| Overfull \hbox (43.50719pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 maximum_distance| Overfull \hbox (6.7573pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 minimum_k| Overfull \hbox (6.7573pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 show_plot| Overfull \hbox (17.25726pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 return_plot| Overfull \hbox (6.7573pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 save_plot| Overfull \hbox (12.06726pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 save_param| Overfull \hbox (48.75717pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 default_save_name| [138] [139] [140] Overfull \hbox (21.71956pt too wide) in paragraph at lines 15921--15921 []\T1/txtt/m/n/10 delaunay_method| Overfull \hbox (74.2194pt too wide) in paragraph at lines 15921--15921 []\T1/txtt/m/n/10 maximum_distance_delaunay| Overfull \hbox (47.96948pt too wide) in paragraph at lines 15921--15921 []\T1/txtt/m/n/10 maximum_distance_knn| Overfull \hbox (16.46957pt too wide) in paragraph at lines 15921--15921 []\T1/txtt/m/n/10 return_gobject| Underfull \hbox (badness 10000) in paragraph at lines 15928--15932 []\T1/qtm/m/n/10 For De-lau-nay [141] [142] [143] [144] [145] Overfull \hbox (4.68492pt too wide) in paragraph at lines 16465--16468 [] [146] Overfull \hbox (3.79921pt too wide) in paragraph at lines 16720--16720 []\T1/txtt/m/n/10 spatial_network_name| [147] [148] Overfull \hbox (3.79921pt too wide) in paragraph at lines 17024--17024 []\T1/txtt/m/n/10 spatial_network_name| [149] [150] [151] Underfull \hbox (badness 10000) in paragraph at lines 17413--17419 [] [152] [153] [154] [155] Overfull \hbox (16.52835pt too wide) in paragraph at lines 17867--17867 []\T1/txtt/m/n/10 expression_values| [156] Overfull \hbox (11.91016pt too wide) in paragraph at lines 17985--17985 []\T1/txtt/m/n/10 expression_values| [157] [158] [159] [160] [161] Underfull \hbox (badness 10000) in paragraph at lines 18674--18677 []\T1/qtm/m/n/10 fully con- [162] Overfull \hbox (0.73529pt too wide) in paragraph at lines 18853--18853 []\T1/txtt/m/n/10 show_cluster_annot| [163] [164] [165] Overfull \hbox (4.64677pt too wide) in paragraph at lines 19335--19335 []\T1/txtt/m/n/10 spatial_network_name| Overfull \hbox (4.64677pt too wide) in paragraph at lines 19335--19335 []\T1/txtt/m/n/10 dim_reduction_to_use| [166] [167] [168] [169] [170] [171] Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 20012--20012 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 di m-Plot2D\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#dim-plot2d>\TS1/qtm/m/n/10 `\T1/qtm /m/n/10 _ list(^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pgobject^^Q)), Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 \T1/qtm/m/n/10 list(^^Pgiotto ob-ject^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^ Pgroup_by^^Q)), list(^^Pcreate mul-ti-ple plots based on Underfull \hbox (badness 6944) in paragraph at lines 20012--20012 \T1/qtm/m/n/10 cell an-no-ta-tion col-umn^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(lis t(^^Pgroup_by_subset^^Q)), list(^^Psubset the group_by Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 \T1/qtm/m/n/10 fac-tor col-umn^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pdim_re duction_to_use^^Q)), list(^^Pdimension re-duc-tion to [172] [173] Underfull \hbox (badness 10000) in paragraph at lines 20134--20134 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20134--20134 \T1/qhv/m/n/10 gu- Overfull \hbox (2.27292pt too wide) in paragraph at lines 20134--20134 \T1/qhv/m/n/10 ment| Overfull \hbox (16.79282pt too wide) in paragraph at lines 20134--20134 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.54265pt too wide) in paragraph at lines 20134--20134 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.29266pt too wide) in paragraph at lines 20134--20134 []\T1/txtt/m/n/10 default_save_name| [174] Underfull \vbox (badness 10000) detected at line 20147 Overfull \vbox (28.11948pt too high) detected at line 20147 [175] [176] Underfull \hbox (badness 10000) in paragraph at lines 20255--20255 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20255--20255 \T1/qhv/m/n/10 gu- Overfull \hbox (2.27292pt too wide) in paragraph at lines 20255--20255 \T1/qhv/m/n/10 ment| Overfull \hbox (16.79282pt too wide) in paragraph at lines 20255--20255 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.54265pt too wide) in paragraph at lines 20255--20255 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.29266pt too wide) in paragraph at lines 20255--20255 []\T1/txtt/m/n/10 default_save_name| Underfull \vbox (badness 10000) detected at line 20268 Overfull \vbox (12.41795pt too high) detected at line 20268 [177] [178] Underfull \hbox (badness 10000) in paragraph at lines 20376--20376 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20376--20376 \T1/qhv/m/n/10 gu- Overfull \hbox (2.27292pt too wide) in paragraph at lines 20376--20376 \T1/qhv/m/n/10 ment| Overfull \hbox (16.79282pt too wide) in paragraph at lines 20376--20376 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.54265pt too wide) in paragraph at lines 20376--20376 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.29266pt too wide) in paragraph at lines 20376--20376 []\T1/txtt/m/n/10 default_save_name| Overfull \vbox (43.47412pt too high) detected at line 20389 [179] [180] Underfull \hbox (badness 10000) in paragraph at lines 20476--20476 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20476--20476 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 20476--20476 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 20476--20476 []\T1/txtt/m/n/10 .. Overfull \vbox (49.87111pt too high) detected at line 20487 [181] [182] Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 20576--20576 \T1/qhv/m/n/10 ment| Overfull \hbox (21.75356pt too wide) in paragraph at lines 20576--20576 []\T1/txtt/m/n/10 gobject| Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 di m-CellPlot2D\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#dim-cellplot2d>\TS1/qtm/m/n/10 `\T1/qtm/m/n/10 _ list(^^Pn^^Q, ^^Q ^^P, Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 \T1/qtm/m/n/10 list(list(list(^^Pdim_reduction_to_use^^Q)), list(^^Pdimension r e-duc-tion to use^^Q)), ^^Pn^^Q, ^^Q ^^P, Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 \T1/qtm/m/n/10 list(list(list(^^Pdim_reduction_name^^Q)), list(^^Pdimension re- duc-tion name^^Q)), ^^Pn^^Q, ^^Q ^^P, Overfull \vbox (30.67413pt too high) detected at line 20589 [183] [184] Underfull \hbox (badness 10000) in paragraph at lines 20739--20739 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20739--20739 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 20739--20739 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 20739--20739 []\T1/txtt/m/n/10 .. Overfull \vbox (26.13272pt too high) detected at line 20754 [185] [186] [187] [188] Overfull \hbox (13.46457pt too wide) in alignment at lines 20877--20887 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 20887--20900 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 20900--20904 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 20904--20906 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 20906--21047 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 21047--21187 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 21187--21327 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 21327--21328 [] [] [189] [190] Underfull \hbox (badness 10000) in paragraph at lines 21409--21409 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 21409--21409 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 21409--21409 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 21409--21409 []\T1/txtt/m/n/10 .. Overfull \vbox (22.51646pt too high) detected at line 21421 [191] [192] [193] [194] Underfull \hbox (badness 10000) in paragraph at lines 21824--21824 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 21824--21824 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 21824--21824 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 21824--21824 []\T1/txtt/m/n/10 .. Underfull \vbox (badness 2600) detected at line 21838 Overfull \vbox (23.21797pt too high) detected at line 21838 [195] [196] Underfull \hbox (badness 10000) in paragraph at lines 21967--21967 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 21967--21967 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 21967--21967 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 21967--21967 []\T1/txtt/m/n/10 .. Overfull \vbox (48.93274pt too high) detected at line 21986 [197] Underfull \vbox (badness 10000) detected at line 21986 Overfull \vbox (47.67393pt too high) detected at line 21986 [198] [199] [200] [201] Underfull \hbox (badness 10000) in paragraph at lines 22541--22541 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 22541--22541 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 22541--22541 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 22541--22541 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 22541--22541 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 sp at-Dim-Gene-Plot2D\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#spat-dim-gene-plot2d>\TS1 /qtm/m/n/10 `\T1/qtm/m/n/10 _ list(^^Pn^^Q, ^^Q ^^P, Underfull \hbox (badness 6961) in paragraph at lines 22541--22541 \T1/qtm/m/n/10 list(list(list(^^Pgobject^^Q)), list(^^Pgiotto ob-ject^^Q)), ^^P n^^Q, ^^Q ^^P, list(list(list(^^Pshow_image^^Q)), list(^^Pshow a [202] Underfull \vbox (badness 10000) detected at line 22556 Overfull \vbox (39.52196pt too high) detected at line 22556 [203] [204] Underfull \hbox (badness 10000) in paragraph at lines 22640--22640 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 22640--22640 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 22640--22640 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 22640--22640 []\T1/txtt/m/n/10 .. Underfull \vbox (badness 10000) detected at line 22659 Overfull \vbox (26.9195pt too high) detected at line 22659 [205] [206] Underfull \hbox (badness 10000) in paragraph at lines 22676--22679 []\TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 spat-Dim-CellPlot2D\TS1/qtm/m/it/10 ` \T1/ qtm/m/n/10 <#spat-dim- [207] Underfull \vbox (badness 10000) detected at line 22798 Underfull \vbox (badness 10000) detected at line 22798 [208] Overfull \hbox (39.7145pt too wide) in alignment at lines 22804--22814 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 22814--22827 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 22827--22831 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 22831--22833 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 22833--22974 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 22974--23114 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 23114--23254 [] [] [209] Overfull \hbox (39.7145pt too wide) in alignment at lines 23254--23381 [] [] [210] [211] [212] Overfull \hbox (13.46457pt too wide) in alignment at lines 23546--23556 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23556--23569 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23569--23573 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23573--23575 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23575--23716 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23716--23856 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23856--23934 [] [] [213] [214] [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 24352--24352 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 24352--24352 \T1/qhv/m/n/10 gu- Overfull \hbox (2.51184pt too wide) in paragraph at lines 24352--24352 \T1/qhv/m/n/10 ment| Overfull \hbox (17.03174pt too wide) in paragraph at lines 24352--24352 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.78157pt too wide) in paragraph at lines 24352--24352 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.53159pt too wide) in paragraph at lines 24352--24352 []\T1/txtt/m/n/10 default_save_name| Underfull \hbox (badness 6792) in paragraph at lines 24352--24352 \T1/qtm/m/n/10 list(^^Pdimension to use on x-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list( list(list(^^Pdim2_to_use^^Q)), list(^^Pdimension to Underfull \hbox (badness 7186) in paragraph at lines 24352--24352 \T1/qtm/m/n/10 use on y-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pdim3_to_ use^^Q)), list(^^Pdimension to use on z-axis^^Q)), Underfull \hbox (badness 7168) in paragraph at lines 24352--24352 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pshow_NN_network^^Q)), list(^ ^Pshow un-der-ly-ing NN net-work^^Q)), ^^Pn^^Q, ^^Q ^^P, [217] [218] Underfull \hbox (badness 10000) in paragraph at lines 24464--24464 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 24464--24464 \T1/qhv/m/n/10 gu- Overfull \hbox (2.51184pt too wide) in paragraph at lines 24464--24464 \T1/qhv/m/n/10 ment| Overfull \hbox (17.03174pt too wide) in paragraph at lines 24464--24464 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.78157pt too wide) in paragraph at lines 24464--24464 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.53159pt too wide) in paragraph at lines 24464--24464 []\T1/txtt/m/n/10 default_save_name| Underfull \hbox (badness 6792) in paragraph at lines 24464--24464 \T1/qtm/m/n/10 list(^^Pdimension to use on x-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list( list(list(^^Pdim2_to_use^^Q)), list(^^Pdimension to Underfull \hbox (badness 7186) in paragraph at lines 24464--24464 \T1/qtm/m/n/10 use on y-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pdim3_to_ use^^Q)), list(^^Pdimension to use on z-axis^^Q)), Underfull \hbox (badness 7168) in paragraph at lines 24464--24464 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pshow_NN_network^^Q)), list(^ ^Pshow un-der-ly-ing NN net-work^^Q)), ^^Pn^^Q, ^^Q ^^P, Overfull \vbox (23.71645pt too high) detected at line 24473 [219] Underfull \hbox (badness 10000) in paragraph at lines 24576--24576 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 24576--24576 \T1/qhv/m/n/10 gu- Overfull \hbox (2.51184pt too wide) in paragraph at lines 24576--24576 \T1/qhv/m/n/10 ment| Overfull \hbox (17.03174pt too wide) in paragraph at lines 24576--24576 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.78157pt too wide) in paragraph at lines 24576--24576 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.53159pt too wide) in paragraph at lines 24576--24576 []\T1/txtt/m/n/10 default_save_name| Underfull \hbox (badness 6792) in paragraph at lines 24576--24576 \T1/qtm/m/n/10 list(^^Pdimension to use on x-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list( list(list(^^Pdim2_to_use^^Q)), list(^^Pdimension to Underfull \hbox (badness 7186) in paragraph at lines 24576--24576 \T1/qtm/m/n/10 use on y-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pdim3_to_ use^^Q)), list(^^Pdimension to use on z-axis^^Q)), Underfull \hbox (badness 7168) in paragraph at lines 24576--24576 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pshow_NN_network^^Q)), list(^ ^Pshow un-der-ly-ing NN net-work^^Q)), ^^Pn^^Q, ^^Q ^^P, [220] [221] Underfull \hbox (badness 5741) in paragraph at lines 24602--24615 \T1/qtm/m/it/10 Plot\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#dim-plot>\TS1/qtm/m/n/1 0 `\T1/qtm/m/n/10 _ , \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 plot-PCA_2D\TS1/qtm/m/ it/10 ` \T1/qtm/m/n/10 <#plot-pca2d>\TS1/qtm/m/n/10 `\T1/qtm/m/n/10 _ , \TS1/qt m/m/it/10 ``\T1/qtm/m/it/10 plot-PCA\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#plot-pc a>\TS1/qtm/m/n/10 `\T1/qtm/m/n/10 _ , \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 plotTS NE_2D\TS1/qtm/m/it/10 ` [222] [223] [224] [225] [226] [227] [228] Underfull \hbox (badness 10000) in paragraph at lines 25784--25788 []\TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 spat-Dim-Gene-Plot2D\TS1/qtm/m/it/10 ` \T1 /qtm/m/n/10 <#spat-dim-gene- [229] Underfull \hbox (badness 10000) in paragraph at lines 26003--26003 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 26003--26003 \T1/qhv/m/n/10 gu- Overfull \hbox (12.7307pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 gobject| Overfull \hbox (80.9805pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 spatial_network_name| Overfull \hbox (49.48059pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 thickness_unit| Overfull \hbox (54.73058pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 slice_thickness| Overfull \hbox (128.23036pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 cell_distance_estimate_method| Overfull \hbox (38.98062pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 extend_ratio| Overfull \hbox (7.48071pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 method| Overfull \hbox (17.98068pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 equation| Overfull \hbox (7.48071pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 point1| Overfull \hbox (7.48071pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 point2| Overfull \hbox (7.48071pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 point3| Overfull \hbox (28.48065pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 normVector| Overfull \hbox (38.98062pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 planeVector1| Overfull \hbox (38.98062pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 planeVector2| Overfull \hbox (33.73064pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 mesh_grid_n| Overfull \hbox (49.48059pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 return_gobject| [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] Overfull \hbox (5.90836pt too wide) in paragraph at lines 27512--27512 []\T1/txtt/m/n/10 edge_weight_range_depletion| Overfull \hbox (11.15834pt too wide) in paragraph at lines 27512--27512 []\T1/txtt/m/n/10 edge_weight_range_enrichment| Overfull \hbox (0.65837pt too wide) in paragraph at lines 27512--27512 []\T1/txtt/m/n/10 only_show_enrichment_edges| [242] Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 27582--27582 \T1/qhv/m/n/10 ment| Overfull \hbox (21.75356pt too wide) in paragraph at lines 27582--27582 []\T1/txtt/m/n/10 gobject| Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 ce ll-Prox-im-i-tyS-pat-Plot2D\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#cell-prox-im-i-t ys-pat-plot2d>\TS1/qtm/m/n/10 `\T1/qtm/m/n/10 _ list(^^Pn^^Q, Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 \T1/qtm/m/n/10 ^^Q ^^P, list(list(list(^^Pinteraction_name^^Q)), list(^^Pcell-c ell in-ter-ac-tion name^^Q)), ^^Pn^^Q, ^^Q ^^P, Overfull \vbox (6.67413pt too high) detected at line 27592 [243] Underfull \hbox (badness 7362) in paragraph at lines 27609--27611 []\TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 cell-Prox-im-i-tyS-pat-Plot2D\TS1/qtm/m/it /10 ` \T1/qtm/m/n/10 <#cell-prox-im-i-tys-pat-plot2d>\TS1/qtm/m/n/10 `\T1/qtm/m /n/10 _ and \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 cell-Prox-im-i-tyS-pat-Plot3D\TS 1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#cell-prox-im-i-tys-pat- [244] [245] [246] [247] [248] [249] Underfull \hbox (badness 10000) in paragraph at lines 28563--28563 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 28563--28563 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 28563--28563 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 28563--28563 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 28563--28563 \T1/qtm/m/n/10 ^^Q ^^P, list(list(list(^^Pgobject^^Q)), list(^^Pgiotto ob-ject^ ^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pexpression_values^^Q)), [250] Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 28626--28626 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 fi nd-ICG\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#find-icg>\TS1/qtm/m/n/10 `\T1/qtm/m/n /10 _ list(^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pgobject^^Q)), Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 \T1/qtm/m/n/10 list(^^Pgiotto ob-ject^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^ Pexpression_values^^Q)), list(^^Pexpression val-ues to Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 \T1/qtm/m/n/10 use^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pselected_genes^^Q) ), list(^^Psubset of se-lected genes (op-tional)^^Q)), Underfull \hbox (badness 7397) in paragraph at lines 28626--28626 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pcluster_column^^Q)), list(^^ Pname of col-umn to use for cell types^^Q)), ^^Pn^^Q, Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 \T1/qtm/m/n/10 ^^Q ^^P, list(list(list(^^Pspatial_network_name^^Q)), list(^^Pna me of spa-tial net-work to use^^Q)), ^^Pn^^Q, ^^Q ^^P, [251] Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 28686--28686 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 fi nd-ICG\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#find-icg>\TS1/qtm/m/n/10 `\T1/qtm/m/n /10 _ list(^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pgobject^^Q)), Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 \T1/qtm/m/n/10 list(^^Pgiotto ob-ject^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^ Pexpression_values^^Q)), list(^^Pexpression val-ues to Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 \T1/qtm/m/n/10 use^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pselected_genes^^Q) ), list(^^Psubset of se-lected genes (op-tional)^^Q)), Underfull \hbox (badness 7397) in paragraph at lines 28686--28686 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pcluster_column^^Q)), list(^^ Pname of col-umn to use for cell types^^Q)), ^^Pn^^Q, Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 \T1/qtm/m/n/10 ^^Q ^^P, list(list(list(^^Pspatial_network_name^^Q)), list(^^Pna me of spa-tial net-work to use^^Q)), ^^Pn^^Q, ^^Q ^^P, [252] [253] [254] Underfull \hbox (badness 10000) in paragraph at lines 29018--29018 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 29018--29018 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 29018--29018 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 29018--29018 []\T1/txtt/m/n/10 .. [255] [256] [257] Underfull \hbox (badness 10000) in paragraph at lines 29381--29381 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 29381--29381 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 29381--29381 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 29381--29381 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 29381--29381 \T1/qtm/m/n/10 list(^^Pn^^Q, ^^Q ^^P, list(list(list(^^PcpgObject^^Q)), list(^^ PICG (in-ter-ac-tion changed gene) score ob-ject^^Q)), Underfull \hbox (badness 5388) in paragraph at lines 29381--29381 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pselected_ints^^Q)), list(^^P subset of se-lected cell-cell in-ter-ac-tions (op-tional)^^Q)), Underfull \hbox (badness 6493) in paragraph at lines 29381--29381 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pselected_genes^^Q)), list(^^ Psubset of se-lected genes (op-tional)^^Q)), ^^Pn^^Q, ^^Q ^^P, [258] Underfull \hbox (badness 10000) in paragraph at lines 29440--29440 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 29440--29440 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 29440--29440 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 29440--29440 []\T1/txtt/m/n/10 .. [259] [260] [261] [262] [263] [264] [265] [266] [267] Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 30525--30525 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 pl ot-Com-bineIn-ter-ac-tion-Changed-Genes\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#plot -com-binein-ter-ac- Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 \T1/qtm/m/n/10 tion-changed-genes>\TS1/qtm/m/n/10 `\T1/qtm/m/n/10 _ list(^^Pn^^ Q, ^^Q ^^P, list(list(list(^^Pgobject^^Q)), list(^^Pgiotto ob-ject^^Q)), ^^Pn^^ Q, ^^Q ^^P, Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 \T1/qtm/m/n/10 list(list(list(^^PcombCpgObject^^Q)), list(^^PICGscores, out-put from com-bineIn-ter-ac-tion-Changed- Underfull \hbox (badness 7925) in paragraph at lines 30525--30525 \T1/qtm/m/n/10 Genes()^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pselected_inter actions^^Q)), list(^^Pinteractions to show^^Q)), ^^Pn^^Q, ^^Q Underfull \hbox (badness 5388) in paragraph at lines 30525--30525 \T1/qtm/m/n/10 ^^P, list(list(list(^^Pselected_gene_to_gene^^Q)), list(^^Ppairw ise gene com-bi-na-tions to show^^Q)), ^^Pn^^Q, ^^Q ^^P, [268] Underfull \hbox (badness 10000) in paragraph at lines 30585--30585 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 30585--30585 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 30585--30585 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 30585--30585 []\T1/txtt/m/n/10 .. [269] [270] [271] [272] [273] Overfull \hbox (9.49155pt too wide) in paragraph at lines 31336--31336 []\T1/txtt/m/n/10 selected_cell_LR| Overfull \hbox (19.99152pt too wide) in paragraph at lines 31336--31336 []\T1/txtt/m/n/10 show_cell_LR_names| Overfull \hbox (14.74153pt too wide) in paragraph at lines 31336--31336 []\T1/txtt/m/n/10 default_save_name| [274] Overfull \hbox (1.10202pt too wide) in paragraph at lines 31496--31496 []\T1/txtt/m/n/10 default_save_name| [275] [276] [277] [278] [279] [280] Chapter 4. [281] [282] [283] [284] [285] [286] [287] [288] Chapter 5. [289] [290 <./1_whole_brain.png>] [291 <./2_whole_brain_clus4.png> <./3_whole_b rain_clus4_noOther.png>] [292 <./4_whole_brain_by_group_leiden_1.png> <./4_whol e_brain_by_group_leiden_2.png>] [293 <./5_whole_brain_HMRF.png> <./5_whole_brai n_by_group_HMRF_1.png>] [294 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_ brain.png>] [295 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>] [296] [297] [298] [299 <./original_clusters_black.png>] Overfull \vbox (3.38263pt too high) detected at line 33290 [300 <./ppt_store_multiple_analyses2.png> <./1_loess_hvg.png>] [301 <./1_group_ hvg.png> <./1_hvg_table.png>] [302 <./2_loess_pca.png> <./2_group_pca.png>] [303 <./3_loess_umap.png>] [304 <./3_group_umap.png>] [305 <./4_spatial_network .png> <./4_large_network.png>] [306 <./4_distance_network.png>] [307 <./5_large _network_genes.png> <./5_large_distance_network_genes.png>] [308] [309] [310] [311 <./2_a_spatplot1.png>] [312 <./2_b_spatplot_image.png>] [313 <./2_c_ spatplot_image_adjusted_1.png>] [314 <./2_c_spatplot_image_adjusted_2.png>] [315 <./2_c_spatplot_image_adjusted_3.png>] [316 <./2_c_spatplot_image_adjusted _4.png>] [317 <./2_c_spatplot_image_adjusted_5.png>] [318 <./2_c_spatplot_image _adjusted_6.png>] [319 <./2_c_spatplot_image_adjusted_7.png>] [320 <./2_c_spatp lot_image_adjusted_8.png>] [321 <./2_c_spatplot_image_adjusted_9.png>] [322 <./ 2_c_spatplot_image_adjusted_10.png>] [323 <./2_c_spatplot_image_adjusted_11.png > <./2_d_original_plot.png>] [324 <./3_a_background_colors.png>] [325 <./3_b_bl ack_background.png>] [326 <./3_c_white_background.png>] [327 <./4_a_external_im age_negated.png>] [328 <./4_b_external_image_charcoal.png>] [329 <./5_1_a_spati al_locations.png>] [330 <./5_1_b_nr_genes.png>] [331 <./5_1_c_nr_genes_black_bg .png>] [332 <./5_1_d_nr_genes_charc_bg.png>] [333 <./5_2_a_UMAP_reduction.png>] [334 <./5_3_a_UMAP_leiden.png>] [335 <./5_4_a_covis_leiden_black.png>] [336 <./ 5_4_b_covis_leiden_negated.png>] [337 <./5_4_c_covis_leiden_charc.png>] [338 <./5_5_a_spatgene_charc_vor.png>] [339 <./5_5_b_spatgene_charc_vor.png>] [340 <./5_6_a_subset_spatgene_charc.png>] [341 <./5_6_b_subset_spatgene_charc_v or.png>] [342 <./1_voronoi.png>] [343 <./2_voronoi_no_others.png>] [344 <./3_vo ronoi_no_others_black_border.png>] [345 <./4_voronoi_spat_dim.png>] [346 <./5_v oronoi_neighbors.png> <./6_original_points.png>] [347 <./7_voronoi_genes.png> < ./8_voronoi_gene_black_bg.png>] [348] Chapter 6. [349] [350] [351] [352 <./3.1_HVGplot.png> <./3.2_screePlot.png>] [353 <./3.3_j ackstrawPlot.png>] [354 <./3.4_PCA.png>] [355 <./3.5_tSNE.png>] [356 <./4.1_UMA P.png>] [357 <./4.2_showClusterHeatmap.png> <./4.3_showClusterDendrogram.png>] [358 <./5.1_violinPlot.png>] [359 <./5.2_plotMetaDataHeatmap.png>] [360 <./6.1_ spatDimPlot2D.png>] [361] [362 <./9.1_spatGenePlot2D.png>] [363 <./10.1_heatmSp atialCorGenes.png>] Overfull \vbox (2.14355pt too high) detected at line 34809 [364 <./10.2_spatCellPlot2D.png>] [365 <./12.1_cellProximityBarplot.png>] [366 <./12.2_spatCellPlot2D.png>] [367 <./12.3_cellProximityHeatmap.png>] [368 <./12.4_cellProximityNetwork.png>] [369 <./12.5_cellProximitySpatPlot2D.pn g>] [370 <./12.6_spatPlot2D.png>] [371 <./13.1_plotCellProximityGenes.png>] Overfull \vbox (2.14355pt too high) detected at line 34991 [372 <./13.2_plotICG.png>] [373 <./14.1_plotCCcomHeatmap.png>] [374 <./14.2_plo tCCcomDotplot.png>] [375 <./14.3_plotRankSpatvsExpr.png>] [376 <./14.4_plotReco very.png>] [377] [378] [379] [380] [381] [382] [383] [384] [385] [386 <./2_a_fi ltergenes.png>] [387 <./2_b_filtercells.png>] [388 <./2_c_filtercombos.png>] [389 <./3_a_screeplot1.png> <./3_b_PCA.png>] [390] [391 <./3_d_UMAP_3D.png> <./ 3_e_TSNE.png>] [392 <./4_a_UMAP1.png>] [393 <./4_b_UMAP_3D.png> <./4_c_spatdimp lot.png>] [394 <./4_e_clusterheatmap.png>] [395 <./4_f_clusterdendrogram.png>] [396 <./5_a_violinplot.png>] [397 <./5_b_metaheatmap.png>] [398 <./6_a_spatdimp lot.png>] [399 <./6_b_dimgeneplot.png> <./6_c_spatgeneplot.png>] [400 <./7_a_sp atplot.png>] [401 <./8_a_plotStatDelaunayNetwork.png>] [402 <./8_b_spatplot.png >] [403 <./8_c_spatplot.png>] [404 <./9_a_spatgeneplot.png>] [405 <./9_b_spatge neplot.png>] [406 <./10_a_heatmspatcor.png>] [407 <./10_b_rankcorgroup.png>] Overfull \vbox (2.14355pt too high) detected at line 36133 [408 <./10_c_spatcellplot.png>] [409 <./12_a_barplot1.png>] [410 <./12_b_heatma p.png>] [411 <./12_c_network.png>] [412 <./12_d_network.png>] [413 <./12_e_spat plot.png>] [414 <./12_e_cellproximity.png>] Underfull \vbox (badness 1158) detected at line 36266 [415 <./13_a_insert.png> <./13_b_crossplot.png>] [416 <./13_c_cross.png>] [417 <./13_d_crossgeneplot.png> <./13_e_crossgene.png>] [418] [419 <./mini_seqF ISH.png>] [420 <./mini_STARmap.png>] [421 <./mini_visium.png>] [422 <./cortex_s vz_location_fields.png>] [423] [424] [425 <./2_a_spatplot.png>] [426 <./3_a_HVG plot2.png>] [427 <./3_b_screeplot2.png> <./3_c_PCA_reduction2.png>] [428 <./3_d _UMAP_reduction2.png>] [429 <./3_e_tSNE_reduction3.png>] [430 <./4_a_UMAP_leide n3.png>] [431 <./4_b_UMAP_leiden_subcluster.png>] [432 <./4_c_heatmap.png>] [433 <./4_d_dendro.png>] [434 <./5_a_covis_leiden3.png>] [435 <./5_b_covis_leid en_selected.png>] Underfull \vbox (badness 10000) detected at line 36683 [436 <./6_a_violinplot_gini2.png>] Underfull \vbox (badness 1320) detected at line 36724 [437 <./6_b_metaheatmap_gini2.png>] [438] [439 <./7_a_violinplot.png>] [440 <./ 7_b_covisualization.png>] [441 <./7_c_heatmap.png>] [442 <./7_d_heatmap_selecte d.png>] [443 <./8_a_grid.png>] [444 <./9_a_spatial_network_delaunay.png> <./9_b _spatial_network_k3.png>] [445 <./9_c_spatial_network_k10.png> <./9_d_spatial_n etwork_dist.png>] [446 <./10_a_spatialgenes_km.png>] Underfull \vbox (badness 10000) detected at line 36909 [447 <./10_b_spatialcoexpression_heatmap.png> <./10_c_spatialcoexpression_rank. png>] [448 <./10_d_spatialcoexpression_metagenes.png>] [449 <./11_HMRF_2_k9_b.2 8.pdf>] [450 <./12_a_barplot_cell_cell_enrichment.png>] [451 <./12_b_heatmap_ce ll_cell_enrichment.png>] [452 <./12_c_network_cell_cell_enrichment.png>] [453 <./12_d_network_cell_cell_enrichment_self.pdf>] [454 <./12_e_cell_cell_enr ichment_selected.png>] [455 <./12_f_cell_cell_enrichment_sel_vs_not.png>] [456 <./13_a_CPG_dotplot.png>] Overfull \vbox (2.14355pt too high) detected at line 37134 [457 <./13_b_ICG_barplot.png>] Underfull \vbox (badness 1194) detected at line 37153 [458 <./14_a_communication_dotplot.png>] [459 <./14_b_expr_vs_spatial_expressio n_rank.png>] [460 <./14_c_spatial_recovery_expression_rank.png>] [461 <./14_d_e xpr_vs_spatial_activity.png>] [462 <./14_e_spatial_recovery_activity.png>] [463] [464] [465 <./2_a_distribution_genes1.png> <./2_b_distribution_cells1.png >] [466 <./2_c_filter_combos.png>] [467 <./2_d_spatial_locations2D.png> <./2_e_ spatial_locations3D.png>] [468 <./3_a_screeplot.png>] [469 <./3_b_UMAP_reductio n.png>] [470 <./4_a_UMAP_leiden.png>] [471 <./5_b_leiden_2D.png>] [472 <./6_a_v iolinplot1.png>] [473 <./6_b_clusterheatmap_markers.png>] [474 <./7_a_clusterhe atmap_markers.png>] [475 <./7_b_clusterheatmap_markers_celltypes.png>] [476 <./ 7_c_umap_cell_types.png> <./7_d_spatPlot_cell_types_all.png>] [477 <./7_e_spatP lot2D_cell_types_all.png>] [478 <./7_f_spatPlot_cell_types_excit.png> <./7_g_sp atPlot2D_cell_types_excit.png>] [479 <./7_h_spatPlot_cell_types_inhib.png>] [480 <./7_i_spatPlot2D_cell_types_inhib.png>] [481 <./7_j_spatPlot_cell_types_O DandAstro.png> <./7_k_spatPlot2D_cell_types_ODandAstro.png>] [482 <./7_l_spatPl ot_cell_types_other.png>] [483 <./7_m_spatPlot2D_cell_types_other.png>] [484] [485 <./2_a_distribution_genes.png>] [486 <./2_b_distribution_cells.png>] [487 <./2_c_distribution_filters.png>] [488 <./2_d_spatial_locations.png> <./3_ a_hvg.png>] [489 <./3_b_signPCs.png> <./3_c_umap.png>] [490 <./4_leiden_0.2.png >] [491 <./5_a_covisualize_leiden_0.2.png>] [492 <./6_a_violinplot.png> <./6_b_ heatmap_leiden_0.2.png>] [493 <./7_a_general_cell_type.png>] [494 <./7_b_dim_pl ot_detailed_cell_type.png> <./7_c_cluster_annotation_heatmap.png>] [495 <./8_ce ll_type_co_vis.png> <./9_a_Rorb_dim_plot.png>] [496 <./9_b_Pcp4_dim_plot.png> < ./9_c_Pcp4_spat_plot.png>] [497 <./9_d_Cux2_dim_plot.png> <./9_e_detailed_cell_ types.png>] [498 <./9_f_Cux2_spat_plot.png> <./9_g_Ctgf_dim_plot.png>] [499 <./ 9_h_Ctgf_spat_plot.png> <./10_a_insert_cross_section_cell_types.png>] [500 <./1 0_b_insert_cross_section_Slc17a7.png> <./10_c_cross_section_spat.png>] [501 <./ 10_d_cross_section_spat3d.png> <./10_e_Slc17a7_cross_section_gene3d.png>] [502] [503 <./visium_technology.png> <./visium_brain_image_summary1.png>] [504 <./2_a_spatplot_image.png>] [505 <./2_b_spatplot_image_adjusted.png>] [506 <./2_c_in_tissue.png>] [507 <./2_d_spatial_locations1.png>] [508 <./2_e_nr _genes.png>] [509 <./3_a_HVGplot.png>] [510 <./3_b_screeplot.png> <./3_c_PCA_re duction.png>] [511 <./3_d_UMAP_reduction.png>] [512 <./3_e_tSNE_reduction.png>] [513 <./4_a_UMAP_leiden1.png>] [514 <./5_a_covis_leiden.png>] [515 <./5_b_nr_ge nes.png>] [516 <./5_c_DEG_subset.png>] Underfull \vbox (badness 10000) detected at line 38334 [517 <./6_a_violinplot_gini.png>] [518 <./6_b_metaheatmap_gini.png> <./6_c_gini _umap.png>] [519] [520 <./6_d_violinplot_scran.png>] [521 <./6_e_metaheatmap_sc ran.png> <./6_f_scran_umap.png>] Overfull \vbox (3.018pt too high) detected at line 38455 [522] [523 <./7_a_metaheatmap2.png>] [524 <./7_b_spatcellplot.png>] [525 <./7_c _spatcellplot.png>] [526 <./7_d_spatDimCellPlot.png>] [527 <./8_grid.png>] [528 <./9_a_knn_network.png>] [529 <./10_a_spatial_genes_km.png>] [530 <./10_b_ spatial_genes_rank.png>] [531 <./10_c_heatmap.png>] [532 <./10_d_spatPlot2D_HMR F.png>] [533] [534 <./mouse_kidney_highres.png>] [535 <./2_a_spatplot_image1.pn g>] [536 <./2_b_spatplot_image_adjusted1.png>] [537 <./2_c_in_tissue1.png>] [538 <./2_d_spatial_locations2.png>] [539 <./2_e_nr_genes1.png>] [540 <./3_a_HV Gplot1.png>] [541 <./3_b_screeplot1.png> <./3_c_PCA_reduction1.png>] [542 <./3_ d_UMAP_reduction1.png>] [543 <./3_e_tSNE_reduction1.png>] [544 <./4_a_UMAP_leid en2.png>] [545 <./5_a_covis_leiden1.png>] [546 <./5_b_nr_genes1.png>] Underfull \vbox (badness 10000) detected at line 38923 [547 <./6_a_violinplot_gini1.png>] [548 <./6_b_metaheatmap_gini1.png> <./6_c_gi ni_umap1.png>] [549] [550 <./6_d_violinplot_scran1.png>] [551 <./6_e_metaheatma p_scran1.png> <./6_f_scran_umap1.png>] [552 <./8_grid1.png>] [553 <./9_a_delaun ay_network.png>] [554 <./9_b_delaunay_network.png>] [555 <./10_a_spatial_genes_ km1.png>] [556 <./10_b_spatial_genes_rank1.png>] [557 <./10_d_Napsa_correlated_ genes.png>] Underfull \vbox (badness 10000) detected at line 39119 [558 <./10_e_heatmap_correlated_genes.png> <./10_f_rank_correlated_groups.png>] [559 <./10_g_spat_enrichment_score_plots.png> <./10_h_spat_enrichment_score_plo ts_genes.png>] [560] [561] [562] Overfull \vbox (6.31403pt too high) detected at line 39374 [563] [564] [565 <./2_a_spatPlot1.png>] [566 <./2_b_spatPlot.png>] [567 <./3_a_ spatPlot.png> <./3_b_PCA1.png>] [568 <./3_c_UMAP1.png>] [569 <./4_a_UMAP2.png>] [570 <./4_b_spatplot.png>] [571 <./5_a_spatdimplot1.png>] [572 <./6_a_metaheatm ap1.png>] [573 <./6_b_violinplot.png>] [574 <./6_c_metaheatmap.png>] [575 <./6_ d_violinplot.png>] [576 <./7_a_metaheatmap1.png>] [577 <./7_b_umap.png>] [578 <./7_c_spatplot1.png>] [579 <./8_a_umap.png>] [580 <./8_b_spatplot1.png>] [581 <./8_c_spatdimplot.png>] [582 <./8_d_umap.png>] [583 <./8_e_spatPlot.png>] [584 <./8_f_spatdimgeneplot.png>] [585] [586 <./osmfish_image_demo.png>] [587] [588 <./2_a_original_clusters.png> <./2_b_original_regions.png>] [589 <./ 2_c_clusterID.png>] [590 <./2_d_total_expr_limits.png>] [591 <./3_a_screeplot2. png> <./3_b_PCA_reduction.png>] [592 <./3_c_UMAP_reduction.png>] [593 <./3_d_UM AP_reduction_expression.png>] [594 <./3_e_tSNE_reduction2.png>] [595 <./4_a_UMA P_hclust.png>] [596 <./4_b_UMAP_kmeans.png>] [597 <./4_c_UMAP_leiden.png>] [598 <./4_d_UMAP_leiden_merged.png>] [599 <./4_e_heatmap.png> <./4_f_dendro.png >] [600 <./5_a_covis_leiden2.png>] [601 <./5_b_covis_leiden_m.png>] [602 <./5_c _covis_leiden_merged_selected.png>] [603 <./5_d_total_expr.png>] [604 <./6_a_vi olinplot2.png>] [605 <./6_b_metaheatmap.png>] [606 <./6_e_metaheatmap_all_genes .png>] [607 <./6_f_metaheatmap_all_genes_names.png>] [608 <./7_a_annotation_lei den_merged_detailed.png>] [609 <./7_b_annotation_leiden_merged_coarse.png>] [610 <./7_c_clusterHeatmap_det_cell_types.png>] [611 <./7_d_heatamp_det_cell_ty pes.png>] [612 <./7_e_metaheatmap.png>] [613 <./8_grid_det_cell_types.png>] [614 <./9_spatial_network_k10.png> <./10_a_spatial_genes_km2.png>] [615 <./11_a _barplot_cell_cell_enrichment.png>] [616 <./11_b_heatmap_cell_cell_enrichment.p ng>] [617 <./11_c_network_cell_cell_enrichment.png>] [618 <./11_d_cell_cell_enr ichment_selected.png>] [619] [620 <./2_a_spatPlot.png>] [621 <./2_b_spatPlot_co lumn.png>] [622 <./2_c_spatPlot_row.png>] [623 <./2_d_spatPlot_hist.png>] [624 <./2_e_spatPlot_hist2.png>] [625] [626 <./3_a_signPCA.png> <./3_b_PCAplot. png>] [627 <./3_c_UMAP.png>] [628 <./4_a_UMAP.png>] [629 <./4_b_UMAP.png>] [630 <./4_c_spatplot.png>] [631 <./4_d_spatPlot.png>] [632 <./5_a_spatdimplot.p ng>] [633 <./5_b_spatdimplot.png>] [634 <./5_c_spatdimplot.png>] [635 <./6_a_me taheatmap.png>] [636 <./6_b_violinplot_gini.png>] [637 <./7_a_metaheatmap.png>] [638 <./7_b_metaheatmap.png>] [639 <./7_c_spatplot.png>] [640 <./7_d_spatplot.p ng>] [641 <./7_e_spatplot.png>] [642 <./7_f_spatplot.png> <./7_g_spatplot_1.png >] [643 <./7_g_spatplot_2.png>] [644 <./7_h_spatdimplot.png>] [645 <./7_i_spatp lot.png>] [646 <./7_j_umap.png>] [647 <./8_a_spatplot.png>] [648 <./12_a_barplo t.png>] [649 <./12_b_network.png>] [650 <./12_c_proxspatplot.png>] [651 <./xx_a _metaheatmap.png>] [652 <./xx_b_spatplot.png>] [653 <./xx_c_spatgeneplot.png>] [654 <./xx_d_umap.png>] [655 <./xx_e_dimGeneplot.png>] [656 <./xx_f_spatplot.pn g>] [657 <./xx_g_spatGeneplot.png>] [658 <./xx_h_umap.png>] [659 <./xx_i_dimGen eplot.png>] [660 <./mouse_SS_cortex_and_subventricular.png> <./merFISH_hypoth_i mage_summary.png>] [661 <./starmap_cortex_image_summary.png> <./visium_brain_im age_summary.png>] [662 <./visium_kidney_image_summary.png> <./CODEX_spleen_imag e_summary.png>] [663 <./osmFISH_SS_cortex_image_summary.png> <./human_cyCIF_PDA C_image_summary.png>] [664] Chapter 7. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.41003 ...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.41003 ...097/ADuTNKaQJdScAAAAAElFTkSuQmCC}.svg}} and a Docker image will b... [665] [666 <./GitHub_Logo.png>] [667] [668 <./01_environments.png>] [669 <./01_ vm.png>] [670 <./02_docker.png> <./03_upload.png>] [671 <./03_view.png>] [672 <./03_googlecloud.png> <./03_url.png>] [673 <./03_cloud.png>] Overfull \hbox (11.18954pt too wide) in paragraph at lines 41389--41393 []\T1/qtm/m/n/10 Step 1 [] [674 <./04_share.png>] Overfull \hbox (11.18954pt too wide) in paragraph at lines 41407--41411 []\T1/qtm/m/n/10 Step 2 [] [675 <./Binder_1.png> <./Binder_2.png> <./Binder_3.png>] [676 <./Binder_4.png>] Chapter 8. [677] Underfull \hbox (badness 10000) in paragraph at lines 41555--41557 []\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 [678] [679] [680] Chapter 9. [681] [682] [683] [684] [685] [686] Chapter 10. [687 <./Index_Fig_A.png>] [688 <./Index_Fig_B.png> <./Index_Fig_C.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.42017 ...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.42017 ...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.42017 ...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.42017 ...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.42019 ...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.42019 ...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.42019 ...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.42019 ...en{}orientation (100 μm and 400 μ m). \sphinxstylestrong{Fig... (./giottoteam-giotto.ind) [689 <./Index_Fig_D.png>] (./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 (693 pages, 348619753 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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[130] [131] [132] Underfull \hbox (badness 5133) in paragraph at lines 14819--14822 []|\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 14854--14857 []|\T1/qtm/m/n/10 Cal-cu-late Gene Sig-na-ture En-rich-ment Score With [133] [134] [135] Overfull \hbox (63.84494pt too wide) in paragraph at lines 15269--15274 [] [136] Underfull \hbox (badness 10000) in paragraph at lines 15425--15425 []\T1/qhv/m/n/10 Ar-gu- Overfull \hbox (14.1738pt too wide) in paragraph at lines 15425--15425 []\T1/txtt/m/n/10 dimensions| Overfull \hbox (45.6737pt too wide) in paragraph at lines 15425--15425 []\T1/txtt/m/n/10 maximum_distance| Overfull \hbox (8.92381pt too wide) in paragraph at lines 15425--15425 []\T1/txtt/m/n/10 minimum_k| Overfull \hbox (35.17374pt too wide) in paragraph at lines 15425--15425 []\T1/txtt/m/n/10 return_gobject| [137] Underfull \hbox (badness 10000) in paragraph at lines 15599--15599 []\T1/qhv/m/n/10 Ar-gu- Overfull \hbox (12.00728pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 dimensions| Overfull \hbox (43.50719pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 maximum_distance| Overfull \hbox (6.7573pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 minimum_k| Overfull \hbox (6.7573pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 show_plot| Overfull \hbox (17.25726pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 return_plot| Overfull \hbox (6.7573pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 save_plot| Overfull \hbox (12.06726pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 save_param| Overfull \hbox (48.75717pt too wide) in paragraph at lines 15599--15599 []\T1/txtt/m/n/10 default_save_name| [138] [139] [140] Overfull \hbox (21.71956pt too wide) in paragraph at lines 15921--15921 []\T1/txtt/m/n/10 delaunay_method| Overfull \hbox (74.2194pt too wide) in paragraph at lines 15921--15921 []\T1/txtt/m/n/10 maximum_distance_delaunay| Overfull \hbox (47.96948pt too wide) in paragraph at lines 15921--15921 []\T1/txtt/m/n/10 maximum_distance_knn| Overfull \hbox (16.46957pt too wide) in paragraph at lines 15921--15921 []\T1/txtt/m/n/10 return_gobject| Underfull \hbox (badness 10000) in paragraph at lines 15928--15932 []\T1/qtm/m/n/10 For De-lau-nay [141] [142] [143] [144] [145] Overfull \hbox (4.68492pt too wide) in paragraph at lines 16465--16468 [] [146] Overfull \hbox (3.79921pt too wide) in paragraph at lines 16720--16720 []\T1/txtt/m/n/10 spatial_network_name| [147] [148] Overfull \hbox (3.79921pt too wide) in paragraph at lines 17024--17024 []\T1/txtt/m/n/10 spatial_network_name| [149] [150] [151] Underfull \hbox (badness 10000) in paragraph at lines 17413--17419 [] [152] [153] [154] [155] Overfull \hbox (16.52835pt too wide) in paragraph at lines 17867--17867 []\T1/txtt/m/n/10 expression_values| [156] Overfull \hbox (11.91016pt too wide) in paragraph at lines 17985--17985 []\T1/txtt/m/n/10 expression_values| [157] [158] [159] [160] [161] Underfull \hbox (badness 10000) in paragraph at lines 18674--18677 []\T1/qtm/m/n/10 fully con- [162] Overfull \hbox (0.73529pt too wide) in paragraph at lines 18853--18853 []\T1/txtt/m/n/10 show_cluster_annot| [163] [164] [165] Overfull \hbox (4.64677pt too wide) in paragraph at lines 19335--19335 []\T1/txtt/m/n/10 spatial_network_name| Overfull \hbox (4.64677pt too wide) in paragraph at lines 19335--19335 []\T1/txtt/m/n/10 dim_reduction_to_use| [166] [167] [168] [169] [170] [171] Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 20012--20012 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 di m-Plot2D\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#dim-plot2d>\TS1/qtm/m/n/10 `\T1/qtm /m/n/10 _ list(^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pgobject^^Q)), Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 \T1/qtm/m/n/10 list(^^Pgiotto ob-ject^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^ Pgroup_by^^Q)), list(^^Pcreate mul-ti-ple plots based on Underfull \hbox (badness 6944) in paragraph at lines 20012--20012 \T1/qtm/m/n/10 cell an-no-ta-tion col-umn^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(lis t(^^Pgroup_by_subset^^Q)), list(^^Psubset the group_by Underfull \hbox (badness 10000) in paragraph at lines 20012--20012 \T1/qtm/m/n/10 fac-tor col-umn^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pdim_re duction_to_use^^Q)), list(^^Pdimension re-duc-tion to [172] [173] Underfull \hbox (badness 10000) in paragraph at lines 20134--20134 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20134--20134 \T1/qhv/m/n/10 gu- Overfull \hbox (2.27292pt too wide) in paragraph at lines 20134--20134 \T1/qhv/m/n/10 ment| Overfull \hbox (16.79282pt too wide) in paragraph at lines 20134--20134 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.54265pt too wide) in paragraph at lines 20134--20134 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.29266pt too wide) in paragraph at lines 20134--20134 []\T1/txtt/m/n/10 default_save_name| [174] Underfull \vbox (badness 10000) detected at line 20147 Overfull \vbox (28.11948pt too high) detected at line 20147 [175] [176] Underfull \hbox (badness 10000) in paragraph at lines 20255--20255 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20255--20255 \T1/qhv/m/n/10 gu- Overfull \hbox (2.27292pt too wide) in paragraph at lines 20255--20255 \T1/qhv/m/n/10 ment| Overfull \hbox (16.79282pt too wide) in paragraph at lines 20255--20255 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.54265pt too wide) in paragraph at lines 20255--20255 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.29266pt too wide) in paragraph at lines 20255--20255 []\T1/txtt/m/n/10 default_save_name| Underfull \vbox (badness 10000) detected at line 20268 Overfull \vbox (12.41795pt too high) detected at line 20268 [177] [178] Underfull \hbox (badness 10000) in paragraph at lines 20376--20376 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20376--20376 \T1/qhv/m/n/10 gu- Overfull \hbox (2.27292pt too wide) in paragraph at lines 20376--20376 \T1/qhv/m/n/10 ment| Overfull \hbox (16.79282pt too wide) in paragraph at lines 20376--20376 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.54265pt too wide) in paragraph at lines 20376--20376 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.29266pt too wide) in paragraph at lines 20376--20376 []\T1/txtt/m/n/10 default_save_name| Overfull \vbox (43.47412pt too high) detected at line 20389 [179] [180] Underfull \hbox (badness 10000) in paragraph at lines 20476--20476 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20476--20476 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 20476--20476 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 20476--20476 []\T1/txtt/m/n/10 .. Overfull \vbox (49.87111pt too high) detected at line 20487 [181] [182] Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 20576--20576 \T1/qhv/m/n/10 ment| Overfull \hbox (21.75356pt too wide) in paragraph at lines 20576--20576 []\T1/txtt/m/n/10 gobject| Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 di m-CellPlot2D\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#dim-cellplot2d>\TS1/qtm/m/n/10 `\T1/qtm/m/n/10 _ list(^^Pn^^Q, ^^Q ^^P, Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 \T1/qtm/m/n/10 list(list(list(^^Pdim_reduction_to_use^^Q)), list(^^Pdimension r e-duc-tion to use^^Q)), ^^Pn^^Q, ^^Q ^^P, Underfull \hbox (badness 10000) in paragraph at lines 20576--20576 \T1/qtm/m/n/10 list(list(list(^^Pdim_reduction_name^^Q)), list(^^Pdimension re- duc-tion name^^Q)), ^^Pn^^Q, ^^Q ^^P, Overfull \vbox (30.67413pt too high) detected at line 20589 [183] [184] Underfull \hbox (badness 10000) in paragraph at lines 20739--20739 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 20739--20739 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 20739--20739 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 20739--20739 []\T1/txtt/m/n/10 .. Overfull \vbox (26.13272pt too high) detected at line 20754 [185] [186] [187] [188] Overfull \hbox (13.46457pt too wide) in alignment at lines 20877--20887 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 20887--20900 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 20900--20904 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 20904--20906 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 20906--21047 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 21047--21187 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 21187--21327 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 21327--21328 [] [] [189] [190] Underfull \hbox (badness 10000) in paragraph at lines 21409--21409 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 21409--21409 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 21409--21409 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 21409--21409 []\T1/txtt/m/n/10 .. Overfull \vbox (22.51646pt too high) detected at line 21421 [191] [192] [193] [194] Underfull \hbox (badness 10000) in paragraph at lines 21824--21824 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 21824--21824 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 21824--21824 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 21824--21824 []\T1/txtt/m/n/10 .. Underfull \vbox (badness 2600) detected at line 21838 Overfull \vbox (23.21797pt too high) detected at line 21838 [195] [196] Underfull \hbox (badness 10000) in paragraph at lines 21967--21967 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 21967--21967 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 21967--21967 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 21967--21967 []\T1/txtt/m/n/10 .. Overfull \vbox (48.93274pt too high) detected at line 21986 [197] Underfull \vbox (badness 10000) detected at line 21986 Overfull \vbox (47.67393pt too high) detected at line 21986 [198] [199] [200] [201] Underfull \hbox (badness 10000) in paragraph at lines 22541--22541 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 22541--22541 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 22541--22541 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 22541--22541 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 22541--22541 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 sp at-Dim-Gene-Plot2D\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#spat-dim-gene-plot2d>\TS1 /qtm/m/n/10 `\T1/qtm/m/n/10 _ list(^^Pn^^Q, ^^Q ^^P, Underfull \hbox (badness 6961) in paragraph at lines 22541--22541 \T1/qtm/m/n/10 list(list(list(^^Pgobject^^Q)), list(^^Pgiotto ob-ject^^Q)), ^^P n^^Q, ^^Q ^^P, list(list(list(^^Pshow_image^^Q)), list(^^Pshow a [202] Underfull \vbox (badness 10000) detected at line 22556 Overfull \vbox (39.52196pt too high) detected at line 22556 [203] [204] Underfull \hbox (badness 10000) in paragraph at lines 22640--22640 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 22640--22640 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 22640--22640 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 22640--22640 []\T1/txtt/m/n/10 .. Underfull \vbox (badness 10000) detected at line 22659 Overfull \vbox (26.9195pt too high) detected at line 22659 [205] [206] Underfull \hbox (badness 10000) in paragraph at lines 22676--22679 []\TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 spat-Dim-CellPlot2D\TS1/qtm/m/it/10 ` \T1/ qtm/m/n/10 <#spat-dim- [207] Underfull \vbox (badness 10000) detected at line 22798 Underfull \vbox (badness 10000) detected at line 22798 [208] Overfull \hbox (39.7145pt too wide) in alignment at lines 22804--22814 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 22814--22827 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 22827--22831 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 22831--22833 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 22833--22974 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 22974--23114 [] [] Overfull \hbox (39.7145pt too wide) in alignment at lines 23114--23254 [] [] [209] Overfull \hbox (39.7145pt too wide) in alignment at lines 23254--23381 [] [] [210] [211] [212] Overfull \hbox (13.46457pt too wide) in alignment at lines 23546--23556 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23556--23569 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23569--23573 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23573--23575 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23575--23716 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23716--23856 [] [] Overfull \hbox (13.46457pt too wide) in alignment at lines 23856--23934 [] [] [213] [214] [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 24352--24352 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 24352--24352 \T1/qhv/m/n/10 gu- Overfull \hbox (2.51184pt too wide) in paragraph at lines 24352--24352 \T1/qhv/m/n/10 ment| Overfull \hbox (17.03174pt too wide) in paragraph at lines 24352--24352 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.78157pt too wide) in paragraph at lines 24352--24352 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.53159pt too wide) in paragraph at lines 24352--24352 []\T1/txtt/m/n/10 default_save_name| Underfull \hbox (badness 6792) in paragraph at lines 24352--24352 \T1/qtm/m/n/10 list(^^Pdimension to use on x-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list( list(list(^^Pdim2_to_use^^Q)), list(^^Pdimension to Underfull \hbox (badness 7186) in paragraph at lines 24352--24352 \T1/qtm/m/n/10 use on y-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pdim3_to_ use^^Q)), list(^^Pdimension to use on z-axis^^Q)), Underfull \hbox (badness 7168) in paragraph at lines 24352--24352 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pshow_NN_network^^Q)), list(^ ^Pshow un-der-ly-ing NN net-work^^Q)), ^^Pn^^Q, ^^Q ^^P, [217] [218] Underfull \hbox (badness 10000) in paragraph at lines 24464--24464 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 24464--24464 \T1/qhv/m/n/10 gu- Overfull \hbox (2.51184pt too wide) in paragraph at lines 24464--24464 \T1/qhv/m/n/10 ment| Overfull \hbox (17.03174pt too wide) in paragraph at lines 24464--24464 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.78157pt too wide) in paragraph at lines 24464--24464 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.53159pt too wide) in paragraph at lines 24464--24464 []\T1/txtt/m/n/10 default_save_name| Underfull \hbox (badness 6792) in paragraph at lines 24464--24464 \T1/qtm/m/n/10 list(^^Pdimension to use on x-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list( list(list(^^Pdim2_to_use^^Q)), list(^^Pdimension to Underfull \hbox (badness 7186) in paragraph at lines 24464--24464 \T1/qtm/m/n/10 use on y-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pdim3_to_ use^^Q)), list(^^Pdimension to use on z-axis^^Q)), Underfull \hbox (badness 7168) in paragraph at lines 24464--24464 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pshow_NN_network^^Q)), list(^ ^Pshow un-der-ly-ing NN net-work^^Q)), ^^Pn^^Q, ^^Q ^^P, Overfull \vbox (23.71645pt too high) detected at line 24473 [219] Underfull \hbox (badness 10000) in paragraph at lines 24576--24576 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 24576--24576 \T1/qhv/m/n/10 gu- Overfull \hbox (2.51184pt too wide) in paragraph at lines 24576--24576 \T1/qhv/m/n/10 ment| Overfull \hbox (17.03174pt too wide) in paragraph at lines 24576--24576 []\T1/txtt/m/n/10 gobject| Overfull \hbox (74.78157pt too wide) in paragraph at lines 24576--24576 []\T1/txtt/m/n/10 dim_reduction_name| Overfull \hbox (69.53159pt too wide) in paragraph at lines 24576--24576 []\T1/txtt/m/n/10 default_save_name| Underfull \hbox (badness 6792) in paragraph at lines 24576--24576 \T1/qtm/m/n/10 list(^^Pdimension to use on x-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list( list(list(^^Pdim2_to_use^^Q)), list(^^Pdimension to Underfull \hbox (badness 7186) in paragraph at lines 24576--24576 \T1/qtm/m/n/10 use on y-axis^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pdim3_to_ use^^Q)), list(^^Pdimension to use on z-axis^^Q)), Underfull \hbox (badness 7168) in paragraph at lines 24576--24576 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pshow_NN_network^^Q)), list(^ ^Pshow un-der-ly-ing NN net-work^^Q)), ^^Pn^^Q, ^^Q ^^P, [220] [221] Underfull \hbox (badness 5741) in paragraph at lines 24602--24615 \T1/qtm/m/it/10 Plot\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#dim-plot>\TS1/qtm/m/n/1 0 `\T1/qtm/m/n/10 _ , \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 plot-PCA_2D\TS1/qtm/m/ it/10 ` \T1/qtm/m/n/10 <#plot-pca2d>\TS1/qtm/m/n/10 `\T1/qtm/m/n/10 _ , \TS1/qt m/m/it/10 ``\T1/qtm/m/it/10 plot-PCA\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#plot-pc a>\TS1/qtm/m/n/10 `\T1/qtm/m/n/10 _ , \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 plotTS NE_2D\TS1/qtm/m/it/10 ` [222] [223] [224] [225] [226] [227] [228] Underfull \hbox (badness 10000) in paragraph at lines 25784--25788 []\TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 spat-Dim-Gene-Plot2D\TS1/qtm/m/it/10 ` \T1 /qtm/m/n/10 <#spat-dim-gene- [229] Underfull \hbox (badness 10000) in paragraph at lines 26003--26003 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 26003--26003 \T1/qhv/m/n/10 gu- Overfull \hbox (12.7307pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 gobject| Overfull \hbox (80.9805pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 spatial_network_name| Overfull \hbox (49.48059pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 thickness_unit| Overfull \hbox (54.73058pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 slice_thickness| Overfull \hbox (128.23036pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 cell_distance_estimate_method| Overfull \hbox (38.98062pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 extend_ratio| Overfull \hbox (7.48071pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 method| Overfull \hbox (17.98068pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 equation| Overfull \hbox (7.48071pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 point1| Overfull \hbox (7.48071pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 point2| Overfull \hbox (7.48071pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 point3| Overfull \hbox (28.48065pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 normVector| Overfull \hbox (38.98062pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 planeVector1| Overfull \hbox (38.98062pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 planeVector2| Overfull \hbox (33.73064pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 mesh_grid_n| Overfull \hbox (49.48059pt too wide) in paragraph at lines 26003--26003 []\T1/txtt/m/n/10 return_gobject| [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] Overfull \hbox (5.90836pt too wide) in paragraph at lines 27512--27512 []\T1/txtt/m/n/10 edge_weight_range_depletion| Overfull \hbox (11.15834pt too wide) in paragraph at lines 27512--27512 []\T1/txtt/m/n/10 edge_weight_range_enrichment| Overfull \hbox (0.65837pt too wide) in paragraph at lines 27512--27512 []\T1/txtt/m/n/10 only_show_enrichment_edges| [242] Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 27582--27582 \T1/qhv/m/n/10 ment| Overfull \hbox (21.75356pt too wide) in paragraph at lines 27582--27582 []\T1/txtt/m/n/10 gobject| Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 ce ll-Prox-im-i-tyS-pat-Plot2D\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#cell-prox-im-i-t ys-pat-plot2d>\TS1/qtm/m/n/10 `\T1/qtm/m/n/10 _ list(^^Pn^^Q, Underfull \hbox (badness 10000) in paragraph at lines 27582--27582 \T1/qtm/m/n/10 ^^Q ^^P, list(list(list(^^Pinteraction_name^^Q)), list(^^Pcell-c ell in-ter-ac-tion name^^Q)), ^^Pn^^Q, ^^Q ^^P, Overfull \vbox (6.67413pt too high) detected at line 27592 [243] Underfull \hbox (badness 7362) in paragraph at lines 27609--27611 []\TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 cell-Prox-im-i-tyS-pat-Plot2D\TS1/qtm/m/it /10 ` \T1/qtm/m/n/10 <#cell-prox-im-i-tys-pat-plot2d>\TS1/qtm/m/n/10 `\T1/qtm/m /n/10 _ and \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 cell-Prox-im-i-tyS-pat-Plot3D\TS 1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#cell-prox-im-i-tys-pat- [244] [245] [246] [247] [248] [249] Underfull \hbox (badness 10000) in paragraph at lines 28563--28563 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 28563--28563 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 28563--28563 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 28563--28563 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 28563--28563 \T1/qtm/m/n/10 ^^Q ^^P, list(list(list(^^Pgobject^^Q)), list(^^Pgiotto ob-ject^ ^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pexpression_values^^Q)), [250] Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 28626--28626 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 fi nd-ICG\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#find-icg>\TS1/qtm/m/n/10 `\T1/qtm/m/n /10 _ list(^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pgobject^^Q)), Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 \T1/qtm/m/n/10 list(^^Pgiotto ob-ject^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^ Pexpression_values^^Q)), list(^^Pexpression val-ues to Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 \T1/qtm/m/n/10 use^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pselected_genes^^Q) ), list(^^Psubset of se-lected genes (op-tional)^^Q)), Underfull \hbox (badness 7397) in paragraph at lines 28626--28626 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pcluster_column^^Q)), list(^^ Pname of col-umn to use for cell types^^Q)), ^^Pn^^Q, Underfull \hbox (badness 10000) in paragraph at lines 28626--28626 \T1/qtm/m/n/10 ^^Q ^^P, list(list(list(^^Pspatial_network_name^^Q)), list(^^Pna me of spa-tial net-work to use^^Q)), ^^Pn^^Q, ^^Q ^^P, [251] Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 28686--28686 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 fi nd-ICG\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#find-icg>\TS1/qtm/m/n/10 `\T1/qtm/m/n /10 _ list(^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pgobject^^Q)), Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 \T1/qtm/m/n/10 list(^^Pgiotto ob-ject^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^ Pexpression_values^^Q)), list(^^Pexpression val-ues to Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 \T1/qtm/m/n/10 use^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pselected_genes^^Q) ), list(^^Psubset of se-lected genes (op-tional)^^Q)), Underfull \hbox (badness 7397) in paragraph at lines 28686--28686 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pcluster_column^^Q)), list(^^ Pname of col-umn to use for cell types^^Q)), ^^Pn^^Q, Underfull \hbox (badness 10000) in paragraph at lines 28686--28686 \T1/qtm/m/n/10 ^^Q ^^P, list(list(list(^^Pspatial_network_name^^Q)), list(^^Pna me of spa-tial net-work to use^^Q)), ^^Pn^^Q, ^^Q ^^P, [252] [253] [254] Underfull \hbox (badness 10000) in paragraph at lines 29018--29018 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 29018--29018 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 29018--29018 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 29018--29018 []\T1/txtt/m/n/10 .. [255] [256] [257] Underfull \hbox (badness 10000) in paragraph at lines 29381--29381 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 29381--29381 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 29381--29381 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 29381--29381 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 29381--29381 \T1/qtm/m/n/10 list(^^Pn^^Q, ^^Q ^^P, list(list(list(^^PcpgObject^^Q)), list(^^ PICG (in-ter-ac-tion changed gene) score ob-ject^^Q)), Underfull \hbox (badness 5388) in paragraph at lines 29381--29381 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pselected_ints^^Q)), list(^^P subset of se-lected cell-cell in-ter-ac-tions (op-tional)^^Q)), Underfull \hbox (badness 6493) in paragraph at lines 29381--29381 \T1/qtm/m/n/10 ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pselected_genes^^Q)), list(^^ Psubset of se-lected genes (op-tional)^^Q)), ^^Pn^^Q, ^^Q ^^P, [258] Underfull \hbox (badness 10000) in paragraph at lines 29440--29440 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 29440--29440 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 29440--29440 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 29440--29440 []\T1/txtt/m/n/10 .. [259] [260] [261] [262] [263] [264] [265] [266] [267] Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 30525--30525 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 []\T1/txtt/m/n/10 .. Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 []\T1/qtm/m/n/10 Ar-gu-ments passed on to \TS1/qtm/m/it/10 ``\T1/qtm/m/it/10 pl ot-Com-bineIn-ter-ac-tion-Changed-Genes\TS1/qtm/m/it/10 ` \T1/qtm/m/n/10 <#plot -com-binein-ter-ac- Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 \T1/qtm/m/n/10 tion-changed-genes>\TS1/qtm/m/n/10 `\T1/qtm/m/n/10 _ list(^^Pn^^ Q, ^^Q ^^P, list(list(list(^^Pgobject^^Q)), list(^^Pgiotto ob-ject^^Q)), ^^Pn^^ Q, ^^Q ^^P, Underfull \hbox (badness 10000) in paragraph at lines 30525--30525 \T1/qtm/m/n/10 list(list(list(^^PcombCpgObject^^Q)), list(^^PICGscores, out-put from com-bineIn-ter-ac-tion-Changed- Underfull \hbox (badness 7925) in paragraph at lines 30525--30525 \T1/qtm/m/n/10 Genes()^^Q)), ^^Pn^^Q, ^^Q ^^P, list(list(list(^^Pselected_inter actions^^Q)), list(^^Pinteractions to show^^Q)), ^^Pn^^Q, ^^Q Underfull \hbox (badness 5388) in paragraph at lines 30525--30525 \T1/qtm/m/n/10 ^^P, list(list(list(^^Pselected_gene_to_gene^^Q)), list(^^Ppairw ise gene com-bi-na-tions to show^^Q)), ^^Pn^^Q, ^^Q ^^P, [268] Underfull \hbox (badness 10000) in paragraph at lines 30585--30585 []\T1/qhv/m/n/10 Ar- Underfull \hbox (badness 10000) in paragraph at lines 30585--30585 \T1/qhv/m/n/10 gu- Overfull \hbox (7.23366pt too wide) in paragraph at lines 30585--30585 \T1/qhv/m/n/10 ment| Underfull \hbox (badness 10000) in paragraph at lines 30585--30585 []\T1/txtt/m/n/10 .. [269] [270] [271] [272] [273] Overfull \hbox (9.49155pt too wide) in paragraph at lines 31336--31336 []\T1/txtt/m/n/10 selected_cell_LR| Overfull \hbox (19.99152pt too wide) in paragraph at lines 31336--31336 []\T1/txtt/m/n/10 show_cell_LR_names| Overfull \hbox (14.74153pt too wide) in paragraph at lines 31336--31336 []\T1/txtt/m/n/10 default_save_name| [274] Overfull \hbox (1.10202pt too wide) in paragraph at lines 31496--31496 []\T1/txtt/m/n/10 default_save_name| [275] [276] [277] [278] [279] [280] Chapter 4. [281] [282] [283] [284] [285] [286] [287] [288] Chapter 5. [289] [290 <./1_whole_brain.png>] [291 <./2_whole_brain_clus4.png> <./3_whole_b rain_clus4_noOther.png>] [292 <./4_whole_brain_by_group_leiden_1.png> <./4_whol e_brain_by_group_leiden_2.png>] [293 <./5_whole_brain_HMRF.png> <./5_whole_brai n_by_group_HMRF_1.png>] [294 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_ brain.png>] [295 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>] [296] [297] [298] [299 <./original_clusters_black.png>] Overfull \vbox (3.38263pt too high) detected at line 33290 [300 <./ppt_store_multiple_analyses2.png> <./1_loess_hvg.png>] [301 <./1_group_ hvg.png> <./1_hvg_table.png>] [302 <./2_loess_pca.png> <./2_group_pca.png>] [303 <./3_loess_umap.png>] [304 <./3_group_umap.png>] [305 <./4_spatial_network .png> <./4_large_network.png>] [306 <./4_distance_network.png>] [307 <./5_large _network_genes.png> <./5_large_distance_network_genes.png>] [308] [309] [310] [311 <./2_a_spatplot1.png>] [312 <./2_b_spatplot_image.png>] [313 <./2_c_ spatplot_image_adjusted_1.png>] [314 <./2_c_spatplot_image_adjusted_2.png>] [315 <./2_c_spatplot_image_adjusted_3.png>] [316 <./2_c_spatplot_image_adjusted _4.png>] [317 <./2_c_spatplot_image_adjusted_5.png>] [318 <./2_c_spatplot_image _adjusted_6.png>] [319 <./2_c_spatplot_image_adjusted_7.png>] [320 <./2_c_spatp lot_image_adjusted_8.png>] [321 <./2_c_spatplot_image_adjusted_9.png>] [322 <./ 2_c_spatplot_image_adjusted_10.png>] [323 <./2_c_spatplot_image_adjusted_11.png > <./2_d_original_plot.png>] [324 <./3_a_background_colors.png>] [325 <./3_b_bl ack_background.png>] [326 <./3_c_white_background.png>] [327 <./4_a_external_im age_negated.png>] [328 <./4_b_external_image_charcoal.png>] [329 <./5_1_a_spati al_locations.png>] [330 <./5_1_b_nr_genes.png>] [331 <./5_1_c_nr_genes_black_bg .png>] [332 <./5_1_d_nr_genes_charc_bg.png>] [333 <./5_2_a_UMAP_reduction.png>] [334 <./5_3_a_UMAP_leiden.png>] [335 <./5_4_a_covis_leiden_black.png>] [336 <./ 5_4_b_covis_leiden_negated.png>] [337 <./5_4_c_covis_leiden_charc.png>] [338 <./5_5_a_spatgene_charc_vor.png>] [339 <./5_5_b_spatgene_charc_vor.png>] [340 <./5_6_a_subset_spatgene_charc.png>] [341 <./5_6_b_subset_spatgene_charc_v or.png>] [342 <./1_voronoi.png>] [343 <./2_voronoi_no_others.png>] [344 <./3_vo ronoi_no_others_black_border.png>] [345 <./4_voronoi_spat_dim.png>] [346 <./5_v oronoi_neighbors.png> <./6_original_points.png>] [347 <./7_voronoi_genes.png> < ./8_voronoi_gene_black_bg.png>] [348] Chapter 6. [349] [350] [351] [352 <./3.1_HVGplot.png> <./3.2_screePlot.png>] [353 <./3.3_j ackstrawPlot.png>] [354 <./3.4_PCA.png>] [355 <./3.5_tSNE.png>] [356 <./4.1_UMA P.png>] [357 <./4.2_showClusterHeatmap.png> <./4.3_showClusterDendrogram.png>] [358 <./5.1_violinPlot.png>] [359 <./5.2_plotMetaDataHeatmap.png>] [360 <./6.1_ spatDimPlot2D.png>] [361] [362 <./9.1_spatGenePlot2D.png>] [363 <./10.1_heatmSp atialCorGenes.png>] Overfull \vbox (2.14355pt too high) detected at line 34809 [364 <./10.2_spatCellPlot2D.png>] [365 <./12.1_cellProximityBarplot.png>] [366 <./12.2_spatCellPlot2D.png>] [367 <./12.3_cellProximityHeatmap.png>] [368 <./12.4_cellProximityNetwork.png>] [369 <./12.5_cellProximitySpatPlot2D.pn g>] [370 <./12.6_spatPlot2D.png>] [371 <./13.1_plotCellProximityGenes.png>] Overfull \vbox (2.14355pt too high) detected at line 34991 [372 <./13.2_plotICG.png>] [373 <./14.1_plotCCcomHeatmap.png>] [374 <./14.2_plo tCCcomDotplot.png>] [375 <./14.3_plotRankSpatvsExpr.png>] [376 <./14.4_plotReco very.png>] [377] [378] [379] [380] [381] [382] [383] [384] [385] [386 <./2_a_fi ltergenes.png>] [387 <./2_b_filtercells.png>] [388 <./2_c_filtercombos.png>] [389 <./3_a_screeplot1.png> <./3_b_PCA.png>] [390] [391 <./3_d_UMAP_3D.png> <./ 3_e_TSNE.png>] [392 <./4_a_UMAP1.png>] [393 <./4_b_UMAP_3D.png> <./4_c_spatdimp lot.png>] [394 <./4_e_clusterheatmap.png>] [395 <./4_f_clusterdendrogram.png>] [396 <./5_a_violinplot.png>] [397 <./5_b_metaheatmap.png>] [398 <./6_a_spatdimp lot.png>] [399 <./6_b_dimgeneplot.png> <./6_c_spatgeneplot.png>] [400 <./7_a_sp atplot.png>] [401 <./8_a_plotStatDelaunayNetwork.png>] [402 <./8_b_spatplot.png >] [403 <./8_c_spatplot.png>] [404 <./9_a_spatgeneplot.png>] [405 <./9_b_spatge neplot.png>] [406 <./10_a_heatmspatcor.png>] [407 <./10_b_rankcorgroup.png>] Overfull \vbox (2.14355pt too high) detected at line 36133 [408 <./10_c_spatcellplot.png>] [409 <./12_a_barplot1.png>] [410 <./12_b_heatma p.png>] [411 <./12_c_network.png>] [412 <./12_d_network.png>] [413 <./12_e_spat plot.png>] [414 <./12_e_cellproximity.png>] Underfull \vbox (badness 1158) detected at line 36266 [415 <./13_a_insert.png> <./13_b_crossplot.png>] [416 <./13_c_cross.png>] [417 <./13_d_crossgeneplot.png> <./13_e_crossgene.png>] [418] [419 <./mini_seqF ISH.png>] [420 <./mini_STARmap.png>] [421 <./mini_visium.png>] [422 <./cortex_s vz_location_fields.png>] [423] [424] [425 <./2_a_spatplot.png>] [426 <./3_a_HVG plot2.png>] [427 <./3_b_screeplot2.png> <./3_c_PCA_reduction2.png>] [428 <./3_d _UMAP_reduction2.png>] [429 <./3_e_tSNE_reduction3.png>] [430 <./4_a_UMAP_leide n3.png>] [431 <./4_b_UMAP_leiden_subcluster.png>] [432 <./4_c_heatmap.png>] [433 <./4_d_dendro.png>] [434 <./5_a_covis_leiden3.png>] [435 <./5_b_covis_leid en_selected.png>] Underfull \vbox (badness 10000) detected at line 36683 [436 <./6_a_violinplot_gini2.png>] Underfull \vbox (badness 1320) detected at line 36724 [437 <./6_b_metaheatmap_gini2.png>] [438] [439 <./7_a_violinplot.png>] [440 <./ 7_b_covisualization.png>] [441 <./7_c_heatmap.png>] [442 <./7_d_heatmap_selecte d.png>] [443 <./8_a_grid.png>] [444 <./9_a_spatial_network_delaunay.png> <./9_b _spatial_network_k3.png>] [445 <./9_c_spatial_network_k10.png> <./9_d_spatial_n etwork_dist.png>] [446 <./10_a_spatialgenes_km.png>] Underfull \vbox (badness 10000) detected at line 36909 [447 <./10_b_spatialcoexpression_heatmap.png> <./10_c_spatialcoexpression_rank. png>] [448 <./10_d_spatialcoexpression_metagenes.png>] [449 <./11_HMRF_2_k9_b.2 8.pdf>] [450 <./12_a_barplot_cell_cell_enrichment.png>] [451 <./12_b_heatmap_ce ll_cell_enrichment.png>] [452 <./12_c_network_cell_cell_enrichment.png>] [453 <./12_d_network_cell_cell_enrichment_self.pdf>] [454 <./12_e_cell_cell_enr ichment_selected.png>] [455 <./12_f_cell_cell_enrichment_sel_vs_not.png>] [456 <./13_a_CPG_dotplot.png>] Overfull \vbox (2.14355pt too high) detected at line 37134 [457 <./13_b_ICG_barplot.png>] Underfull \vbox (badness 1194) detected at line 37153 [458 <./14_a_communication_dotplot.png>] [459 <./14_b_expr_vs_spatial_expressio n_rank.png>] [460 <./14_c_spatial_recovery_expression_rank.png>] [461 <./14_d_e xpr_vs_spatial_activity.png>] [462 <./14_e_spatial_recovery_activity.png>] [463] [464] [465 <./2_a_distribution_genes1.png> <./2_b_distribution_cells1.png >] [466 <./2_c_filter_combos.png>] [467 <./2_d_spatial_locations2D.png> <./2_e_ spatial_locations3D.png>] [468 <./3_a_screeplot.png>] [469 <./3_b_UMAP_reductio n.png>] [470 <./4_a_UMAP_leiden.png>] [471 <./5_b_leiden_2D.png>] [472 <./6_a_v iolinplot1.png>] [473 <./6_b_clusterheatmap_markers.png>] [474 <./7_a_clusterhe atmap_markers.png>] [475 <./7_b_clusterheatmap_markers_celltypes.png>] [476 <./ 7_c_umap_cell_types.png> <./7_d_spatPlot_cell_types_all.png>] [477 <./7_e_spatP lot2D_cell_types_all.png>] [478 <./7_f_spatPlot_cell_types_excit.png> <./7_g_sp atPlot2D_cell_types_excit.png>] [479 <./7_h_spatPlot_cell_types_inhib.png>] [480 <./7_i_spatPlot2D_cell_types_inhib.png>] [481 <./7_j_spatPlot_cell_types_O DandAstro.png> <./7_k_spatPlot2D_cell_types_ODandAstro.png>] [482 <./7_l_spatPl ot_cell_types_other.png>] [483 <./7_m_spatPlot2D_cell_types_other.png>] [484] [485 <./2_a_distribution_genes.png>] [486 <./2_b_distribution_cells.png>] [487 <./2_c_distribution_filters.png>] [488 <./2_d_spatial_locations.png> <./3_ a_hvg.png>] [489 <./3_b_signPCs.png> <./3_c_umap.png>] [490 <./4_leiden_0.2.png >] [491 <./5_a_covisualize_leiden_0.2.png>] [492 <./6_a_violinplot.png> <./6_b_ heatmap_leiden_0.2.png>] [493 <./7_a_general_cell_type.png>] [494 <./7_b_dim_pl ot_detailed_cell_type.png> <./7_c_cluster_annotation_heatmap.png>] [495 <./8_ce ll_type_co_vis.png> <./9_a_Rorb_dim_plot.png>] [496 <./9_b_Pcp4_dim_plot.png> < ./9_c_Pcp4_spat_plot.png>] [497 <./9_d_Cux2_dim_plot.png> <./9_e_detailed_cell_ types.png>] [498 <./9_f_Cux2_spat_plot.png> <./9_g_Ctgf_dim_plot.png>] [499 <./ 9_h_Ctgf_spat_plot.png> <./10_a_insert_cross_section_cell_types.png>] [500 <./1 0_b_insert_cross_section_Slc17a7.png> <./10_c_cross_section_spat.png>] [501 <./ 10_d_cross_section_spat3d.png> <./10_e_Slc17a7_cross_section_gene3d.png>] [502] [503 <./visium_technology.png> <./visium_brain_image_summary1.png>] [504 <./2_a_spatplot_image.png>] [505 <./2_b_spatplot_image_adjusted.png>] [506 <./2_c_in_tissue.png>] [507 <./2_d_spatial_locations1.png>] [508 <./2_e_nr _genes.png>] [509 <./3_a_HVGplot.png>] [510 <./3_b_screeplot.png> <./3_c_PCA_re duction.png>] [511 <./3_d_UMAP_reduction.png>] [512 <./3_e_tSNE_reduction.png>] [513 <./4_a_UMAP_leiden1.png>] [514 <./5_a_covis_leiden.png>] [515 <./5_b_nr_ge nes.png>] [516 <./5_c_DEG_subset.png>] Underfull \vbox (badness 10000) detected at line 38334 [517 <./6_a_violinplot_gini.png>] [518 <./6_b_metaheatmap_gini.png> <./6_c_gini _umap.png>] [519] [520 <./6_d_violinplot_scran.png>] [521 <./6_e_metaheatmap_sc ran.png> <./6_f_scran_umap.png>] Overfull \vbox (3.018pt too high) detected at line 38455 [522] [523 <./7_a_metaheatmap2.png>] [524 <./7_b_spatcellplot.png>] [525 <./7_c _spatcellplot.png>] [526 <./7_d_spatDimCellPlot.png>] [527 <./8_grid.png>] [528 <./9_a_knn_network.png>] [529 <./10_a_spatial_genes_km.png>] [530 <./10_b_ spatial_genes_rank.png>] [531 <./10_c_heatmap.png>] [532 <./10_d_spatPlot2D_HMR F.png>] [533] [534 <./mouse_kidney_highres.png>] [535 <./2_a_spatplot_image1.pn g>] [536 <./2_b_spatplot_image_adjusted1.png>] [537 <./2_c_in_tissue1.png>] [538 <./2_d_spatial_locations2.png>] [539 <./2_e_nr_genes1.png>] [540 <./3_a_HV Gplot1.png>] [541 <./3_b_screeplot1.png> <./3_c_PCA_reduction1.png>] [542 <./3_ d_UMAP_reduction1.png>] [543 <./3_e_tSNE_reduction1.png>] [544 <./4_a_UMAP_leid en2.png>] [545 <./5_a_covis_leiden1.png>] [546 <./5_b_nr_genes1.png>] Underfull \vbox (badness 10000) detected at line 38923 [547 <./6_a_violinplot_gini1.png>] [548 <./6_b_metaheatmap_gini1.png> <./6_c_gi ni_umap1.png>] [549] [550 <./6_d_violinplot_scran1.png>] [551 <./6_e_metaheatma p_scran1.png> <./6_f_scran_umap1.png>] [552 <./8_grid1.png>] [553 <./9_a_delaun ay_network.png>] [554 <./9_b_delaunay_network.png>] [555 <./10_a_spatial_genes_ km1.png>] [556 <./10_b_spatial_genes_rank1.png>] [557 <./10_d_Napsa_correlated_ genes.png>] Underfull \vbox (badness 10000) detected at line 39119 [558 <./10_e_heatmap_correlated_genes.png> <./10_f_rank_correlated_groups.png>] [559 <./10_g_spat_enrichment_score_plots.png> <./10_h_spat_enrichment_score_plo ts_genes.png>] [560] [561] [562] Overfull \vbox (6.31403pt too high) detected at line 39374 [563] [564] [565 <./2_a_spatPlot1.png>] [566 <./2_b_spatPlot.png>] [567 <./3_a_ spatPlot.png> <./3_b_PCA1.png>] [568 <./3_c_UMAP1.png>] [569 <./4_a_UMAP2.png>] [570 <./4_b_spatplot.png>] [571 <./5_a_spatdimplot1.png>] [572 <./6_a_metaheatm ap1.png>] [573 <./6_b_violinplot.png>] [574 <./6_c_metaheatmap.png>] [575 <./6_ d_violinplot.png>] [576 <./7_a_metaheatmap1.png>] [577 <./7_b_umap.png>] [578 <./7_c_spatplot1.png>] [579 <./8_a_umap.png>] [580 <./8_b_spatplot1.png>] [581 <./8_c_spatdimplot.png>] [582 <./8_d_umap.png>] [583 <./8_e_spatPlot.png>] [584 <./8_f_spatdimgeneplot.png>] [585] [586 <./osmfish_image_demo.png>] [587] [588 <./2_a_original_clusters.png> <./2_b_original_regions.png>] [589 <./ 2_c_clusterID.png>] [590 <./2_d_total_expr_limits.png>] [591 <./3_a_screeplot2. png> <./3_b_PCA_reduction.png>] [592 <./3_c_UMAP_reduction.png>] [593 <./3_d_UM AP_reduction_expression.png>] [594 <./3_e_tSNE_reduction2.png>] [595 <./4_a_UMA P_hclust.png>] [596 <./4_b_UMAP_kmeans.png>] [597 <./4_c_UMAP_leiden.png>] [598 <./4_d_UMAP_leiden_merged.png>] [599 <./4_e_heatmap.png> <./4_f_dendro.png >] [600 <./5_a_covis_leiden2.png>] [601 <./5_b_covis_leiden_m.png>] [602 <./5_c _covis_leiden_merged_selected.png>] [603 <./5_d_total_expr.png>] [604 <./6_a_vi olinplot2.png>] [605 <./6_b_metaheatmap.png>] [606 <./6_e_metaheatmap_all_genes .png>] [607 <./6_f_metaheatmap_all_genes_names.png>] [608 <./7_a_annotation_lei den_merged_detailed.png>] [609 <./7_b_annotation_leiden_merged_coarse.png>] [610 <./7_c_clusterHeatmap_det_cell_types.png>] [611 <./7_d_heatamp_det_cell_ty pes.png>] [612 <./7_e_metaheatmap.png>] [613 <./8_grid_det_cell_types.png>] [614 <./9_spatial_network_k10.png> <./10_a_spatial_genes_km2.png>] [615 <./11_a _barplot_cell_cell_enrichment.png>] [616 <./11_b_heatmap_cell_cell_enrichment.p ng>] [617 <./11_c_network_cell_cell_enrichment.png>] [618 <./11_d_cell_cell_enr ichment_selected.png>] [619] [620 <./2_a_spatPlot.png>] [621 <./2_b_spatPlot_co lumn.png>] [622 <./2_c_spatPlot_row.png>] [623 <./2_d_spatPlot_hist.png>] [624 <./2_e_spatPlot_hist2.png>] [625] [626 <./3_a_signPCA.png> <./3_b_PCAplot. png>] [627 <./3_c_UMAP.png>] [628 <./4_a_UMAP.png>] [629 <./4_b_UMAP.png>] [630 <./4_c_spatplot.png>] [631 <./4_d_spatPlot.png>] [632 <./5_a_spatdimplot.p ng>] [633 <./5_b_spatdimplot.png>] [634 <./5_c_spatdimplot.png>] [635 <./6_a_me taheatmap.png>] [636 <./6_b_violinplot_gini.png>] [637 <./7_a_metaheatmap.png>] [638 <./7_b_metaheatmap.png>] [639 <./7_c_spatplot.png>] [640 <./7_d_spatplot.p ng>] [641 <./7_e_spatplot.png>] [642 <./7_f_spatplot.png> <./7_g_spatplot_1.png >] [643 <./7_g_spatplot_2.png>] [644 <./7_h_spatdimplot.png>] [645 <./7_i_spatp lot.png>] [646 <./7_j_umap.png>] [647 <./8_a_spatplot.png>] [648 <./12_a_barplo t.png>] [649 <./12_b_network.png>] [650 <./12_c_proxspatplot.png>] [651 <./xx_a _metaheatmap.png>] [652 <./xx_b_spatplot.png>] [653 <./xx_c_spatgeneplot.png>] [654 <./xx_d_umap.png>] [655 <./xx_e_dimGeneplot.png>] [656 <./xx_f_spatplot.pn g>] [657 <./xx_g_spatGeneplot.png>] [658 <./xx_h_umap.png>] [659 <./xx_i_dimGen eplot.png>] [660 <./mouse_SS_cortex_and_subventricular.png> <./merFISH_hypoth_i mage_summary.png>] [661 <./starmap_cortex_image_summary.png> <./visium_brain_im age_summary.png>] [662 <./visium_kidney_image_summary.png> <./CODEX_spleen_imag e_summary.png>] [663 <./osmFISH_SS_cortex_image_summary.png> <./human_cyCIF_PDA C_image_summary.png>] [664] Chapter 7. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.41003 ...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.41003 ...097/ADuTNKaQJdScAAAAAElFTkSuQmCC}.svg}} and a Docker image will b... [665] [666 <./GitHub_Logo.png>] [667] [668 <./01_environments.png>] [669 <./01_ vm.png>] [670 <./02_docker.png> <./03_upload.png>] [671 <./03_view.png>] [672 <./03_googlecloud.png> <./03_url.png>] [673 <./03_cloud.png>] Overfull \hbox (11.18954pt too wide) in paragraph at lines 41389--41393 []\T1/qtm/m/n/10 Step 1 [] [674 <./04_share.png>] Overfull \hbox (11.18954pt too wide) in paragraph at lines 41407--41411 []\T1/qtm/m/n/10 Step 2 [] [675 <./Binder_1.png> <./Binder_2.png> <./Binder_3.png>] [676 <./Binder_4.png>] Chapter 8. [677] Underfull \hbox (badness 10000) in paragraph at lines 41555--41557 []\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 [678] [679] [680] Chapter 9. [681] [682] [683] [684] [685] [686] Chapter 10. [687 <./Index_Fig_A.png>] [688 <./Index_Fig_B.png> <./Index_Fig_C.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.42017 ...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.42017 ...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.42017 ...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.42017 ...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.42019 ...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.42019 ...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.42019 ...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.42019 ...en{}orientation (100 μm and 400 μ m). \sphinxstylestrong{Fig... (./giottoteam-giotto.ind) [689 <./Index_Fig_D.png>] (./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 (693 pages, 348619753 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: 2022-09-08T18:52:42.288437Z, end-time: 2022-09-08T18:52:42.370726Z, 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: 2022-09-08T18:52:42.592782Z, end-time: 2022-09-08T18:53:24.842030Z, duration: 42, 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 462 source files that are out of date updating environment: [new config] 462 added, 0 changed, 0 removed reading sources... 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[100%] trygiotto /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:95: WARNING: unknown document: installGiottoEnvironmentFunction /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:97: WARNING: unknown document: removeGiottoEnvironment /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:99: WARNING: unknown document: checkGiottoEnvironment /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:230: WARNING: unknown document: /subsections/md_rst/get10XMatrix /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:232: WARNING: unknown document: /subsections/md_rst/get10XMatrix_h5 /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/documentation.rst:409: WARNING: unknown document: /subsections/md_rst/findMarkersFunction /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/master/docs/source/gettingstarted.rst:224: WARNING: undefined label: creategiottoinstructions /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