Read the Docs build information
Build id: 991153
Project: giottoteam-giotto
Version: suite
Commit: d61ed4805424f8059d3035b54eec70afc17c0ff5
Date: 2022-06-24T20:03:02.031237Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-06-24T20:03:05.437588Z, end-time: 2022-06-24T20:04:15.020585Z, duration: 69, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/sistia01/Giotto.git .
Cloning into '.'...

[rtd-command-info] start-time: 2022-06-24T20:04:15.298997Z, end-time: 2022-06-24T20:04:30.367423Z, duration: 15, exit-code: 0
git checkout --force origin/suite
Note: switching to 'origin/suite'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at d61ed480 moved m2r2 to requirements.txt

[rtd-command-info] start-time: 2022-06-24T20:04:30.562259Z, end-time: 2022-06-24T20:04:30.657967Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-06-24T20:04:40.069524Z, end-time: 2022-06-24T20:04:44.620515Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-06-24T20:04:44.810480Z, end-time: 2022-06-24T20:04:46.633018Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (22.1.2)
Collecting setuptools<58.3.0
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Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 62.6.0
    Uninstalling setuptools-62.6.0:
      Successfully uninstalled setuptools-62.6.0
Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2022-06-24T20:04:46.826385Z, end-time: 2022-06-24T20:04:55.202175Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2
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  Preparing metadata (setup.py): started
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Collecting docutils>=0.11
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Collecting requests>=2.5.0
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Collecting sphinxcontrib-serializinghtml>=1.1.5
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Collecting snowballstemmer>=1.1
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Collecting packaging
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Collecting sphinxcontrib-htmlhelp>=2.0.0
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Collecting babel>=1.3
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Collecting sphinxcontrib-qthelp
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Collecting imagesize
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Collecting Pygments>=2.0
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Collecting Jinja2>=2.3
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Collecting docutils>=0.11
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Collecting pytz>=2015.7
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Collecting zipp>=0.5
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Collecting charset-normalizer~=2.0.0
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Collecting urllib3<1.27,>=1.21.1
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Collecting pyparsing!=3.0.5,>=2.0.2
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23773 sha256=e3671d95d10607f13f2f9ef047fedcd7d09e403b4f7c2a2e8e8bd16ca4d34521
  Stored in directory: /tmp/pip-ephem-wheel-cache-m999ylfz/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=805d788367c2254902ce1c7a0e4ab546e26c51496235dcf8bd74f2c367e0f53f
  Stored in directory: /tmp/pip-ephem-wheel-cache-m999ylfz/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: snowballstemmer, pytz, mock, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, requests, packaging, Jinja2, importlib-metadata, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.6.15 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 importlib-metadata-4.11.4 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.8 recommonmark-0.5.0 requests-2.28.0 snowballstemmer-2.2.0 sphinx-5.0.2 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.2.0 urllib3-1.26.9 zipp-3.8.0

[rtd-command-info] start-time: 2022-06-24T20:04:55.542445Z, end-time: 2022-06-24T20:05:08.682094Z, duration: 13, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting bluepy
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Collecting sphinx==3.4.3
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Collecting readthedocs-sphinx-search==0.1.0
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Collecting m2r2
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Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (2.28.0)
Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (1.0.2)
Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/envs/suite/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 3)) (0.17.1)
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[rtd-command-info] start-time: 2022-06-24T20:05:10.624481Z, end-time: 2022-06-24T20:05:10.695807Z, duration: 0, exit-code: 0
cat docs/source/conf.py
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
#import os
#import sys
#sys.path.insert(0, os.path.abspath('.'))


# -- Project information -----------------------------------------------------

project = 'Giotto'
copyright = '2021, Ruben Dries, Qian Zhu, Huipeng Li, Rui Dong, Guo-Cheng Yuan'
author = 'Developed by Ruben Dries, Qian Zhu, Huipeng Li, Rui Dong, Guo-Cheng Yuan.'

# The full version, including alpha/beta/rc tags
release = '1.0'


# -- General configuration ---------------------------------------------------

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
#import os 
#import sys 
#from sphinx.application import Sphinx

import sphinx_rtd_theme

extensions = [
'sphinx.ext.autosectionlabel', 
'sphinx.ext.autodoc',
'sphinx_rtd_theme',
'sphinx_design',
'sphinx_copybutton',
'sphinx_toolbox', 
'sphinx_toolbox.shields',
'sphinx_toolbox.github',
#'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': "suite",
    'version_slug': "suite",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ],
    'downloads': [ 
    ("pdf", "//giottoteam-giotto.readthedocs-hosted.com/_/downloads/en/suite/pdf/"),
    ("html", "//giottoteam-giotto.readthedocs-hosted.com/_/downloads/en/suite/htmlzip/"),
    ("epub", "//giottoteam-giotto.readthedocs-hosted.com/_/downloads/en/suite/epub/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'giottoteam-giotto',
    'name': u'Giotto',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://giottoteam-giotto.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/source/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'sistia01',
    'proxied_api_host': '/_',
    'github_repo': 'Giotto',
    'github_version': 'suite',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'suite',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'suite',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'd61ed480',
}

# 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/991153/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2022-06-24T20:05:10.987714Z, end-time: 2022-06-24T20:06:05.269081Z, duration: 54, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v3.4.3
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no content permitted.

unicode:: 0xA0
   :trim:


  ``binSpectMultiMatrix``
  ===========================

  binSpectMultiMatrix

  Description
  -----------

  binSpect for a single spatial network and a provided expression matrix

  Usage
  -----

  .. code-block:: r

    binSpectMultiMatrix(
      expression_matrix,
      spatial_networks,
      bin_method = c("kmeans", "rank"),
      subset_feats = NULL,
      kmeans_algo = c("kmeans", "kmeans_arma", "kmeans_arma_subset"),
      nstart = 3,
      iter_max = 10,
      extreme_nr = 50,
      sample_nr = 50,
      percentage_rank = c(10, 30),
      do_fisher_test = TRUE,
      adjust_method = "fdr",
      calc_hub = FALSE,
      hub_min_int = 3,
      get_av_expr = TRUE,
      get_high_expr = TRUE,
      implementation = c("data.table", "simple", "matrix"),
      group_size = "automatic",
      do_parallel = TRUE,
      cores = NA,
      verbose = T,
      knn_params = NULL,
      set.seed = NULL,
      summarize = c("adj.p.value", "p.value")
    )

  Arguments
  ---------

  .. list-table::
    :header-rows: 1

    * - Argument
      - Description
    * - ``expression_matrix``
      - expression matrix
    * - ``spatial_networks``
      - list of spatial networks in data.table format
    * - ``bin_method``
      - method to binarize gene expression
    * - ``subset_feats``
      - only select a subset of features to test
    * - ``kmeans_algo``
      - kmeans algorithm to use (kmeans, kmeans_arma, kmeans_arma_subset)
    * - ``nstart``
      - kmeans: nstart parameter
    * - ``iter_max``
      - kmeans: iter.max parameter
    * - ``extreme_nr``
      - number of top and bottom cells (see details)
    * - ``sample_nr``
      - total number of cells to sample (see details)
    * - ``percentage_rank``
      - vector of percentages of top cells for binarization
    * - ``do_fisher_test``
      - perform fisher test
    * - ``adjust_method``
      - p-value adjusted method to use (see `\ ``p.adjust`` <#p.adjust>`_ )
    * - ``calc_hub``
      - calculate the number of hub cells
    * - ``hub_min_int``
      - minimum number of cell-cell interactions for a hub cell
    * - ``get_av_expr``
      - calculate the average expression per gene of the high expressing cells
    * - ``get_high_expr``
      - calculate the number of high expressing cells  per gene
    * - ``implementation``
      - enrichment implementation (data.table, simple, matrix)
    * - ``group_size``
      - number of genes to process together with data.table implementation (default = automatic)
    * - ``do_parallel``
      - run calculations in parallel with mclapply
    * - ``cores``
      - number of cores to use if do_parallel = TRUE
    * - ``verbose``
      - be verbose
    * - ``knn_params``
      - list of parameters to create spatial kNN network
    * - ``set.seed``
      - set a seed before kmeans binarization
    * - ``summarize``
      - summarize the p-values or adjusted p-values


  Value
  -----

  data.table with results
<rst_prolog>:3: WARNING: Substitution definition "nbsp" empty or invalid.

.. |nbsp| unicode:: 0xA0
   :trim:


  ``binSpectMultiMatrix``
  ===========================

  binSpectMultiMatrix

  Description
  -----------

  binSpect for a single spatial network and a provided expression matrix

  Usage
  -----

  .. code-block:: r

    binSpectMultiMatrix(
      expression_matrix,
      spatial_networks,
      bin_method = c("kmeans", "rank"),
      subset_feats = NULL,
      kmeans_algo = c("kmeans", "kmeans_arma", "kmeans_arma_subset"),
      nstart = 3,
      iter_max = 10,
      extreme_nr = 50,
      sample_nr = 50,
      percentage_rank = c(10, 30),
      do_fisher_test = TRUE,
      adjust_method = "fdr",
      calc_hub = FALSE,
      hub_min_int = 3,
      get_av_expr = TRUE,
      get_high_expr = TRUE,
      implementation = c("data.table", "simple", "matrix"),
      group_size = "automatic",
      do_parallel = TRUE,
      cores = NA,
      verbose = T,
      knn_params = NULL,
      set.seed = NULL,
      summarize = c("adj.p.value", "p.value")
    )

  Arguments
  ---------

  .. list-table::
    :header-rows: 1

    * - Argument
      - Description
    * - ``expression_matrix``
      - expression matrix
    * - ``spatial_networks``
      - list of spatial networks in data.table format
    * - ``bin_method``
      - method to binarize gene expression
    * - ``subset_feats``
      - only select a subset of features to test
    * - ``kmeans_algo``
      - kmeans algorithm to use (kmeans, kmeans_arma, kmeans_arma_subset)
    * - ``nstart``
      - kmeans: nstart parameter
    * - ``iter_max``
      - kmeans: iter.max parameter
    * - ``extreme_nr``
      - number of top and bottom cells (see details)
    * - ``sample_nr``
      - total number of cells to sample (see details)
    * - ``percentage_rank``
      - vector of percentages of top cells for binarization
    * - ``do_fisher_test``
      - perform fisher test
    * - ``adjust_method``
      - p-value adjusted method to use (see `\ ``p.adjust`` <#p.adjust>`_ )
    * - ``calc_hub``
      - calculate the number of hub cells
    * - ``hub_min_int``
      - minimum number of cell-cell interactions for a hub cell
    * - ``get_av_expr``
      - calculate the average expression per gene of the high expressing cells
    * - ``get_high_expr``
      - calculate the number of high expressing cells  per gene
    * - ``implementation``
      - enrichment implementation (data.table, simple, matrix)
    * - ``group_size``
      - number of genes to process together with data.table implementation (default = automatic)
    * - ``do_parallel``
      - run calculations in parallel with mclapply
    * - ``cores``
      - number of cores to use if do_parallel = TRUE
    * - ``verbose``
      - be verbose
    * - ``knn_params``
      - list of parameters to create spatial kNN network
    * - ``set.seed``
      - set a seed before kmeans binarization
    * - ``summarize``
      - summarize the p-values or adjusted p-values


  Value
  -----

  data.table with results
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writing output... [ 99%] subsections/trygiotto/binder
writing output... [ 99%] subsections/trygiotto/docker
writing output... [ 99%] subsections/trygiotto/terra
writing output... [ 99%] tipsandtricks
writing output... [100%] trygiotto

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no content permitted.

unicode:: 0xA0
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  ``binSpectMultiMatrix``
  ===========================

  binSpectMultiMatrix

  Description
  -----------

  binSpect for a single spatial network and a provided expression matrix

  Usage
  -----

  .. code-block:: r

    binSpectMultiMatrix(
      expression_matrix,
      spatial_networks,
      bin_method = c("kmeans", "rank"),
      subset_feats = NULL,
      kmeans_algo = c("kmeans", "kmeans_arma", "kmeans_arma_subset"),
      nstart = 3,
      iter_max = 10,
      extreme_nr = 50,
      sample_nr = 50,
      percentage_rank = c(10, 30),
      do_fisher_test = TRUE,
      adjust_method = "fdr",
      calc_hub = FALSE,
      hub_min_int = 3,
      get_av_expr = TRUE,
      get_high_expr = TRUE,
      implementation = c("data.table", "simple", "matrix"),
      group_size = "automatic",
      do_parallel = TRUE,
      cores = NA,
      verbose = T,
      knn_params = NULL,
      set.seed = NULL,
      summarize = c("adj.p.value", "p.value")
    )

  Arguments
  ---------

  .. list-table::
    :header-rows: 1

    * - Argument
      - Description
    * - ``expression_matrix``
      - expression matrix
    * - ``spatial_networks``
      - list of spatial networks in data.table format
    * - ``bin_method``
      - method to binarize gene expression
    * - ``subset_feats``
      - only select a subset of features to test
    * - ``kmeans_algo``
      - kmeans algorithm to use (kmeans, kmeans_arma, kmeans_arma_subset)
    * - ``nstart``
      - kmeans: nstart parameter
    * - ``iter_max``
      - kmeans: iter.max parameter
    * - ``extreme_nr``
      - number of top and bottom cells (see details)
    * - ``sample_nr``
      - total number of cells to sample (see details)
    * - ``percentage_rank``
      - vector of percentages of top cells for binarization
    * - ``do_fisher_test``
      - perform fisher test
    * - ``adjust_method``
      - p-value adjusted method to use (see `\ ``p.adjust`` <#p.adjust>`_ )
    * - ``calc_hub``
      - calculate the number of hub cells
    * - ``hub_min_int``
      - minimum number of cell-cell interactions for a hub cell
    * - ``get_av_expr``
      - calculate the average expression per gene of the high expressing cells
    * - ``get_high_expr``
      - calculate the number of high expressing cells  per gene
    * - ``implementation``
      - enrichment implementation (data.table, simple, matrix)
    * - ``group_size``
      - number of genes to process together with data.table implementation (default = automatic)
    * - ``do_parallel``
      - run calculations in parallel with mclapply
    * - ``cores``
      - number of cores to use if do_parallel = TRUE
    * - ``verbose``
      - be verbose
    * - ``knn_params``
      - list of parameters to create spatial kNN network
    * - ``set.seed``
      - set a seed before kmeans binarization
    * - ``summarize``
      - summarize the p-values or adjusted p-values


  Value
  -----

  data.table with results
<rst_prolog>:3: WARNING: Substitution definition "nbsp" empty or invalid.

.. |nbsp| unicode:: 0xA0
   :trim:


  ``binSpectMultiMatrix``
  ===========================

  binSpectMultiMatrix

  Description
  -----------

  binSpect for a single spatial network and a provided expression matrix

  Usage
  -----

  .. code-block:: r

    binSpectMultiMatrix(
      expression_matrix,
      spatial_networks,
      bin_method = c("kmeans", "rank"),
      subset_feats = NULL,
      kmeans_algo = c("kmeans", "kmeans_arma", "kmeans_arma_subset"),
      nstart = 3,
      iter_max = 10,
      extreme_nr = 50,
      sample_nr = 50,
      percentage_rank = c(10, 30),
      do_fisher_test = TRUE,
      adjust_method = "fdr",
      calc_hub = FALSE,
      hub_min_int = 3,
      get_av_expr = TRUE,
      get_high_expr = TRUE,
      implementation = c("data.table", "simple", "matrix"),
      group_size = "automatic",
      do_parallel = TRUE,
      cores = NA,
      verbose = T,
      knn_params = NULL,
      set.seed = NULL,
      summarize = c("adj.p.value", "p.value")
    )

  Arguments
  ---------

  .. list-table::
    :header-rows: 1

    * - Argument
      - Description
    * - ``expression_matrix``
      - expression matrix
    * - ``spatial_networks``
      - list of spatial networks in data.table format
    * - ``bin_method``
      - method to binarize gene expression
    * - ``subset_feats``
      - only select a subset of features to test
    * - ``kmeans_algo``
      - kmeans algorithm to use (kmeans, kmeans_arma, kmeans_arma_subset)
    * - ``nstart``
      - kmeans: nstart parameter
    * - ``iter_max``
      - kmeans: iter.max parameter
    * - ``extreme_nr``
      - number of top and bottom cells (see details)
    * - ``sample_nr``
      - total number of cells to sample (see details)
    * - ``percentage_rank``
      - vector of percentages of top cells for binarization
    * - ``do_fisher_test``
      - perform fisher test
    * - ``adjust_method``
      - p-value adjusted method to use (see `\ ``p.adjust`` <#p.adjust>`_ )
    * - ``calc_hub``
      - calculate the number of hub cells
    * - ``hub_min_int``
      - minimum number of cell-cell interactions for a hub cell
    * - ``get_av_expr``
      - calculate the average expression per gene of the high expressing cells
    * - ``get_high_expr``
      - calculate the number of high expressing cells  per gene
    * - ``implementation``
      - enrichment implementation (data.table, simple, matrix)
    * - ``group_size``
      - number of genes to process together with data.table implementation (default = automatic)
    * - ``do_parallel``
      - run calculations in parallel with mclapply
    * - ``cores``
      - number of cores to use if do_parallel = TRUE
    * - ``verbose``
      - be verbose
    * - ``knn_params``
      - list of parameters to create spatial kNN network
    * - ``set.seed``
      - set a seed before kmeans binarization
    * - ``summarize``
      - summarize the p-values or adjusted p-values


  Value
  -----

  data.table with results
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done
processing giotto.tex... index gettingstarted documentation subsections/md_rst/installGiottoEnvironment subsections/md_rst/removeGiottoEnvironment subsections/md_rst/checkGiottoEnvironment subsections/md_rst/createGiottoInstructions subsections/md_rst/readGiottoInstructions subsections/md_rst/showGiottoInstructions subsections/md_rst/changeGiottoInstructions subsections/md_rst/replaceGiottoInstructions subsections/md_rst/getSpatialDataset subsections/md_rst/readExprMatrix subsections/md_rst/get10Xmatrix subsections/md_rst/get10Xmatrix_h5 subsections/md_rst/stitchFieldCoordinates subsections/md_rst/stitchTileCoordinates subsections/md_rst/estimateImageBg subsections/md_rst/changeImageBg subsections/md_rst/createGiottoImage subsections/md_rst/addGiottoImage subsections/md_rst/addGiottoImageToSpatPlot subsections/md_rst/showGiottoImageNames subsections/md_rst/updateGiottoImage subsections/md_rst/plotGiottoImage subsections/md_rst/createGiottoObject subsections/md_rst/createGiottoVisiumObject subsections/md_rst/createGiottoObjectSubcellular subsections/md_rst/pDataDT subsections/md_rst/fDataDT subsections/md_rst/showProcessingSteps subsections/md_rst/calculateMetaTable subsections/md_rst/calculateMetaTableCells subsections/md_rst/combineMetadata subsections/md_rst/createMetagenes subsections/md_rst/findNetworkNeighbors subsections/md_rst/get_expression_values subsections/md_rst/set_expression_values subsections/md_rst/get_spatial_locations subsections/md_rst/set_spatial_locations subsections/md_rst/get_dimReduction subsections/md_rst/set_dimReduction subsections/md_rst/get_NearestNetwork subsections/md_rst/set_NearestNetwork subsections/md_rst/get_spatialNetwork subsections/md_rst/set_spatialNetwork subsections/md_rst/get_spatialGrid subsections/md_rst/set_spatialGrid subsections/md_rst/get_polygon_info subsections/md_rst/set_polygon_info subsections/md_rst/get_feature_info subsections/md_rst/set_feature_info subsections/md_rst/get_spatial_enrichment subsections/md_rst/set_spatial_enrichment subsections/md_rst/showGiottoExpression subsections/md_rst/showGiottoSpatLocs subsections/md_rst/showGiottoDimRed subsections/md_rst/showGiottoSpatNetworks subsections/md_rst/showGiottoSpatGrids subsections/md_rst/showGiottoSpatialInfo subsections/md_rst/showGiottoFeatInfo subsections/md_rst/showGiottoSpatEnrichments subsections/md_rst/filterGiotto subsections/md_rst/subsetGiotto subsections/md_rst/subsetGiottoLocs subsections/md_rst/joinGiottoObjects subsections/md_rst/normalizeGiotto subsections/md_rst/adjustGiottoMatrix subsections/md_rst/annotateGiotto subsections/md_rst/removeCellAnnotation subsections/md_rst/removeFeatAnnotation subsections/md_rst/addCellMetadata subsections/md_rst/addFeatMetadata subsections/md_rst/addFeatStatistics subsections/md_rst/addCellStatistics subsections/md_rst/addStatistics subsections/md_rst/addFeatsPerc subsections/md_rst/addCellIntMetadata subsections/md_rst/calculateHVG subsections/md_rst/signPCA subsections/md_rst/screePlot subsections/md_rst/jackstrawPlot subsections/md_rst/runPCA subsections/md_rst/runUMAP subsections/md_rst/runtSNE subsections/md_rst/createNearestNetwork subsections/md_rst/addNetworkLayout subsections/md_rst/clusterCells subsections/md_rst/doLeidenCluster subsections/md_rst/doLouvainCluster subsections/md_rst/doKmeans subsections/md_rst/doHclust subsections/md_rst/subClusterCells subsections/md_rst/doLeidenSubCluster subsections/md_rst/doLouvainSubCluster subsections/md_rst/getClusterSimilarity subsections/md_rst/mergeClusters subsections/md_rst/getDendrogramSplits subsections/md_rst/findMarkers subsections/md_rst/findMarkers_one_vs_all subsections/md_rst/findGiniMarkers subsections/md_rst/findGiniMarkers_one_vs_all subsections/md_rst/findScranMarkers subsections/md_rst/findScranMarkers_one_vs_all subsections/md_rst/findMastMarkers subsections/md_rst/findMastMarkers_one_vs_all subsections/md_rst/showClusterHeatmap subsections/md_rst/showClusterDendrogram subsections/md_rst/plotHeatmap subsections/md_rst/plotMetaDataHeatmap subsections/md_rst/plotMetaDataCellsHeatmap subsections/md_rst/violinPlot subsections/md_rst/makeSignMatrixPAGE subsections/md_rst/makeSignMatrixRank subsections/md_rst/runSpatialEnrich subsections/md_rst/runPAGEEnrich subsections/md_rst/runRankEnrich subsections/md_rst/runHyperGeometricEnrich subsections/md_rst/makeSignMatrixDWLSfromMatrix subsections/md_rst/makeSignMatrixDWLS subsections/md_rst/runSpatialDeconv subsections/md_rst/runDWLSDeconv subsections/md_rst/spatNetwDistributionsDistance subsections/md_rst/spatNetwDistributionsKneighbors subsections/md_rst/spatNetwDistributions subsections/md_rst/createSpatialDelaunayNetwork subsections/md_rst/plotStatDelaunayNetwork subsections/md_rst/createSpatialKNNnetwork subsections/md_rst/createSpatialNetwork subsections/md_rst/annotateSpatialNetwork subsections/md_rst/annotateSpatialGrid subsections/md_rst/createSpatialGrid subsections/md_rst/binSpectSingleMatrix subsections/md_rst/binSpectMultiMatrix subsections/md_rst/binSpectSingle subsections/md_rst/binSpectMulti subsections/md_rst/binSpect subsections/md_rst/spatialDE subsections/md_rst/spatialAEH subsections/md_rst/trendSceek subsections/md_rst/spark subsections/md_rst/simulateOneGenePatternGiottoObject subsections/md_rst/runPatternSimulation subsections/md_rst/clusterSpatialCorGenes subsections/md_rst/detectSpatialCorGenes subsections/md_rst/heatmSpatialCorGenes subsections/md_rst/showSpatialCorGenes subsections/md_rst/rankSpatialCorGroups subsections/md_rst/doHMRF subsections/md_rst/loadHMRF subsections/md_rst/viewHMRFresults subsections/md_rst/writeHMRFresults subsections/md_rst/addHMRF subsections/md_rst/viewHMRFresults2D subsections/md_rst/viewHMRFresults3D subsections/md_rst/dimPlot subsections/md_rst/plotUMAP subsections/md_rst/plotTSNE subsections/md_rst/plotPCA subsections/md_rst/dimGenePlot subsections/md_rst/dimCellPlot subsections/md_rst/spatPlot subsections/md_rst/spatCellPlot subsections/md_rst/spatDimPlot subsections/md_rst/spatDimCellPlot subsections/md_rst/dimPlot3D subsections/md_rst/plotUMAP_3D subsections/md_rst/plotTSNE_3D subsections/md_rst/plotPCA_3D subsections/md_rst/spatPlot3D subsections/md_rst/spatDimPlot3D subsections/md_rst/createCrossSection subsections/md_rst/crossSectionGenePlot subsections/md_rst/crossSectionPlot subsections/md_rst/crossSectionGenePlot3D subsections/md_rst/crossSectionPlot3D subsections/md_rst/insertCrossSectionSpatPlot3D subsections/md_rst/insertCrossSectionGenePlot3D subsections/md_rst/cellProximityEnrichment subsections/md_rst/cellProximityBarplot subsections/md_rst/cellProximityHeatmap subsections/md_rst/cellProximityNetwork subsections/md_rst/cellProximitySpatPlot subsections/md_rst/cellProximitySpatPlot3D subsections/md_rst/findInteractionChangedFeats subsections/md_rst/findICF subsections/md_rst/filterInteractionChangedFeats subsections/md_rst/filterICF subsections/md_rst/exprCellCellcom subsections/md_rst/spatCellCellcom subsections/md_rst/plotCCcomDotplot subsections/md_rst/plotRankSpatvsExpr subsections/md_rst/plotRecovery subsections/md_rst/seuratToGiotto development additionalinformation contribute subsections/tipsandtricks/NEWS subsections/detailed_workflow tipsandtricks subsections/tipsandtricks/giottoclass subsections/tipsandtricks/howtosubsetgiottoobject subsections/tipsandtricks/howtovisualizeandsaveplots subsections/tipsandtricks/testandstoremultipleanayses subsections/tipsandtricks/waystovisualizespatialdata subsections/tipsandtricks/workingwithimages subsections/tipsandtricks/visualizewithvoronoiplots datasets trygiotto subsections/trygiotto/binder subsections/trygiotto/docker subsections/trygiotto/terra errorsfaqsandtips github_issues 
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/home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/documentation.rst:140: WARNING: unknown document: /subsections/md_rst/getGiottoImage
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build succeeded, 453 warnings.

The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
(use `make latexpdf' here to do that automatically).
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[rtd-command-info] start-time: 2022-06-24T20:06:48.745484Z, end-time: 2022-06-24T20:06:48.809724Z, duration: 0, exit-code: 0
cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

[rtd-command-info] start-time: 2022-06-24T20:06:49.025604Z, end-time: 2022-06-24T20:09:25.355080Z, duration: 156, exit-code: 0
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Chapter 6.
[275] [276 <./1_whole_brain.png>] [277 <./2_whole_brain_clus4.png> <./3_whole_b
rain_clus4_noOther.png>] [278 <./4_whole_brain_by_group_leiden_1.png> <./4_whol
e_brain_by_group_leiden_2.png>] [279 <./5_whole_brain_HMRF.png> <./5_whole_brai
n_by_group_HMRF_1.png>] [280 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_
brain.png>] [281 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>]
[282] [283] [284 <./original_clusters_black.png>] [285 <./ppt_store_multiple_an
alyses2.png>] [286 <./1_loess_hvg.png> <./1_group_hvg.png>] [287 <./1_hvg_table
.png> <./2_loess_pca.png>] [288 <./2_group_pca.png> <./3_loess_umap.png>]
[289 <./3_group_umap.png>] [290 <./4_spatial_network.png> <./4_large_network.pn
g>] [291 <./4_distance_network.png>] [292 <./5_large_network_genes.png> <./5_la
rge_distance_network_genes.png>] [293] [294] [295] [296 <./2_a_spatplot1.png>]
[297 <./2_b_spatplot_image.png>] [298 <./2_c_spatplot_image_adjusted_1.png>]
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g>] [320 <./5_4_a_covis_leiden_black.png>] [321 <./5_4_b_covis_leiden_negated.p
ng>] [322 <./5_4_c_covis_leiden_charc.png>] [323 <./5_5_a_spatgene_charc_vor.pn
g>] [324 <./5_5_b_spatgene_charc_vor.png>] [325 <./5_6_a_subset_spatgene_charc.
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Chapter 8.

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Chapter 11.
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Chapter 12.
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Chapter 13.
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Chapter 14.

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Chapter 15.
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Chapter 1.
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Chapter 2.
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Chapter 3.
[261] [262] [263] [264] [265] [266]
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Chapter 4.
[269] [270]
Chapter 5.
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Chapter 6.
[275] [276 <./1_whole_brain.png>] [277 <./2_whole_brain_clus4.png> <./3_whole_b
rain_clus4_noOther.png>] [278 <./4_whole_brain_by_group_leiden_1.png> <./4_whol
e_brain_by_group_leiden_2.png>] [279 <./5_whole_brain_HMRF.png> <./5_whole_brai
n_by_group_HMRF_1.png>] [280 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_
brain.png>] [281 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>]
[282] [283] [284 <./original_clusters_black.png>] [285 <./ppt_store_multiple_an
alyses2.png>] [286 <./1_loess_hvg.png> <./1_group_hvg.png>] [287 <./1_hvg_table
.png> <./2_loess_pca.png>] [288 <./2_group_pca.png> <./3_loess_umap.png>]
[289 <./3_group_umap.png>] [290 <./4_spatial_network.png> <./4_large_network.pn
g>] [291 <./4_distance_network.png>] [292 <./5_large_network_genes.png> <./5_la
rge_distance_network_genes.png>] [293] [294] [295] [296 <./2_a_spatplot1.png>]
[297 <./2_b_spatplot_image.png>] [298 <./2_c_spatplot_image_adjusted_1.png>]
[299 <./2_c_spatplot_image_adjusted_2.png>] [300 <./2_c_spatplot_image_adjusted
_3.png>] [301 <./2_c_spatplot_image_adjusted_4.png>] [302 <./2_c_spatplot_image
_adjusted_5.png>] [303 <./2_c_spatplot_image_adjusted_6.png>] [304 <./2_c_spatp
lot_image_adjusted_7.png>] [305 <./2_c_spatplot_image_adjusted_8.png>] [306 <./
2_c_spatplot_image_adjusted_9.png>] [307 <./2_c_spatplot_image_adjusted_10.png>
] [308 <./2_c_spatplot_image_adjusted_11.png> <./2_d_original_plot.png>]
[309 <./3_a_background_colors.png>] [310 <./3_b_black_background.png>] [311 <./
3_c_white_background.png>] [312 <./4_a_external_image_negated.png>] [313 <./4_b
_external_image_charcoal.png>] [314 <./5_1_a_spatial_locations.png>] [315 <./5_
1_b_nr_genes.png>] [316 <./5_1_c_nr_genes_black_bg.png>] [317 <./5_1_d_nr_genes
_charc_bg.png>] [318 <./5_2_a_UMAP_reduction.png>] [319 <./5_3_a_UMAP_leiden.pn
g>] [320 <./5_4_a_covis_leiden_black.png>] [321 <./5_4_b_covis_leiden_negated.p
ng>] [322 <./5_4_c_covis_leiden_charc.png>] [323 <./5_5_a_spatgene_charc_vor.pn
g>] [324 <./5_5_b_spatgene_charc_vor.png>] [325 <./5_6_a_subset_spatgene_charc.
png>] [326 <./5_6_b_subset_spatgene_charc_vor.png>] [327 <./1_voronoi.png>]
[328 <./2_voronoi_no_others.png>] [329 <./3_voronoi_no_others_black_border.png>
] [330 <./4_voronoi_spat_dim.png>] [331 <./5_voronoi_neighbors.png> <./6_origin
al_points.png>] [332 <./7_voronoi_genes.png> <./8_voronoi_gene_black_bg.png>]
[333] [334]
Chapter 7.
[335 <./visium_kidney_image_summary.png>] [336 <./visium_brain_image_summary.pn
g>] [337 <./visium_prostate_summary.png> <./coming_soon_summary.png>] [338 <./c
ortex_image_summary.png> <./osmFISH_SS_cortex_image_summary.png>] [339]
[340]
Chapter 8.

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                                                   and a Docker image will b...


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                                                   and a Docker image will b...

[341] [342 <./GitHub_Logo.png>] [343] [344 <./01_environments.png>] [345 <./01_
vm.png>] [346 <./02_docker.png> <./03_upload.png>] [347 <./03_view.png>]
[348 <./03_googlecloud.png> <./03_url.png>] [349 <./03_cloud.png>]
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\T1/ptm/m/n/10 Below is an ex-am-ple of run-ning [][]\T1/ptm/m/it/10 Binder.[][
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[350 <./04_share.png>] [351 <./Binder_1.png> <./Binder_2.png>] [352 <./Binder_3
.png> <./Binder_4.png>]
Chapter 9.
[353] [354] [355] [356]
Chapter 10.
[357] [358] [359] [360] [361] [362]
Chapter 11.
[363 <./Giotto_to_suite.png>] [364]
Chapter 12.
[365 <./input_Compatibility.png> <./data_structure_Data_Structure.png>]
[366 <./analysis.png>]
Chapter 13.
[367] [368]
Chapter 14.

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[369] [370]
Chapter 15.
(./giottoteam-giotto.ind) [371] (./giottoteam-giotto.aux)

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Chapter 1.
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[7] [8] [9 <./icons_configuration.png>] [10 <./icons_giotto.png> <./icons_proce
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Chapter 2.
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Chapter 3.
[261] [262] [263] [264] [265] [266]
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Chapter 4.
[269] [270]
Chapter 5.
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Chapter 6.
[275] [276 <./1_whole_brain.png>] [277 <./2_whole_brain_clus4.png> <./3_whole_b
rain_clus4_noOther.png>] [278 <./4_whole_brain_by_group_leiden_1.png> <./4_whol
e_brain_by_group_leiden_2.png>] [279 <./5_whole_brain_HMRF.png> <./5_whole_brai
n_by_group_HMRF_1.png>] [280 <./5_whole_brain_by_group_HMRF_2.png> <./6_subset_
brain.png>] [281 <./6_subset_brain_nr_genes.png> <./7_DG_loc_subset.png>]
[282] [283] [284 <./original_clusters_black.png>] [285 <./ppt_store_multiple_an
alyses2.png>] [286 <./1_loess_hvg.png> <./1_group_hvg.png>] [287 <./1_hvg_table
.png> <./2_loess_pca.png>] [288 <./2_group_pca.png> <./3_loess_umap.png>]
[289 <./3_group_umap.png>] [290 <./4_spatial_network.png> <./4_large_network.pn
g>] [291 <./4_distance_network.png>] [292 <./5_large_network_genes.png> <./5_la
rge_distance_network_genes.png>] [293] [294] [295] [296 <./2_a_spatplot1.png>]
[297 <./2_b_spatplot_image.png>] [298 <./2_c_spatplot_image_adjusted_1.png>]
[299 <./2_c_spatplot_image_adjusted_2.png>] [300 <./2_c_spatplot_image_adjusted
_3.png>] [301 <./2_c_spatplot_image_adjusted_4.png>] [302 <./2_c_spatplot_image
_adjusted_5.png>] [303 <./2_c_spatplot_image_adjusted_6.png>] [304 <./2_c_spatp
lot_image_adjusted_7.png>] [305 <./2_c_spatplot_image_adjusted_8.png>] [306 <./
2_c_spatplot_image_adjusted_9.png>] [307 <./2_c_spatplot_image_adjusted_10.png>
] [308 <./2_c_spatplot_image_adjusted_11.png> <./2_d_original_plot.png>]
[309 <./3_a_background_colors.png>] [310 <./3_b_black_background.png>] [311 <./
3_c_white_background.png>] [312 <./4_a_external_image_negated.png>] [313 <./4_b
_external_image_charcoal.png>] [314 <./5_1_a_spatial_locations.png>] [315 <./5_
1_b_nr_genes.png>] [316 <./5_1_c_nr_genes_black_bg.png>] [317 <./5_1_d_nr_genes
_charc_bg.png>] [318 <./5_2_a_UMAP_reduction.png>] [319 <./5_3_a_UMAP_leiden.pn
g>] [320 <./5_4_a_covis_leiden_black.png>] [321 <./5_4_b_covis_leiden_negated.p
ng>] [322 <./5_4_c_covis_leiden_charc.png>] [323 <./5_5_a_spatgene_charc_vor.pn
g>] [324 <./5_5_b_spatgene_charc_vor.png>] [325 <./5_6_a_subset_spatgene_charc.
png>] [326 <./5_6_b_subset_spatgene_charc_vor.png>] [327 <./1_voronoi.png>]
[328 <./2_voronoi_no_others.png>] [329 <./3_voronoi_no_others_black_border.png>
] [330 <./4_voronoi_spat_dim.png>] [331 <./5_voronoi_neighbors.png> <./6_origin
al_points.png>] [332 <./7_voronoi_genes.png> <./8_voronoi_gene_black_bg.png>]
[333] [334]
Chapter 7.
[335 <./visium_kidney_image_summary.png>] [336 <./visium_brain_image_summary.pn
g>] [337 <./visium_prostate_summary.png> <./coming_soon_summary.png>] [338 <./c
ortex_image_summary.png> <./osmFISH_SS_cortex_image_summary.png>] [339]
[340]
Chapter 8.

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                                                   and a Docker image will b...


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                                                   and a Docker image will b...

[341] [342 <./GitHub_Logo.png>] [343] [344 <./01_environments.png>] [345 <./01_
vm.png>] [346 <./02_docker.png> <./03_upload.png>] [347 <./03_view.png>]
[348 <./03_googlecloud.png> <./03_url.png>] [349 <./03_cloud.png>]
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\T1/ptm/m/n/10 Below is an ex-am-ple of run-ning [][]\T1/ptm/m/it/10 Binder.[][
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[350 <./04_share.png>] [351 <./Binder_1.png> <./Binder_2.png>] [352 <./Binder_3
.png> <./Binder_4.png>]
Chapter 9.
[353] [354] [355] [356]
Chapter 10.
[357] [358] [359] [360] [361] [362]
Chapter 11.
[363 <./Giotto_to_suite.png>] [364]
Chapter 12.
[365 <./input_Compatibility.png> <./data_structure_Data_Structure.png>]
[366 <./analysis.png>]
Chapter 13.
[367] [368]
Chapter 14.

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[369] [370]
Chapter 15.
(./giottoteam-giotto.ind) [371] (./giottoteam-giotto.aux)

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[rtd-command-info] start-time: 2022-06-24T20:09:25.824801Z, end-time: 2022-06-24T20:09:25.919398Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/_build/latex/giottoteam-giotto.pdf /home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/artifacts/suite/sphinx_pdf/giottoteam-giotto.pdf


[rtd-command-info] start-time: 2022-06-24T20:09:26.123530Z, end-time: 2022-06-24T20:10:15.256627Z, duration: 49, exit-code: 0
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no content permitted.

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  ``binSpectMultiMatrix``
  ===========================

  binSpectMultiMatrix

  Description
  -----------

  binSpect for a single spatial network and a provided expression matrix

  Usage
  -----

  .. code-block:: r

    binSpectMultiMatrix(
      expression_matrix,
      spatial_networks,
      bin_method = c("kmeans", "rank"),
      subset_feats = NULL,
      kmeans_algo = c("kmeans", "kmeans_arma", "kmeans_arma_subset"),
      nstart = 3,
      iter_max = 10,
      extreme_nr = 50,
      sample_nr = 50,
      percentage_rank = c(10, 30),
      do_fisher_test = TRUE,
      adjust_method = "fdr",
      calc_hub = FALSE,
      hub_min_int = 3,
      get_av_expr = TRUE,
      get_high_expr = TRUE,
      implementation = c("data.table", "simple", "matrix"),
      group_size = "automatic",
      do_parallel = TRUE,
      cores = NA,
      verbose = T,
      knn_params = NULL,
      set.seed = NULL,
      summarize = c("adj.p.value", "p.value")
    )

  Arguments
  ---------

  .. list-table::
    :header-rows: 1

    * - Argument
      - Description
    * - ``expression_matrix``
      - expression matrix
    * - ``spatial_networks``
      - list of spatial networks in data.table format
    * - ``bin_method``
      - method to binarize gene expression
    * - ``subset_feats``
      - only select a subset of features to test
    * - ``kmeans_algo``
      - kmeans algorithm to use (kmeans, kmeans_arma, kmeans_arma_subset)
    * - ``nstart``
      - kmeans: nstart parameter
    * - ``iter_max``
      - kmeans: iter.max parameter
    * - ``extreme_nr``
      - number of top and bottom cells (see details)
    * - ``sample_nr``
      - total number of cells to sample (see details)
    * - ``percentage_rank``
      - vector of percentages of top cells for binarization
    * - ``do_fisher_test``
      - perform fisher test
    * - ``adjust_method``
      - p-value adjusted method to use (see `\ ``p.adjust`` <#p.adjust>`_ )
    * - ``calc_hub``
      - calculate the number of hub cells
    * - ``hub_min_int``
      - minimum number of cell-cell interactions for a hub cell
    * - ``get_av_expr``
      - calculate the average expression per gene of the high expressing cells
    * - ``get_high_expr``
      - calculate the number of high expressing cells  per gene
    * - ``implementation``
      - enrichment implementation (data.table, simple, matrix)
    * - ``group_size``
      - number of genes to process together with data.table implementation (default = automatic)
    * - ``do_parallel``
      - run calculations in parallel with mclapply
    * - ``cores``
      - number of cores to use if do_parallel = TRUE
    * - ``verbose``
      - be verbose
    * - ``knn_params``
      - list of parameters to create spatial kNN network
    * - ``set.seed``
      - set a seed before kmeans binarization
    * - ``summarize``
      - summarize the p-values or adjusted p-values


  Value
  -----

  data.table with results
<rst_prolog>:3: WARNING: Substitution definition "nbsp" empty or invalid.

.. |nbsp| unicode:: 0xA0
   :trim:


  ``binSpectMultiMatrix``
  ===========================

  binSpectMultiMatrix

  Description
  -----------

  binSpect for a single spatial network and a provided expression matrix

  Usage
  -----

  .. code-block:: r

    binSpectMultiMatrix(
      expression_matrix,
      spatial_networks,
      bin_method = c("kmeans", "rank"),
      subset_feats = NULL,
      kmeans_algo = c("kmeans", "kmeans_arma", "kmeans_arma_subset"),
      nstart = 3,
      iter_max = 10,
      extreme_nr = 50,
      sample_nr = 50,
      percentage_rank = c(10, 30),
      do_fisher_test = TRUE,
      adjust_method = "fdr",
      calc_hub = FALSE,
      hub_min_int = 3,
      get_av_expr = TRUE,
      get_high_expr = TRUE,
      implementation = c("data.table", "simple", "matrix"),
      group_size = "automatic",
      do_parallel = TRUE,
      cores = NA,
      verbose = T,
      knn_params = NULL,
      set.seed = NULL,
      summarize = c("adj.p.value", "p.value")
    )

  Arguments
  ---------

  .. list-table::
    :header-rows: 1

    * - Argument
      - Description
    * - ``expression_matrix``
      - expression matrix
    * - ``spatial_networks``
      - list of spatial networks in data.table format
    * - ``bin_method``
      - method to binarize gene expression
    * - ``subset_feats``
      - only select a subset of features to test
    * - ``kmeans_algo``
      - kmeans algorithm to use (kmeans, kmeans_arma, kmeans_arma_subset)
    * - ``nstart``
      - kmeans: nstart parameter
    * - ``iter_max``
      - kmeans: iter.max parameter
    * - ``extreme_nr``
      - number of top and bottom cells (see details)
    * - ``sample_nr``
      - total number of cells to sample (see details)
    * - ``percentage_rank``
      - vector of percentages of top cells for binarization
    * - ``do_fisher_test``
      - perform fisher test
    * - ``adjust_method``
      - p-value adjusted method to use (see `\ ``p.adjust`` <#p.adjust>`_ )
    * - ``calc_hub``
      - calculate the number of hub cells
    * - ``hub_min_int``
      - minimum number of cell-cell interactions for a hub cell
    * - ``get_av_expr``
      - calculate the average expression per gene of the high expressing cells
    * - ``get_high_expr``
      - calculate the number of high expressing cells  per gene
    * - ``implementation``
      - enrichment implementation (data.table, simple, matrix)
    * - ``group_size``
      - number of genes to process together with data.table implementation (default = automatic)
    * - ``do_parallel``
      - run calculations in parallel with mclapply
    * - ``cores``
      - number of cores to use if do_parallel = TRUE
    * - ``verbose``
      - be verbose
    * - ``knn_params``
      - list of parameters to create spatial kNN network
    * - ``set.seed``
      - set a seed before kmeans binarization
    * - ``summarize``
      - summarize the p-values or adjusted p-values


  Value
  -----

  data.table with results
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/home/docs/checkouts/readthedocs.org/user_builds/giottoteam-giotto/checkouts/suite/docs/source/documentation.rst:140: WARNING: unknown document: /subsections/md_rst/getGiottoImage
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