Merge branch 'main' of github.com:saezlab/FUNKI

saezlab · Apr 8, 2024 · 347afc4 · 347afc4
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diff --git a/docs/doctrees/analysis.doctree b/docs/doctrees/analysis.doctree
diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/docs/doctrees/input.doctree b/docs/doctrees/input.doctree
diff --git a/docs/doctrees/link_license.doctree b/docs/doctrees/link_license.doctree
diff --git a/docs/doctrees/plots.doctree b/docs/doctrees/plots.doctree
diff --git a/docs/doctrees/preprocessing.doctree b/docs/doctrees/preprocessing.doctree
diff --git a/docs/html/.buildinfo b/docs/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: e236f0c5063ef81a3fc85d883fdde236
+config: 3deed59d0a3ec42b6b33f42f7748f628
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/html/_static/pygments.css b/docs/html/_static/pygments.css
@@ -17,6 +17,7 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */
 .highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
 .highlight .gr { color: #FF0000 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #00A000 } /* Generic.Inserted */

diff --git a/docs/html/analysis.html b/docs/html/analysis.html
@@ -3,10 +3,10 @@
 <html lang="en" data-content_root="./">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>funki.analysis &#8212; FUNKI documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/classic.css?v=7663fcb8" />
 
     <script src="_static/documentation_options.js?v=d45e8c67"></script>
@@ -46,6 +46,38 @@ <h3>Navigation</h3>
 
   <section id="module-funki.analysis">
 <span id="funki-analysis"></span><h1>funki.analysis<a class="headerlink" href="#module-funki.analysis" title="Link to this heading">¶</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="funki.analysis.enrich">
+<span class="sig-prename descclassname"><span class="pre">funki.analysis.</span></span><span class="sig-name descname"><span class="pre">enrich</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">net</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">methods</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#funki.analysis.enrich" title="Link to this definition">¶</a></dt>
+<dd><p>Performs enrichment analysis using <a class="reference external" href="https://decoupler-py.readthedocs.io/en/latest/index.html">Decoupler</a> based on a given network
+(e.g. gene set collection) and statistical method(s).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>data</strong> (<a class="reference internal" href="input.html#funki.input.DataSet" title="funki.input.DataSet"><code class="xref py py-class docutils literal notranslate"><span class="pre">funki.input.DataSet</span></code></a>) – The data set from which to perform the enrichment</p></li>
+<li><p><strong>net</strong> (<a class="reference external" href="https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.html">pandas.DataFrame</a>) – The network linking the features of the data to the attributes
+(e.g. pathways, gene sets, transcription factors, etc.)</p></li>
+<li><p><strong>methods</strong> (<em>NoneType</em><em> | </em><em>str</em><em> | </em><em>list</em><em>[</em><em>str</em><em>]</em>) – Which statistical method(s) to use in order to compute the
+enrichment, defaults to <code class="docutils literal notranslate"><span class="pre">None</span></code>. If none is provided, uses <code class="docutils literal notranslate"><span class="pre">'mlm'</span></code>,
+<code class="docutils literal notranslate"><span class="pre">'ulm'</span></code> and <code class="docutils literal notranslate"><span class="pre">'wsum'</span></code>. The option <code class="docutils literal notranslate"><span class="pre">'all'</span></code> performs all methods. To
+see all the available methods, you can run <a class="reference external" href="https://decoupler-py.readthedocs.io/en/latest/generated/decoupler.show_methods.html#decoupler.show_methods">decoupler.show_methods()</a>
+function</p></li>
+<li><p><strong>**kwargs</strong> – Other keyword arguments that passed to</p></li>
+</ul>
+</dd>
+</dl>
+<p><a class="reference external" href="https://decoupler-py.readthedocs.io/en/latest/generated/decoupler.decouple.html#decoupler.decouple">decoupler.decouple()</a> function
+:type **kwargs: optional</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><code class="docutils literal notranslate"><span class="pre">None</span></code>, results are stored inplace of the passed <code class="docutils literal notranslate"><span class="pre">data</span></code> object</p>
+</dd>
+<dt class="field-even">Return type<span class="colon">:</span></dt>
+<dd class="field-even"><p>NoneType</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="funki.analysis.sc_clustering">
 <span class="sig-prename descclassname"><span class="pre">funki.analysis.</span></span><span class="sig-name descname"><span class="pre">sc_clustering</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alg</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'leiden'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resolution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#funki.analysis.sc_clustering" title="Link to this definition">¶</a></dt>
@@ -67,6 +99,12 @@ <h3>Navigation</h3>
 <a class="reference external" href="https://scanpy.readthedocs.io/en/latest/api/generated/scanpy.pp.neighbors.html">scanpy.pp.neighbors()</a> function</p></li>
 </ul>
 </dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="docutils literal notranslate"><span class="pre">None</span></code>, results are stored inplace of the passed <code class="docutils literal notranslate"><span class="pre">data</span></code> object</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>NoneType</p>
+</dd>
 </dl>
 </dd></dl>
 
@@ -106,6 +144,7 @@ <h3>Navigation</h3>
     <h3><a href="index.html">Table of Contents</a></h3>
     <ul>
 <li><a class="reference internal" href="#">funki.analysis</a><ul>
+<li><a class="reference internal" href="#funki.analysis.enrich"><code class="docutils literal notranslate"><span class="pre">enrich()</span></code></a></li>
 <li><a class="reference internal" href="#funki.analysis.sc_clustering"><code class="docutils literal notranslate"><span class="pre">sc_clustering()</span></code></a></li>
 <li><a class="reference internal" href="#funki.analysis.sc_trans_qc_metrics"><code class="docutils literal notranslate"><span class="pre">sc_trans_qc_metrics()</span></code></a></li>
 </ul>

diff --git a/docs/html/genindex.html b/docs/html/genindex.html
@@ -5,7 +5,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Index &#8212; FUNKI documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/classic.css?v=7663fcb8" />
 
     <script src="_static/documentation_options.js?v=d45e8c67"></script>
@@ -41,6 +41,7 @@ <h1 id="index">Index</h1>
 <div class="genindex-jumpbox">
  <a href="#C"><strong>C</strong></a>
  | <a href="#D"><strong>D</strong></a>
+ | <a href="#E"><strong>E</strong></a>
  | <a href="#F"><strong>F</strong></a>
  | <a href="#H"><strong>H</strong></a>
  | <a href="#M"><strong>M</strong></a>
@@ -65,6 +66,14 @@ <h2 id="D">D</h2>
   </ul></td>
 </tr></table>
 
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="analysis.html#funki.analysis.enrich">enrich() (in module funki.analysis)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="F">F</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>

diff --git a/docs/html/index.html b/docs/html/index.html
@@ -3,10 +3,10 @@
 <html lang="en" data-content_root="./">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>Welcome to FUNKI &#8212; FUNKI documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/classic.css?v=7663fcb8" />
 
     <script src="_static/documentation_options.js?v=d45e8c67"></script>
@@ -92,6 +92,7 @@ <h2>Documentation<a class="headerlink" href="#documentation" title="Link to this
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="analysis.html">funki.analysis</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="analysis.html#funki.analysis.enrich"><code class="docutils literal notranslate"><span class="pre">enrich()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="analysis.html#funki.analysis.sc_clustering"><code class="docutils literal notranslate"><span class="pre">sc_clustering()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="analysis.html#funki.analysis.sc_trans_qc_metrics"><code class="docutils literal notranslate"><span class="pre">sc_trans_qc_metrics()</span></code></a></li>
 </ul>

diff --git a/docs/html/input.html b/docs/html/input.html
@@ -3,10 +3,10 @@
 <html lang="en" data-content_root="./">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>funki.input &#8212; FUNKI documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/classic.css?v=7663fcb8" />
 
     <script src="_static/documentation_options.js?v=d45e8c67"></script>

diff --git a/docs/html/link_license.html b/docs/html/link_license.html
@@ -3,10 +3,10 @@
 <html lang="en" data-content_root="./">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>License &#8212; FUNKI documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/classic.css?v=7663fcb8" />
 
     <script src="_static/documentation_options.js?v=d45e8c67"></script>

diff --git a/docs/html/objects.inv b/docs/html/objects.inv
diff --git a/docs/html/plots.html b/docs/html/plots.html
@@ -3,10 +3,10 @@
 <html lang="en" data-content_root="./">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>funki.plots &#8212; FUNKI documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/classic.css?v=7663fcb8" />
 
     <script src="_static/documentation_options.js?v=d45e8c67"></script>

diff --git a/docs/html/preprocessing.html b/docs/html/preprocessing.html
@@ -3,10 +3,10 @@
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   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>funki.preprocessing &#8212; FUNKI documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/classic.css?v=7663fcb8" />
 
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diff --git a/docs/html/py-modindex.html b/docs/html/py-modindex.html
@@ -5,7 +5,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Python Module Index &#8212; FUNKI documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
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diff --git a/docs/html/search.html b/docs/html/search.html
@@ -5,7 +5,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Search &#8212; FUNKI documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/classic.css?v=7663fcb8" />
 
 

diff --git a/docs/html/searchindex.js b/docs/html/searchindex.js