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nargesr committed Sep 4, 2024
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# 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: b4b62d77d49bef1e217ef279564429a8
config: e1f0dd8b2dba20b0198db35fc13d8c7f
tags: 645f666f9bcd5a90fca523b33c5a78b7
128 changes: 88 additions & 40 deletions docs/html/_modules/Topyfic/analysis.html
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75 changes: 51 additions & 24 deletions docs/html/_modules/Topyfic/topic.html
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<!DOCTYPE html>

<html lang="en">
<html lang="en" data-content_root="../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Topyfic.topic &#8212; Topyfic 0.0.11 documentation</title>
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../../_static/bootstrap-sphinx.css" />
<link rel="stylesheet" type="text/css" href="../../_static/graphviz.css" />
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<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
<meta charset='utf-8'>
Expand Down Expand Up @@ -101,7 +99,18 @@

<div class="container">
<div class="row">
<div class="body col-md-12 content" role="main">
<div class="col-md-3">
<div id="sidebar" class="bs-sidenav" role="complementary">
<form action="../../search.html" method="get">
<div class="form-group">
<input type="text" name="q" class="form-control" placeholder="Search" />
</div>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
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<div class="body col-md-9 content" role="main">

<h1>Source code for Topyfic.topic</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">sys</span>
Expand All @@ -119,8 +128,10 @@ <h1>Source code for Topyfic.topic</h1><div class="highlight"><pre>
<span class="kn">from</span> <span class="nn">Topyfic.utilsAnalyseModel</span> <span class="kn">import</span> <span class="n">GSEA</span><span class="p">,</span> <span class="n">functional_enrichment_analysis</span>


<div class="viewcode-block" id="Topic"><a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic">[docs]</a><span class="k">class</span> <span class="nc">Topic</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;</span>
<div class="viewcode-block" id="Topic">
<a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic">[docs]</a>
<span class="k">class</span> <span class="nc">Topic</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> A class saved topic along with other useful information</span>

<span class="sd"> :param topic_id: ID of topic which is unique</span>
Expand Down Expand Up @@ -161,8 +172,10 @@ <h1>Source code for Topyfic.topic</h1><div class="highlight"><pre>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">topic_information</span> <span class="o">=</span> <span class="n">topic_information</span>

<div class="viewcode-block" id="Topic.update_gene_information"><a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic.update_gene_information">[docs]</a> <span class="k">def</span> <span class="nf">update_gene_information</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">gene_information</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<div class="viewcode-block" id="Topic.update_gene_information">
<a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic.update_gene_information">[docs]</a>
<span class="k">def</span> <span class="nf">update_gene_information</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">gene_information</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> update/add genes information for each topics</span>

<span class="sd"> :param gene_information: dataframe contains genes information we would like to add/update (the index should be same as an index of gene_information in class)</span>
Expand All @@ -172,14 +185,17 @@ <h1>Source code for Topyfic.topic</h1><div class="highlight"><pre>
<span class="bp">self</span><span class="o">.</span><span class="n">gene_information</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">same_columns</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">gene_information</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">gene_information</span><span class="p">,</span> <span class="n">gene_information</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span></div>

<div class="viewcode-block" id="Topic.functional_enrichment_analysis"><a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic.functional_enrichment_analysis">[docs]</a> <span class="k">def</span> <span class="nf">functional_enrichment_analysis</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>

<div class="viewcode-block" id="Topic.functional_enrichment_analysis">
<a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic.functional_enrichment_analysis">[docs]</a>
<span class="k">def</span> <span class="nf">functional_enrichment_analysis</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="nb">type</span><span class="p">,</span>
<span class="n">organism</span><span class="p">,</span>
<span class="n">sets</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">p_value</span><span class="o">=</span><span class="mf">0.05</span><span class="p">,</span>
<span class="n">file_format</span><span class="o">=</span><span class="s2">&quot;pdf&quot;</span><span class="p">,</span>
<span class="n">file_name</span><span class="o">=</span><span class="s2">&quot;functional_enrichment_analysis&quot;</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Doing functional enrichment analysis including GO, KEGG and REACTOME</span>

<span class="sd"> :param type: indicate the type of databases which it should be one of &quot;GO&quot;, &quot;REACTOME&quot;</span>
Expand Down Expand Up @@ -207,15 +223,18 @@ <h1>Source code for Topyfic.topic</h1><div class="highlight"><pre>
<span class="n">file_format</span><span class="o">=</span><span class="n">file_format</span><span class="p">,</span>
<span class="n">file_name</span><span class="o">=</span><span class="n">file_name</span><span class="p">)</span></div>

<div class="viewcode-block" id="Topic.GSEA"><a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic.GSEA">[docs]</a> <span class="k">def</span> <span class="nf">GSEA</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>

<div class="viewcode-block" id="Topic.GSEA">
<a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic.GSEA">[docs]</a>
<span class="k">def</span> <span class="nf">GSEA</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="n">gene_sets</span><span class="o">=</span><span class="s1">&#39;GO_Biological_Process_2021&#39;</span><span class="p">,</span>
<span class="n">p_value</span><span class="o">=</span><span class="mf">0.05</span><span class="p">,</span>
<span class="n">table</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">plot</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">file_format</span><span class="o">=</span><span class="s2">&quot;pdf&quot;</span><span class="p">,</span>
<span class="n">file_name</span><span class="o">=</span><span class="s2">&quot;GSEA&quot;</span><span class="p">,</span>
<span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Doing Gene Set Enrichment Analysis on based on the topic weights using GSEAPY package.</span>

<span class="sd"> :param gene_sets: Enrichr Library name or .gmt gene sets file or dict of gene sets. (you can add any Enrichr Libraries from here: https://maayanlab.cloud/Enrichr/#stats)</span>
Expand Down Expand Up @@ -256,8 +275,11 @@ <h1>Source code for Topyfic.topic</h1><div class="highlight"><pre>

<span class="k">return</span> <span class="n">GSEA_df</span></div>

<div class="viewcode-block" id="Topic.gene_weight_variance"><a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic.gene_weight_variance">[docs]</a> <span class="k">def</span> <span class="nf">gene_weight_variance</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">save</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>

<div class="viewcode-block" id="Topic.gene_weight_variance">
<a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic.gene_weight_variance">[docs]</a>
<span class="k">def</span> <span class="nf">gene_weight_variance</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">save</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> calculate the gene weight variance</span>

<span class="sd"> :param save: added as an information to the Topic (default: True)</span>
Expand All @@ -273,8 +295,11 @@ <h1>Source code for Topyfic.topic</h1><div class="highlight"><pre>

<span class="k">return</span> <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Gene weight variance for given topic is </span><span class="si">{</span><span class="n">variance</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span></div>

<div class="viewcode-block" id="Topic.write_topic_yaml"><a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic.write_topic_yaml">[docs]</a> <span class="k">def</span> <span class="nf">write_topic_yaml</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">topic_id</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">model_yaml_path</span><span class="o">=</span><span class="s2">&quot;model.yaml&quot;</span><span class="p">,</span> <span class="n">topic_yaml_path</span><span class="o">=</span><span class="s2">&quot;topic.yaml&quot;</span><span class="p">,</span> <span class="n">save</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>

<div class="viewcode-block" id="Topic.write_topic_yaml">
<a class="viewcode-back" href="../../api.html#Topyfic.topic.Topic.write_topic_yaml">[docs]</a>
<span class="k">def</span> <span class="nf">write_topic_yaml</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">topic_id</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">model_yaml_path</span><span class="o">=</span><span class="s2">&quot;model.yaml&quot;</span><span class="p">,</span> <span class="n">topic_yaml_path</span><span class="o">=</span><span class="s2">&quot;topic.yaml&quot;</span><span class="p">,</span> <span class="n">save</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> write topic in YAML format</span>

<span class="sd"> :param topic_id: unique topic ID (default is topic ID)</span>
Expand Down Expand Up @@ -309,7 +334,9 @@ <h1>Source code for Topyfic.topic</h1><div class="highlight"><pre>
<span class="k">else</span><span class="p">:</span>
<span class="n">yaml_string</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">topic_yaml</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;The Topic YAML is:&quot;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">yaml_string</span><span class="p">)</span></div></div>
<span class="nb">print</span><span class="p">(</span><span class="n">yaml_string</span><span class="p">)</span></div>
</div>

</pre></div>

</div>
Expand All @@ -324,7 +351,7 @@ <h1>Source code for Topyfic.topic</h1><div class="highlight"><pre>
</p>
<p>
&copy; Copyright 2022, Narges Rezaie.<br/>
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 5.0.2.<br/>
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 8.0.2.<br/>
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