deploy: 9acfabe

sysbio-curie · Aug 19, 2024 · b681093 · b681093
commit b681093
Show file tree

Hide file tree

Showing 123 changed files with 45,140 additions and 0 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -0,0 +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: 6d926d0751bafd1a7e10e49a516e7997
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.nojekyll b/.nojekyll
diff --git a/_autosummary/neko._visual.visualize_network.NetworkVisualizer.render.html b/_autosummary/neko._visual.visualize_network.NetworkVisualizer.render.html
@@ -0,0 +1,165 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>neko._visual.visualize_network.NetworkVisualizer.render &mdash; neko  documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
+    <link rel="shortcut icon" href="../_static/neko_logo.png"/>
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+    <link rel="next" title="neko._visual.visualize_network.NetworkVisualizer.yfiles_visual" href="neko._visual.visualize_network.NetworkVisualizer.yfiles_visual.html" />
+    <link rel="prev" title="neko._visual.visualize_network.NetworkVisualizer.tissue_mapping" href="neko._visual.visualize_network.NetworkVisualizer.tissue_mapping.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+          <a href="../contents.html">
+
+              <img src="../_static/neko_logo.png" class="logo" alt="Logo"/>
+          </a>
+              <div class="version">
+                0.9.1
+              </div>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">API Reference</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../api.html">API Reference</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../api.html#network-class">Network Class</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../api.html#method-details">Method Details</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.add_edge.html">neko.core.network.Network.add_edge</a></li>
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.remove_node.html">neko.core.network.Network.remove_node</a></li>
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.add_node.html">neko.core.network.Network.add_node</a></li>
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.complete_connection.html">neko.core.network.Network.complete_connection</a></li>
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.connect_component.html">neko.core.network.Network.connect_component</a></li>
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.connect_genes_to_phenotype.html">neko.core.network.Network.connect_genes_to_phenotype</a></li>
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.connect_nodes.html">neko.core.network.Network.connect_nodes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.connect_subgroup.html">neko.core.network.Network.connect_subgroup</a></li>
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.connect_to_upstream_nodes.html">neko.core.network.Network.connect_to_upstream_nodes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.convert_edgelist_into_genesymbol.html">neko.core.network.Network.convert_edgelist_into_genesymbol</a></li>
+<li class="toctree-l3"><a class="reference internal" href="neko.core.network.Network.is_connected.html">neko.core.network.Network.is_connected</a></li>
+<li class="toctree-l3 current"><a class="reference internal" href="../api.html#networkvisualizer-class-methods">NetworkVisualizer Class Methods</a><ul class="current">
+<li class="toctree-l4"><a class="reference internal" href="neko._visual.visualize_network.NetworkVisualizer.tissue_mapping.html">neko._visual.visualize_network.NetworkVisualizer.tissue_mapping</a></li>
+<li class="toctree-l4 current"><a class="current reference internal" href="#">neko._visual.visualize_network.NetworkVisualizer.render</a></li>
+<li class="toctree-l4"><a class="reference internal" href="neko._visual.visualize_network.NetworkVisualizer.yfiles_visual.html">neko._visual.visualize_network.NetworkVisualizer.yfiles_visual</a></li>
+<li class="toctree-l4"><a class="reference internal" href="neko._visual.visualize_network.NetworkVisualizer.vis_comparison.html">neko._visual.visualize_network.NetworkVisualizer.vis_comparison</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html#other-modules">Other Modules</a></li>
+</ul>
+</li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Notebooks</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../notebooks/1_network_building.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../notebooks/2_add_resources.html">Build network using user-defined resources</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../notebooks/3_stepwise_connection.html">Stepwise connection: a focus on the INE algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../notebooks/4_Connect_upstream.html">Connect to upstream components</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../notebooks/5_build_phosphosite_network.html">Build network based on kinase-phosphosite interactions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../notebooks/6_ontology.html">Connect to downstream Gene Ontology terms.</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../notebooks/7_tissue_mapping.html">Map tissue expression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../notebooks/8_Compare_networks.html">Network comparison</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../notebooks/9-Recreating_famous_pathways.html">Re-creating famous pathways from SIGNOR and WIKIPATHWAYS using NeKo</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../contents.html">neko</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../contents.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../api.html">API Reference</a></li>
+      <li class="breadcrumb-item active">neko._visual.visualize_network.NetworkVisualizer.render</li>
+      <li class="wy-breadcrumbs-aside">
+              <a href="/~https://github.com/sysbio-curie/neko/blob/main/docs/_autosummary/neko._visual.visualize_network.NetworkVisualizer.render.rst" class="fa fa-github"> Edit on GitHub</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <section id="neko-visual-visualize-network-networkvisualizer-render">
+<h1>neko._visual.visualize_network.NetworkVisualizer.render<a class="headerlink" href="#neko-visual-visualize-network-networkvisualizer-render" title="Link to this heading"></a></h1>
+<dl class="py method">
+<dt class="sig sig-object py" id="neko._visual.visualize_network.NetworkVisualizer.render">
+<span class="sig-prename descclassname"><span class="pre">NetworkVisualizer.</span></span><span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'network'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">view</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">highlight_nodes</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="n"><span class="pre">highlight_color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'lightyellow'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#neko._visual.visualize_network.NetworkVisualizer.render" title="Link to this definition"></a></dt>
+<dd><p>Render the graph.</p>
+<dl class="simple">
+<dt>Args:</dt><dd><p>output_file (str): The name of the output file.
+view (bool): If True, display the graph.
+highlight_nodes (list): List of nodes to highlight.
+highlight_color (str): Color to use for highlighting nodes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+        <a href="neko._visual.visualize_network.NetworkVisualizer.tissue_mapping.html" class="btn btn-neutral float-left" title="neko._visual.visualize_network.NetworkVisualizer.tissue_mapping" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="neko._visual.visualize_network.NetworkVisualizer.yfiles_visual.html" class="btn btn-neutral float-right" title="neko._visual.visualize_network.NetworkVisualizer.yfiles_visual" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+    </div>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2022-2024, Sysbio-Curie.</p>
+  </div>
+
+
+
+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>