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example_script.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>4. Example scripts — pyGCluster 0.18.4 documentation</title>
<link rel="stylesheet" href="_static/default.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
VERSION: '0.18.4',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="top" title="pyGCluster 0.18.4 documentation" href="index.html" />
<link rel="prev" title="3. Usage" href="usage.html" />
</head>
<body>
<div class="related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
accesskey="I">index</a></li>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
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accesskey="P">previous</a> |</li>
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</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body">
<div class="section" id="example-scripts">
<h1>4. Example scripts<a class="headerlink" href="#example-scripts" title="Permalink to this headline">¶</a></h1>
<div class="section" id="testscript-to-demonstrate-functionality-of-pygcluster">
<h2>4.1. Testscript to demonstrate functionality of pyGCluster<a class="headerlink" href="#testscript-to-demonstrate-functionality-of-pygcluster" title="Permalink to this headline">¶</a></h2>
<p>This script imports the data of Hoehner et al. (2013) and executes pyGCluster
with 250,000 iterations of resampling. pyGCluster will evoke 4 threads
(if possible), which each require approx. 1.5GB RAM. Please make sure you have
enough RAM available (4 threads in all require approx. 6GB RAM).
Duration will be approx. 2 hours to complete 250,000 iterations on 4 threads.</p>
<p>Usage:</p>
<p>./example-script.py</p>
<p>If this script is executed in pyGCluster/exampleScripts, the command would be:</p>
<p>./example_script.py ../exampleFiles/hoehner_dataset.csv</p>
</div>
<div class="section" id="nodemap-and-heatmap-example">
<h2>4.2. Nodemap and heatmap example<a class="headerlink" href="#nodemap-and-heatmap-example" title="Permalink to this headline">¶</a></h2>
<p>The figure shows an example of a nodemap generated by pyGCluster, taken from the publication manuscript.</p>
<div class="figure align-left">
<img alt="_images/_Fig1.png" src="_images/_Fig1.png" />
</div>
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</div>
<p>(Modified from Jaeger et al. 2013)</p>
</div>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar">
<div class="sphinxsidebarwrapper">
<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">4. Example scripts</a><ul>
<li><a class="reference internal" href="#testscript-to-demonstrate-functionality-of-pygcluster">4.1. Testscript to demonstrate functionality of pyGCluster</a></li>
<li><a class="reference internal" href="#nodemap-and-heatmap-example">4.2. Nodemap and heatmap example</a></li>
</ul>
</li>
</ul>
<h4>Previous topic</h4>
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title="previous chapter">3. Usage</a></p>
<h3>This Page</h3>
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<li><a href="_sources/example_script.txt"
rel="nofollow">Show Source</a></li>
</ul>
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</form>
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Enter search terms or a module, class or function name.
</p>
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<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
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</div>
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<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
>index</a></li>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
<a href="usage.html" title="3. Usage"
>previous</a> |</li>
<li><a href="index.html">pyGCluster 0.18.4 documentation</a> »</li>
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© Copyright 2013, Daniel Jaeger, Johannes Barth, Anna Niehues and Christian Fufezan.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
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