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--- a +++ b/doc/_build/html/index.html @@ -0,0 +1,170 @@ + +<!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="X-UA-Compatible" content="IE=Edge" /> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <title>Multi-omics Autoencoder Integration (maui) — 0.1 documentation</title> + <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></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> + <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="shortcut icon" href="_static/icons8-beach-30.png"/> + <link rel="index" title="Index" href="genindex.html" /> + <link rel="search" title="Search" href="search.html" /> + <link rel="next" title="Multi-modal Autoencoders" href="autoencoder-integration.html" /> + + <link rel="stylesheet" href="_static/custom.css" type="text/css" /> + + + <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" /> + + </head><body> + + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + + + <div class="body" role="main"> + + <div class="section" id="multi-omics-autoencoder-integration-maui"> +<h1>Multi-omics Autoencoder Integration (maui)<a class="headerlink" href="#multi-omics-autoencoder-integration-maui" title="Permalink to this headline">¶</a></h1> +<p>maui is an autoencoder-based framework for multi-omics data analysis. It consists of two main modules, <a class="reference internal" href="maui.html"><span class="doc">The Maui Class</span></a>, and <a class="reference internal" href="utils.html"><span class="doc">Maui Utilities</span></a>. For an introduction of the use of autoencoders for multi-omics integration, see <a class="reference internal" href="autoencoder-integration.html"><span class="doc">Multi-modal Autoencoders</span></a>.</p> +<div class="section" id="table-of-contents"> +<h2>Table of contents<a class="headerlink" href="#table-of-contents" title="Permalink to this headline">¶</a></h2> +<div class="toctree-wrapper compound"> +<ul> +<li class="toctree-l1"><a class="reference internal" href="autoencoder-integration.html">Multi-modal Autoencoders</a><ul> +<li class="toctree-l2"><a class="reference internal" href="autoencoder-integration.html#variational-autoencoders">Variational Autoencoders</a></li> +<li class="toctree-l2"><a class="reference internal" href="autoencoder-integration.html#stacked-autoencoders">Stacked Autoencoders</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="data-normalization.html">Data and Normalization</a></li> +<li class="toctree-l1"><a class="reference internal" href="filtering-and-merging-latent-factors.html">Filtering and Merging latent factors</a><ul> +<li class="toctree-l2"><a class="reference internal" href="filtering-and-merging-latent-factors.html#dropping-unexplanatory-latent-factors">Dropping unexplanatory latent factors</a></li> +<li class="toctree-l2"><a class="reference internal" href="filtering-and-merging-latent-factors.html#merging-similar-latent-factors">Merging similar latent factors</a></li> +<li class="toctree-l2"><a class="reference internal" href="filtering-and-merging-latent-factors.html#supervised-filtering-of-latent-factors">Supervised filtering of latent factors</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="saving-and-loading-models.html">Saving and loading models</a><ul> +<li class="toctree-l2"><a class="reference internal" href="saving-and-loading-models.html#saving-a-trained-model-to-disk">Saving a trained model to disk</a></li> +<li class="toctree-l2"><a class="reference internal" href="saving-and-loading-models.html#loading-a-model-from-disk">Loading a model from disk</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="maui.html">The Maui Class</a></li> +<li class="toctree-l1"><a class="reference internal" href="utils.html">Maui Utilities</a></li> +</ul> +</div> +</div> +<div class="section" id="quickstart"> +<h2>Quickstart<a class="headerlink" href="#quickstart" title="Permalink to this headline">¶</a></h2> +<p>The <code class="docutils literal notranslate"><span class="pre">Maui</span></code> class implements <code class="docutils literal notranslate"><span class="pre">scikit-learn</span></code>’s <code class="docutils literal notranslate"><span class="pre">BaseEstimator</span></code>. In order to infer latent factors in multi-omics data, first instantiate a <code class="docutils literal notranslate"><span class="pre">Maui</span></code> model with the desired parameters, and then fit it to some data:</p> +<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">maui</span> <span class="kn">import</span> <span class="n">Maui</span> + +<span class="n">maui_model</span> <span class="o">=</span> <span class="n">maui</span><span class="o">.</span><span class="n">Maui</span><span class="p">(</span><span class="n">n_hidden</span><span class="o">=</span><span class="p">[</span><span class="mi">900</span><span class="p">],</span> <span class="n">n_latent</span><span class="o">=</span><span class="mi">70</span><span class="p">,</span> <span class="n">epochs</span><span class="o">=</span><span class="mi">100</span><span class="p">)</span> +<span class="n">z</span> <span class="o">=</span> <span class="n">maui_model</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">({</span><span class="s1">'mRNA'</span><span class="p">:</span> <span class="n">gex</span><span class="p">,</span> <span class="s1">'Mutations'</span><span class="p">:</span> <span class="n">mut</span><span class="p">,</span> <span class="s1">'CNV'</span><span class="p">:</span> <span class="n">cnv</span><span class="p">})</span> +</pre></div> +</div> +<p>This will instantiate a maui model with one hidden layer of 900 nodes, and a middle layer of 70 nodes, which will be traiend for 100 epochs. It then feeds the multi-omics data in <code class="docutils literal notranslate"><span class="pre">gex</span></code>, <code class="docutils literal notranslate"><span class="pre">mut</span></code>, and <code class="docutils literal notranslate"><span class="pre">cnv</span></code> to the fitting procedure. The omics data (<code class="docutils literal notranslate"><span class="pre">gex</span></code> et. al.) are <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> objects of dimension (n_features, n_samples). The return object <code class="docutils literal notranslate"><span class="pre">z</span></code> is a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> (n_samples, n_latent), and may be used for further analysis.</p> +<p>In order to check the model’s convergance, the <code class="docutils literal notranslate"><span class="pre">hist</span></code> object may be inspected, and plotted:</p> +<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">maui_model</span><span class="o">.</span><span class="n">hist</span><span class="o">.</span><span class="n">plot</span><span class="p">()</span> +</pre></div> +</div> +<img alt="_images/hist.png" src="_images/hist.png" /> +<p>For a more comprehensive example, check out <a class="reference external" href="https://github.com/BIMSBbioinfo/maui/blob/master/vignette/maui_vignette.ipynb">our vignette</a>.</p> +<div class="section" id="indices-and-tables"> +<h3>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h3> +<ul class="simple"> +<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li> +<li><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></li> +<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li> +</ul> +</div> +</div> +</div> + + + </div> + + </div> + </div> + <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> + <div class="sphinxsidebarwrapper"> + <p class="logo"><a href="#"> + <img class="logo" src="_static/hex-maui.png" alt="Logo"/> + </a></p> +<h1 class="logo"><a href="#"></a></h1> + + + + + + + + +<h3>Navigation</h3> +<ul> +<li class="toctree-l1"><a class="reference internal" href="autoencoder-integration.html">Multi-modal Autoencoders</a></li> +<li class="toctree-l1"><a class="reference internal" href="data-normalization.html">Data and Normalization</a></li> +<li class="toctree-l1"><a class="reference internal" href="filtering-and-merging-latent-factors.html">Filtering and Merging latent factors</a></li> +<li class="toctree-l1"><a class="reference internal" href="saving-and-loading-models.html">Saving and loading models</a></li> +<li class="toctree-l1"><a class="reference internal" href="maui.html">The Maui Class</a></li> +<li class="toctree-l1"><a class="reference internal" href="utils.html">Maui Utilities</a></li> +</ul> + +<div class="relations"> +<h3>Related Topics</h3> +<ul> + <li><a href="#">Documentation overview</a><ul> + <li>Next: <a href="autoencoder-integration.html" title="next chapter">Multi-modal Autoencoders</a></li> + </ul></li> +</ul> +</div> +<div id="searchbox" style="display: none" role="search"> + <h3>Quick search</h3> + <div class="searchformwrapper"> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + </div> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + + + + + + + + + </div> + </div> + <div class="clearer"></div> + </div> + <div class="footer"> + ©2018, Jonathan Ronen, Altuna Akalin. + + | + Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.2</a> + & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a> + + | + <a href="_sources/index.rst.txt" + rel="nofollow">Page source</a> + </div> + + + + + </body> +</html> \ No newline at end of file