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<section id="spapros-se-select-pca-genes">
<h1>spapros.se.select_pca_genes<a class="headerlink" href="#spapros-se-select-pca-genes" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="spapros.se.select_pca_genes">
<span class="sig-prename descclassname"><span class="pre">spapros.se.</span></span><span class="sig-name descname"><span class="pre">select_pca_genes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">adata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variance_scaled</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">absolute</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_pcs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">20</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">penalty_keys</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">corr_penalty</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">inplace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">progress</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">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spapros.se.select_pca_genes" title="Permalink to this definition"></a></dt>
<dd><p>Select n features based on pca loadings.</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>adata</strong> (<em>AnnData</em>) – Data with log normalised counts in adata.X.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – Number of selected features.</p></li>
<li><p><strong>variance_scaled</strong> (<em>bool</em>) – If <cite>True</cite>, loadings are defined as <cite>eigenvector_component * sqrt(eigenvalue)</cite>.
If False loadings are defined as eigenvector_component.</p></li>
<li><p><strong>absolute</strong> (<em>bool</em>) – Take absolute value of loadings.</p></li>
<li><p><strong>n_pcs</strong> (<em>int</em>) – Number of PCs used to calculate loadings sums.</p></li>
<li><p><strong>penalty_keys</strong> (<em>list</em>) – List of keys for columns in adata.var that are multiplied with the scores.</p></li>
<li><p><strong>corr_penalty</strong> (<em>Optional</em><em>[</em><em>Callable</em><em>]</em>) – Function that maps values from [0,1] to [0,1]. It describes an iterative penalty function
that is applied on pca selected genes. The highest correlation with already selected genes
to the next selected genes are penalized according the given function. (max correlation is
recomputed after each selected gene).</p></li>
<li><p><strong>inplace</strong> (<em>bool</em>) – Save results in <code class="xref py py-attr docutils literal notranslate"><span class="pre">adata.var</span></code> or return dataframe.</p></li>
<li><p><strong>progress</strong> (<em>Optional</em><em>[</em><em>Progress</em><em>]</em>) – <code class="xref py py-attr docutils literal notranslate"><span class="pre">rich.Progress</span></code> object if progress bars should be shown.</p></li>
<li><p><strong>level</strong> (<em>int</em>) – Progress bar level.</p></li>
<li><p><strong>verbosity</strong> (<em>int</em>) – Verbosity level.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><blockquote>
<div><p>pd.DataFrame (like adata.var) with columns:</p>
<blockquote>
<div><ul class="simple">
<li><p>’selection’: bool indicator of selected genes</p></li>
<li><p>’selection_score’: pca loadings based score of each gene</p></li>
<li><p>’selection_ranking’: ranking according selection scores</p></li>
</ul>
</div></blockquote>
</div></blockquote>
<ul class="simple">
<li><dl class="simple">
<dt>if inplace:</dt><dd><p>Save results in <cite>adata.var[[‘selection’,’selection_score’,’selection_ranking’]]</cite>.</p>
</dd>
</dl>
</li>
</ul>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><ul class="simple">
<li><p>if not inplace</p></li>
</ul>
</p>
</dd>
</dl>
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