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<section id="spapros-se-probesetselector-plot-clf-genes">
<h1>spapros.se.ProbesetSelector.plot_clf_genes<a class="headerlink" href="#spapros-se-probesetselector-plot-clf-genes" title="Permalink to this heading"></a></h1>
<dl class="py method">
<dt class="sig sig-object py" id="spapros.se.ProbesetSelector.plot_clf_genes">
<span class="sig-prename descclassname"><span class="pre">ProbesetSelector.</span></span><span class="sig-name descname"><span class="pre">plot_clf_genes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">basis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'X_umap'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">celltypes</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">till_rank</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">importance_th</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">add_marker_genes</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">neighbors_params</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">umap_params</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spapros.se.ProbesetSelector.plot_clf_genes" title="Permalink to this definition"></a></dt>
<dd><p>Plot umaps of selected genes needed for cell type classification of each cell type.</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>basis</strong> (<em>str</em>) – Name of the <code class="docutils literal notranslate"><span class="pre">obsm</span></code> embedding to use.</p></li>
<li><p><strong>celltypes</strong> (<em>Optional</em><em>[</em><em>List</em><em>[</em><em>str</em><em>]</em><em>]</em>) – Subset of cell types for which to plot decision genes. If <cite>None</cite>, <code class="xref py py-attr docutils literal notranslate"><span class="pre">celltypes</span></code> is used.</p></li>
<li><p><strong>till_rank</strong> (<em>Optional</em><em>[</em><em>int</em><em>]</em>) – Plot decision genes only up to the given tree rank of the probeset list.</p></li>
<li><p><strong>importance_th</strong> (<em>Optional</em><em>[</em><em>float</em><em>]</em>) – Only plot genes with a tree feature importance above the given threshold.</p></li>
<li><p><strong>add_marker_genes</strong> (<em>bool</em>) – Whether to add subplots for marker genes from <code class="xref py py-attr docutils literal notranslate"><span class="pre">marker_list</span></code> for each celltype.
TODO: what about cell types that only occur in the marker list?</p></li>
<li><p><strong>neighbors_params</strong> (<em>dict</em>) – Parameters for <code class="xref py py-meth docutils literal notranslate"><span class="pre">sc.pp.neighbors()</span></code>. Only applicable if <code class="docutils literal notranslate"><span class="pre">adata.obsm[basis]</span></code> does not exist.
TODO: do we rly need that parameter? Would be fine to always expect a pre calculated embedding!</p></li>
<li><p><strong>umap_params</strong> (<em>dict</em>) – Parameters for <code class="xref py py-meth docutils literal notranslate"><span class="pre">sc.tl.umap()</span></code>. Only applicable if <code class="docutils literal notranslate"><span class="pre">adata.obsm[basis]</span></code> does not exist.
TODO: do we rly need that parameter? Would be fine to always expect a pre calculated embedding!</p></li>
<li><p><strong>kwargs</strong> – Keyword arguments of <a class="reference internal" href="../pl/spapros.pl.selection_histogram.html#spapros.pl.selection_histogram" title="spapros.pl.selection_histogram"><code class="xref py py-func docutils literal notranslate"><span class="pre">selection_histogram()</span></code></a>.</p></li>
</ul>
</dd>
</dl>
<p class="rubric">Example</p>
<p>(Takes a few minutes to calculate)</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">spapros</span> <span class="k">as</span> <span class="nn">sp</span>
<span class="n">adata</span> <span class="o">=</span> <span class="n">sp</span><span class="o">.</span><span class="n">ut</span><span class="o">.</span><span class="n">get_processed_pbmc_data</span><span class="p">()</span>
<span class="n">selector</span> <span class="o">=</span> <span class="n">sp</span><span class="o">.</span><span class="n">se</span><span class="o">.</span><span class="n">ProbesetSelector</span><span class="p">(</span><span class="n">adata</span><span class="p">,</span> <span class="s2">"celltype"</span><span class="p">,</span> <span class="n">n</span><span class="o">=</span><span class="mi">30</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">selector</span><span class="o">.</span><span class="n">select_probeset</span><span class="p">()</span>
<span class="n">selector</span><span class="o">.</span><span class="n">plot_clf_genes</span><span class="p">(</span><span class="n">n_cols</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span><span class="n">celltypes</span><span class="o">=</span><span class="p">[</span><span class="s2">"FCGR3A+ Monocytes"</span><span class="p">,</span><span class="s2">"Megakaryocytes"</span><span class="p">])</span>
</pre></div>
</div>
<img alt="../_images/Selector_plot_clf_genes.png" src="../_images/Selector_plot_clf_genes.png" />
<p>TODO: this function and pl.clf_genes_umaps need to be tested on all argument combinations + can be optimized.</p>
</dd></dl>
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