deploy: 937ec5b

Author: AnneHartebrodt

.doctrees/environment.pickle

@@ -349,23 +349,9 @@
 <h1>netmap.downstream.clustering.downstream_recipe<a class="headerlink" href="#netmap-downstream-clustering-downstream-recipe" title="Link to this heading">¶</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="netmap.downstream.clustering.downstream_recipe">
-<span class="sig-prename descclassname"><span class="pre">netmap.downstream.clustering.</span></span><span class="sig-name descname"><span class="pre">downstream_recipe</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">grn_adata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{'knn_neighbors':</span> <span class="pre">50,</span> <span class="pre">'leiden_resolution':</span> <span class="pre">0.1,</span> <span class="pre">'min_cells':</span> <span class="pre">1,</span> <span class="pre">'n_components':</span> <span class="pre">100,</span> <span class="pre">'n_neighbors':</span> <span class="pre">30}</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">AnnData</span></span></span><a class="headerlink" href="#netmap.downstream.clustering.downstream_recipe" title="Link to this definition">¶</a></dt>
-<dd><p>Minimal downstream processing for GRN object. Runs sc.pca (without scaling),
-sc.neighbours, sc.leiden, sc. umap</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>grn_adata</strong> (<em>AnnData</em>) – A GRN anndata object to process</p></li>
-<li><p><strong>config</strong> (<em>dict</em>) – Parameters for the processing</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p><strong>grn_adata</strong> – Processed Anndata object</p>
-</dd>
-<dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>AnnData</p>
-</dd>
-</dl>
+<span class="sig-prename descclassname"><span class="pre">netmap.downstream.clustering.</span></span><span class="sig-name descname"><span class="pre">downstream_recipe</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">grn_adata</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> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">AnnData</span></span></span><a class="headerlink" href="#netmap.downstream.clustering.downstream_recipe" title="Link to this definition">¶</a></dt>
+<dd><p>Runs sc.pca, sc.neighbors, sc.leiden, and sc.umap.
+Parameters are pulled from kwargs, with defaults provided.</p>
 </dd></dl>
 
 </section>

.doctrees/generated/netmap.downstream.clustering.doctree

@@ -352,10 +352,10 @@
 <table class="autosummary longtable docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p><a class="reference internal" href="netmap.downstream.clustering.downstream_recipe.html#netmap.downstream.clustering.downstream_recipe" title="netmap.downstream.clustering.downstream_recipe"><code class="xref py py-obj docutils literal notranslate"><span class="pre">downstream_recipe</span></code></a></p></td>
-<td><p>Minimal downstream processing for GRN object.</p></td>
+<td><p>Runs sc.pca, sc.neighbors, sc.leiden, and sc.umap.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="netmap.downstream.clustering.process.html#netmap.downstream.clustering.process" title="netmap.downstream.clustering.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a></p></td>
-<td><p>Wrapper function for convenience processing and clustering</p></td>
+<td><p>Wrapper function that passes all extra keyword arguments to downstream_recipe.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="netmap.downstream.clustering.spectral_clustering.html#netmap.downstream.clustering.spectral_clustering" title="netmap.downstream.clustering.spectral_clustering"><code class="xref py py-obj docutils literal notranslate"><span class="pre">spectral_clustering</span></code></a></p></td>
 <td><p>Run sklearn spectral clustering on the neighbour matrix in the anndata object.</p></td>

.doctrees/generated/netmap.downstream.clustering.downstream_recipe.doctree

@@ -349,24 +349,8 @@
 <h1>netmap.downstream.clustering.process<a class="headerlink" href="#netmap-downstream-clustering-process" title="Link to this heading">¶</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="netmap.downstream.clustering.process">
-<span class="sig-prename descclassname"><span class="pre">netmap.downstream.clustering.</span></span><span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">grn_adata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_clu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">key_added</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'spectral'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#netmap.downstream.clustering.process" title="Link to this definition">¶</a></dt>
-<dd><p>Wrapper function for convenience processing and clustering</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>grn_adata</strong> (<em>AnnData</em>) – A GRN anndata object to process</p></li>
-<li><p><strong>n_clu</strong> (<em>int</em>) – Number of clusters to compute</p></li>
-<li><p><strong>key_added</strong> (<em>str</em>) – The key to add the new labelling to [Default: spectral]</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p><strong>grn_adata</strong> – Processed Anndata object with an additional column in the .obs
-slot of the object named <cite>key_added</cite></p>
-</dd>
-<dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>AnnData</p>
-</dd>
-</dl>
+<span class="sig-prename descclassname"><span class="pre">netmap.downstream.clustering.</span></span><span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">grn_adata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_clu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">key_added</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'spectral'</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="#netmap.downstream.clustering.process" title="Link to this definition">¶</a></dt>
+<dd><p>Wrapper function that passes all extra keyword arguments to downstream_recipe.</p>
 </dd></dl>
 
 </section>