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fix yaml #52

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35 changes: 0 additions & 35 deletions .readthedocs.yaml
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<title>Utilities - scenvi 0.3.2 documentation</title>
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<p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
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<li class="toctree-l1"><a class="reference internal" href="ENVI.html">ENVI</a></li>
<li class="toctree-l1 current current-page"><a class="current reference internal" href="#">Utilities</a></li>
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<article role="main">
<section id="module-scenvi.utils">
<span id="utilities"></span><h1>Utilities<a class="headerlink" href="#module-scenvi.utils" title="Link to this heading">¶</a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="scenvi.utils.compute_covet">
<span class="sig-prename descclassname"><span class="pre">scenvi.utils.</span></span><span class="sig-name descname"><span class="pre">compute_covet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">spatial_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">g</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">64</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genes</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">spatial_key</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'spatial'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_key</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#scenvi.utils.compute_covet" title="Link to this definition">¶</a></dt>
<dd><p>Compute niche covariance matrices for spatial data, run with scenvi.compute_covet</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>(</strong><strong>anndata</strong><strong>)</strong> (<em>spatial_data</em>) – anndata with spatial data, with an obsm indicating spatial location of spot/segmented cell</p></li>
<li><p><strong>(</strong><strong>int</strong><strong>)</strong> (<em>g</em>) – number of nearest neighbours to define niche (default 8)</p></li>
<li><p><strong>(</strong><strong>int</strong><strong>)</strong> – number of HVG to compute COVET representation on (default 64)</p></li>
<li><p><strong>str</strong><strong>)</strong> (<em>genes</em><em> (</em><em>list of</em>) – list of genes to keep for niche covariance (default []</p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> (<em>batch_key</em>) – obsm key name with physical location of spots/cells (default ‘spatial’)</p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> – obs key name of batch/sample of spatial data (default ‘batch’ if in spatial_data.obs, else -1)</p></li>
</ul>
</dd>
<dt class="field-even">Return COVET<span class="colon">:</span></dt>
<dd class="field-even"><p>niche covariance matrices</p>
</dd>
<dt class="field-odd">Return COVET_SQRT<span class="colon">:</span></dt>
<dd class="field-odd"><p>matrix square-root of niche covariance matrices for approximate OT</p>
</dd>
<dt class="field-even">Return CovGenes<span class="colon">:</span></dt>
<dd class="field-even"><p>list of genes selected for COVET representation</p>
</dd>
</dl>
</dd></dl>

<section id="envi">
<h1>ENVI<a class="headerlink" href="#envi" title="Link to this heading">¶</a></h1>
</section>

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<li><a class="reference internal" href="#">Utilities</a><ul>
<li><a class="reference internal" href="#scenvi.utils.compute_covet"><code class="docutils literal notranslate"><span class="pre">compute_covet()</span></code></a></li>
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<meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="#" /><link rel="search" title="Search" href="search.html" />

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<section class="genindex-section">
<h1 id="index">Index</h1>
<div class="genindex-jumpbox"><a href="#C"><strong>C</strong></a> | <a href="#E"><strong>E</strong></a> | <a href="#I"><strong>I</strong></a> | <a href="#L"><strong>L</strong></a> | <a href="#M"><strong>M</strong></a> | <a href="#S"><strong>S</strong></a> | <a href="#T"><strong>T</strong></a></div>
<div class="genindex-jumpbox"></div>
</section>
<section id="C" class="genindex-section">
<h2>C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="utils.html#scenvi.utils.compute_covet">compute_covet() (in module scenvi.utils)</a>
</li>
</ul></td>
</tr></table>
</section>

<section id="E" class="genindex-section">
<h2>E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="ENVI.html#scenvi.ENVI.ENVI">ENVI (class in scenvi.ENVI)</a>
</li>
</ul></td>
</tr></table>
</section>

<section id="I" class="genindex-section">
<h2>I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="ENVI.html#scenvi.ENVI.ENVI.impute_genes">impute_genes() (scenvi.ENVI.ENVI method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="ENVI.html#scenvi.ENVI.ENVI.infer_niche_celltype">infer_niche_celltype() (scenvi.ENVI.ENVI method)</a>
</li>
<li><a href="ENVI.html#scenvi.ENVI.ENVI.infer_niche_covet">infer_niche_covet() (scenvi.ENVI.ENVI method)</a>
</li>
</ul></td>
</tr></table>
</section>

<section id="L" class="genindex-section">
<h2>L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="ENVI.html#scenvi.ENVI.ENVI.latent_rep">latent_rep() (scenvi.ENVI.ENVI method)</a>
</li>
</ul></td>
</tr></table>
</section>

<section id="M" class="genindex-section">
<h2>M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
module

<ul>
<li><a href="ENVI.html#module-scenvi.ENVI">scenvi.ENVI</a>
</li>
<li><a href="utils.html#module-scenvi.utils">scenvi.utils</a>
</li>
</ul></li>
</ul></td>
</tr></table>
</section>

<section id="S" class="genindex-section">
<h2>S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
scenvi.ENVI

<ul>
<li><a href="ENVI.html#module-scenvi.ENVI">module</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
scenvi.utils

<ul>
<li><a href="utils.html#module-scenvi.utils">module</a>
</li>
</ul></li>
</ul></td>
</tr></table>
</section>

<section id="T" class="genindex-section">
<h2>T</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="ENVI.html#scenvi.ENVI.ENVI.train">train() (scenvi.ENVI.ENVI method)</a>
</li>
</ul></td>
</tr></table>
</section>


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# Sphinx inventory version 2
# Project: scenvi
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2 changes: 1 addition & 1 deletion docs/build/pre_built_html/search.html → docs/build/html/search.html
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<meta name="viewport" content="width=device-width,initial-scale=1"/>
<meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="#" />

<!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 --><title>Search - scenvi 0.3.2 documentation</title><link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
<!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 --><title>Search - scenvi 0.3.2 documentation</title><link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
<link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=135e06be" />
<link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=36a5483c" />

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