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14 changes: 12 additions & 2 deletions _autosummary/cellxgene_census.download_source_h5ad.html
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<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
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<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
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</div>
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<div itemprop="articleBody">

<section id="cellxgene-census-download-source-h5ad">
<h1>cellxgene_census.download_source_h5ad<a class="headerlink" href="#cellxgene-census-download-source-h5ad" title="Permalink to this heading"></a></h1>
<h1>cellxgene_census.download_source_h5ad<a class="headerlink" href="#cellxgene-census-download-source-h5ad" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="cellxgene_census.download_source_h5ad">
<span class="sig-prename descclassname"><span class="pre">cellxgene_census.</span></span><span class="sig-name descname"><span class="pre">download_source_h5ad</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">census_version</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'stable'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#cellxgene_census.download_source_h5ad" title="Permalink to this definition"></a></dt>
<span class="sig-prename descclassname"><span class="pre">cellxgene_census.</span></span><span class="sig-name descname"><span class="pre">download_source_h5ad</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">census_version</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'stable'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">progress_bar</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#cellxgene_census.download_source_h5ad" title="Permalink to this definition"></a></dt>
<dd><p>Download the source H5AD dataset, for the given <cite>dataset_id</cite>, to the user-specified
file name.</p>
<dl class="field-list simple">
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<li><p><strong>dataset_id</strong> – Fetch the source (original) H5AD associated with this <code class="docutils literal notranslate"><span class="pre">dataset_id</span></code>.</p></li>
<li><p><strong>to_path</strong> – The file name where the downloaded H5AD will be written. Must not already exist.</p></li>
<li><p><strong>census_version</strong> – The census version name. Defaults to <code class="docutils literal notranslate"><span class="pre">&quot;stable&quot;</span></code>.</p></li>
<li><p><strong>progress_bar</strong> – Whether to display a progress bar. Defaults to <code class="docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
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<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/doctools.js"></script>
<script src="../_static/sphinx_highlight.js"></script>
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<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>


</div>
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<div itemprop="articleBody">

<section id="cellxgene-census-experimental-get-all-available-embeddings">
<h1>cellxgene_census.experimental.get_all_available_embeddings<a class="headerlink" href="#cellxgene-census-experimental-get-all-available-embeddings" title="Permalink to this heading"></a></h1>
<h1>cellxgene_census.experimental.get_all_available_embeddings<a class="headerlink" href="#cellxgene-census-experimental-get-all-available-embeddings" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="cellxgene_census.experimental.get_all_available_embeddings">
<span class="sig-prename descclassname"><span class="pre">cellxgene_census.experimental.</span></span><span class="sig-name descname"><span class="pre">get_all_available_embeddings</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">census_version</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><span class="pre">list</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><span class="pre">dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cellxgene_census.experimental.get_all_available_embeddings" title="Permalink to this definition"></a></dt>
<span class="sig-prename descclassname"><span class="pre">cellxgene_census.experimental.</span></span><span class="sig-name descname"><span class="pre">get_all_available_embeddings</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">census_version</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><span class="pre">list</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><span class="pre">dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cellxgene_census.experimental.get_all_available_embeddings" title="Permalink to this definition"></a></dt>
<dd><p>Return a dictionary of all available embeddings for a given Census version.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/doctools.js"></script>
<script src="../_static/sphinx_highlight.js"></script>
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<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
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</div>
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<div itemprop="articleBody">

<section id="cellxgene-census-experimental-get-all-census-versions-with-embedding">
<h1>cellxgene_census.experimental.get_all_census_versions_with_embedding<a class="headerlink" href="#cellxgene-census-experimental-get-all-census-versions-with-embedding" title="Permalink to this heading"></a></h1>
<h1>cellxgene_census.experimental.get_all_census_versions_with_embedding<a class="headerlink" href="#cellxgene-census-experimental-get-all-census-versions-with-embedding" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="cellxgene_census.experimental.get_all_census_versions_with_embedding">
<span class="sig-prename descclassname"><span class="pre">cellxgene_census.experimental.</span></span><span class="sig-name descname"><span class="pre">get_all_census_versions_with_embedding</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">embedding_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">embedding_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'obs_embedding'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><span class="pre">list</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cellxgene_census.experimental.get_all_census_versions_with_embedding" title="Permalink to this definition"></a></dt>
<span class="sig-prename descclassname"><span class="pre">cellxgene_census.experimental.</span></span><span class="sig-name descname"><span class="pre">get_all_census_versions_with_embedding</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">embedding_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">embedding_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'obs_embedding'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><span class="pre">list</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cellxgene_census.experimental.get_all_census_versions_with_embedding" title="Permalink to this definition"></a></dt>
<dd><p>Get a list of all census versions that contain a specific embedding.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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