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ebezzi committed Apr 4, 2024
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<li class="toctree-l4"><a class="reference internal" href="#cellxgene_census.experimental.get_embedding_metadata"><code class="docutils literal notranslate"><span class="pre">get_embedding_metadata()</span></code></a></li>
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<h1>cellxgene_census.get_presence_matrix<a class="headerlink" href="#cellxgene-census-get-presence-matrix" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="cellxgene_census.get_presence_matrix">
<span class="sig-prename descclassname"><span class="pre">cellxgene_census.</span></span><span class="sig-name descname"><span class="pre">get_presence_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">census</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://tiledbsoma.readthedocs.io/en/latest/_autosummary/tiledbsoma.Collection.html#tiledbsoma.Collection" title="(in TileDB-SOMA-Py)"><span class="pre">Collection</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">measurement_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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'RNA'</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.scipy.org/doc/scipy/reference/generated/scipy.sparse.csr_matrix.html#scipy.sparse.csr_matrix" title="(in SciPy v1.12.0)"><span class="pre">csr_matrix</span></a></span></span><a class="headerlink" href="#cellxgene_census.get_presence_matrix" title="Permalink to this definition"></a></dt>
<dd><p>Read the feature dataset presence matrix and return as a <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.csr_array.html#scipy.sparse.csr_array" title="(in SciPy v1.12.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">scipy.sparse.csr_array</span></code></a>. The
<span class="sig-prename descclassname"><span class="pre">cellxgene_census.</span></span><span class="sig-name descname"><span class="pre">get_presence_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">census</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://tiledbsoma.readthedocs.io/en/latest/_autosummary/tiledbsoma.Collection.html#tiledbsoma.Collection" title="(in TileDB-SOMA-Py)"><span class="pre">Collection</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">measurement_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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'RNA'</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.scipy.org/doc/scipy/reference/generated/scipy.sparse.csr_matrix.html#scipy.sparse.csr_matrix" title="(in SciPy v1.13.0)"><span class="pre">csr_matrix</span></a></span></span><a class="headerlink" href="#cellxgene_census.get_presence_matrix" title="Permalink to this definition"></a></dt>
<dd><p>Read the feature dataset presence matrix and return as a <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.csr_array.html#scipy.sparse.csr_array" title="(in SciPy v1.13.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">scipy.sparse.csr_array</span></code></a>. The
returned sparse matrix is indexed on the first dimension by the dataset <code class="docutils literal notranslate"><span class="pre">soma_joinid</span></code> values,
and on the second dimension by the <code class="docutils literal notranslate"><span class="pre">var</span></code> <a class="reference external" href="https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code></a> <code class="docutils literal notranslate"><span class="pre">soma_joinid</span></code> values.</p>
<dl class="field-list simple">
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</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.csr_array.html#scipy.sparse.csr_array" title="(in SciPy v1.12.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">scipy.sparse.csr_array</span></code></a> object containing the presence matrix.</p>
<dd class="field-even"><p>A <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.csr_array.html#scipy.sparse.csr_array" title="(in SciPy v1.13.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">scipy.sparse.csr_array</span></code></a> object containing the presence matrix.</p>
</dd>
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – if the organism cannot be found.</p>
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cellxgene\_census.experimental.get\_all\_available\_embeddings
==============================================================

.. currentmodule:: cellxgene_census.experimental

.. autofunction:: get_all_available_embeddings
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cellxgene\_census.experimental.get\_all\_census\_versions\_with\_embedding
==========================================================================

.. currentmodule:: cellxgene_census.experimental

.. autofunction:: get_all_census_versions_with_embedding
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cellxgene\_census.experimental.get\_embedding\_metadata\_by\_name
=================================================================

.. currentmodule:: cellxgene_census.experimental

.. autofunction:: get_embedding_metadata_by_name
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