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<li><a class="reference internal" href="#deepof.post_hoc.compute_transition_matrix_per_condition"><code class="docutils literal notranslate"><span class="pre">compute_transition_matrix_per_condition()</span></code></a></li>
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<section id="deepof-post-hoc-compute-transition-matrix-per-condition">
<h1>deepof.post_hoc.compute_transition_matrix_per_condition<a class="headerlink" href="#deepof-post-hoc-compute-transition-matrix-per-condition" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="deepof.post_hoc.compute_transition_matrix_per_condition">
<span class="sig-prename descclassname"><span class="pre">deepof.post_hoc.</span></span><span class="sig-name descname"><span class="pre">compute_transition_matrix_per_condition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">embedding</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">deepof_table_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">soft_counts</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">deepof_table_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">breaks</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">deepof_table_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exp_conditions</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silence_diagonal</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bin_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bin_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></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>, <em class="sig-param"><span class="n"><span class="pre">normalize</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></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><a class="headerlink" href="#deepof.post_hoc.compute_transition_matrix_per_condition" title="Permalink to this definition"></a></dt>
<dd><p>Compute the transition matrices specific to each condition.</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>embedding</strong> (<a class="reference internal" href="deepof.data.TableDict.html#deepof.data.TableDict" title="deepof.data.TableDict"><em>TableDict</em></a>) – A dictionary of embeddings, where the keys are the names of the experimental conditions, and the values are the embeddings for each condition.</p></li>
<li><p><strong>soft_counts</strong> (<a class="reference internal" href="deepof.data.TableDict.html#deepof.data.TableDict" title="deepof.data.TableDict"><em>TableDict</em></a>) – A dictionary of soft counts, where the keys are the names of the experimental conditions, and the values are the soft counts for each condition.</p></li>
<li><p><strong>breaks</strong> (<a class="reference internal" href="deepof.data.TableDict.html#deepof.data.TableDict" title="deepof.data.TableDict"><em>TableDict</em></a>) – A dictionary of breaks, where the keys are the names of the experimental conditions, and the values are the breaks for each condition.</p></li>
<li><p><strong>exp_conditions</strong> (<em>dict</em>) – A dictionary of experimental conditions, where the keys are the names of the experiments, and the values are the names of their corresponding</p></li>
<li><p><strong>silence_diagonal</strong> (<em>bool</em>) – If True, diagonal elements on the transition matrix are set to zero.</p></li>
<li><p><strong>bin_size</strong> (<em>int</em>) – The size of the time bins to use. If None, the embeddings are not binned.</p></li>
<li><p><strong>bin_index</strong> (<em>int</em>) – The index of the bin to use. If None, the embeddings are not binned.</p></li>
<li><p><strong>aggregate</strong> (<em>str</em>) – Whether to aggregate the embeddings across time.</p></li>
<li><p><strong>normalize</strong> (<em>str</em>) – Whether to normalize the population of each cluster across conditions.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A dictionary of transition matrices, where the keys are the names of the experimental
conditions, and the values are the transition matrices for each condition.</p>
</dd>
</dl>
</dd></dl>
</section>
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