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<section id="pyflowbat-package">
<h1>pyflowbat package<a class="headerlink" href="#pyflowbat-package" title="Permalink to this headline">#</a></h1>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">#</a></h2>
</section>
<section id="module-pyflowbat.gating">
<span id="pyflowbat-gating-module"></span><h2>pyflowbat.gating module<a class="headerlink" href="#module-pyflowbat.gating" title="Permalink to this headline">#</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.gating.find_percentile">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.gating.</span></span><span class="sig-name descname"><span class="pre">find_percentile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">workspace</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pyflowbat.pyflowbat.Workspace" title="pyflowbat.pyflowbat.Workspace"><span class="pre">pyflowbat.pyflowbat.Workspace</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">sample_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sample_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">percentile</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="headerlink" href="#pyflowbat.gating.find_percentile" title="Permalink to this definition">#</a></dt>
<dd><p>Finds the specified percentile of the data in a given channel
a PyFlowBAT sample.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>workspace</strong> (<a class="reference internal" href="#pyflowbat.pyflowbat.Workspace" title="pyflowbat.pyflowbat.Workspace"><em>pyflowbat.pyflowbat.Workspace</em></a>) – the PyFlowBAT Workspace containing the sample
whose percentile is desired.</p></li>
<li><p><strong>sample_collection_name</strong> (<em>str</em>) – the name of the sample collection
containing the sample whose percentile is desired</p></li>
<li><p><strong>sample_name</strong> (<em>str</em>) – the name of the sample whose percentile
is desired</p></li>
<li><p><strong>channel_name</strong> (<em>str</em>) – the name of the channel whose percentile
is desired</p></li>
<li><p><strong>percentile</strong> (<em>float</em>) – the desired percentile</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the desired percentile of the data in the specified channel
of the PyFlowBAT sample</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.gating.gate_heks">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.gating.</span></span><span class="sig-name descname"><span class="pre">gate_heks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_to_gate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">limits</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</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">'same'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">samples</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">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></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="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">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pyflowbat.gating.gate_heks" title="Permalink to this definition">#</a></dt>
<dd><p>Gates all samples in a collection for HEK 293FT by finding the
most extreme valleys in the FSC-A and SSC-A channels.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data_to_gate</strong> (<em>pyflowbat.pyflowbat.SampleCollection</em>) – the PyFlowBAT sample collection to gate;
NOTE: this parameter is provided to by the
<cite>pyflowbat.pyflowbat.Workspace.apply_gate</cite> method and should
NOT be specified by the user</p></li>
<li><p><strong>limits</strong> (<em>dict</em><em>[</em><em>str</em><em>, </em><em>list</em><em>[</em><em>float</em><em>]</em><em>]</em>) – the limits of the FSC-A and SSC-A channels;
NOTE: this parameter is provided to by the
<cite>pyflowbat.pyflowbat.Workspace.apply_gate</cite> method and should
NOT be specified by the user, to specify this parameter’s
value, change the value of <cite>limits</cite> within the Workspace in
which this gate is being applied</p></li>
<li><p><strong>method</strong> (<em>str</em>) – whether or not to use a unique gate for each
sample in the collection or the same gate for all samples,
options are “unique” or “same”,
defaults to “same”</p></li>
<li><p><strong>samples</strong> (<em>Optional</em><em>[</em><em>list</em><em>[</em><em>str</em><em>]</em><em>]</em>) – the samples to use to define the gate if the
“same” method is used,
defaults to None</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the gated PyFlowBAT sample collection</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>pyflowbat.pyflowbat.SampleCollection</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.gating.gate_high_low">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.gating.</span></span><span class="sig-name descname"><span class="pre">gate_high_low</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_to_gate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gating_channel_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">high</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">float</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">low</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">float</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="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">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pyflowbat.gating.gate_high_low" title="Permalink to this definition">#</a></dt>
<dd><p>Gates all samples in a collection within an upper and lower
bound in a specified channel.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data_to_gate</strong> (<em>pyflowbat.pyflowbat.SampleCollection</em>) – the PyFlowBAT sample collection to gate;
NOTE: this parameter is provided to by the
<cite>pyflowbat.pyflowbat.Workspace.apply_gate</cite> method and should
NOT be specified by the user</p></li>
<li><p><strong>gating_channel_name</strong> (<em>str</em>) – the name of the channel to gate
the samples</p></li>
<li><p><strong>high</strong> (<em>Optional</em><em>[</em><em>float</em><em>]</em>) – the upper bound</p></li>
<li><p><strong>low</strong> (<em>Optional</em><em>[</em><em>float</em><em>]</em>) – the lower bound</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the gated PyFlowBAT sample collection</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>pyflowbat.pyflowbat.SampleCollection</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.gating.gate_singlets">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.gating.</span></span><span class="sig-name descname"><span class="pre">gate_singlets</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_to_gate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">a</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">10000000000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">b</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">20000</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">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pyflowbat.gating.gate_singlets" title="Permalink to this definition">#</a></dt>
<dd><p>Gates all samples in a collection for singlets by drawing a tilted
ellipse.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data_to_gate</strong> (<em>pyflowbat.pyflowbat.SampleCollection</em>) – the PyFlowBAT sample collection to gat
NOTE: this parameter is provided to by the
<cite>pyflowbat.pyflowbat.Workspace.apply_gate</cite> method and should
NOT be specified by the user</p></li>
<li><p><strong>a</strong> (<em>float</em>) – the long axis of the ellipse surrounding the singlets,
defaults to 1*10**10</p></li>
<li><p><strong>b</strong> (<em>float</em>) – the short axis of the ellipse surrounding the singlets,
defaults to 2*10**4</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the gated PyFlowBAT sample collection</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>pyflowbat.pyflowbat.SampleCollection</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pyflowbat.operations">
<span id="pyflowbat-operations-module"></span><h2>pyflowbat.operations module<a class="headerlink" href="#module-pyflowbat.operations" title="Permalink to this headline">#</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.operations.apply_conversion_factor">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.operations.</span></span><span class="sig-name descname"><span class="pre">apply_conversion_factor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">factor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="headerlink" href="#pyflowbat.operations.apply_conversion_factor" title="Permalink to this definition">#</a></dt>
<dd><p>Given a number x and a conversion factor, returns x multiplied by the factor.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>x</strong> (<em>float</em>) – the value to convert</p></li>
<li><p><strong>factor</strong> (<em>float</em>) – the conversion factor to apply to x</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>x multiplied by the conversion factor</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.operations.channel_mean">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.operations.</span></span><span class="sig-name descname"><span class="pre">channel_mean</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">FlowCal.io.FCSData</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="headerlink" href="#pyflowbat.operations.channel_mean" title="Permalink to this definition">#</a></dt>
<dd><p>Computes the mean value of a given channel of FCS data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data</strong> (<em>FlowCal.io.FCSData</em>) – the FCS data with the desired mean</p></li>
<li><p><strong>channel_name</strong> (<em>str</em>) – the name of the channel of the desired mean</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the mean value of the specified channel of the specified FCS sample</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.operations.compute_conversion_factor_stdErr">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.operations.</span></span><span class="sig-name descname"><span class="pre">compute_conversion_factor_stdErr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">factor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">factor_err</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="headerlink" href="#pyflowbat.operations.compute_conversion_factor_stdErr" title="Permalink to this definition">#</a></dt>
<dd><p>Computes the standard error of the conversion factor multiplication.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>x</strong> (<em>float</em>) – the value being converted</p></li>
<li><p><strong>factor</strong> (<em>float</em>) – the conversion factor being applied</p></li>
<li><p><strong>factor_err</strong> (<em>float</em>) – the standard error of the conversion factor</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the standard error of the conversion</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.operations.non_negative">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.operations.</span></span><span class="sig-name descname"><span class="pre">non_negative</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="headerlink" href="#pyflowbat.operations.non_negative" title="Permalink to this definition">#</a></dt>
<dd><p>Given a number x, returns the x if x is non-negative and 0 otherwise.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>x</strong> (<em>float</em>) – a number</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>x if x is non-negative and 0 otherwise</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.operations.split_sample_name">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.operations.</span></span><span class="sig-name descname"><span class="pre">split_sample_name</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">→</span> <span class="sig-return-typehint"><span class="pre">str</span></span></span><a class="headerlink" href="#pyflowbat.operations.split_sample_name" title="Permalink to this definition">#</a></dt>
<dd><p>Splits a string by a character.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>name</strong> (<em>str</em>) – the string to split</p></li>
<li><p><strong>by</strong> (<em>str</em>) – the character to split by</p></li>
<li><p><strong>index</strong> (<em>int</em>) – the index of the split string to return</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the string at the specified index of the provided string split by the specified character</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pyflowbat.pyflowbat">
<span id="pyflowbat-pyflowbat-module"></span><h2>pyflowbat.pyflowbat module<a class="headerlink" href="#module-pyflowbat.pyflowbat" title="Permalink to this headline">#</a></h2>
<dl class="py class">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.StatisticsExtraction">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pyflowbat.pyflowbat.</span></span><span class="sig-name descname"><span class="pre">StatisticsExtraction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sample_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">statistics_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">not_include</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pyflowbat.pyflowbat.StatisticsExtraction" title="Permalink to this definition">#</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A class containing a rule for extracting statistics from a
sample collection.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sample_collection_name</strong> (<em>str</em>) – the name of the sample collection
in the workspace from which to extract the statistics</p></li>
<li><p><strong>statistics_collection_name</strong> (<em>str</em>) – the name of the statistics
collection to create/extract statistics into</p></li>
<li><p><strong>include</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the list of keywords in the names of samples
that must be present to extract statistics from that
sample, all keywords must be present in a sample’s name
for statistics to be extracted from it</p></li>
<li><p><strong>not_include</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the list of keywords in the names of
samples that must not be present to extract statistics
from that sample, all keywords must not be present in a
sample’s name for statistics to be extracted from it</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pyflowbat.pyflowbat.</span></span><span class="sig-name descname"><span class="pre">Workspace</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">stylesheet</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</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">{'axes.axisbelow':</span> <span class="pre">True,</span> <span class="pre">'axes.edgecolor':</span> <span class="pre">'B0B0B0',</span> <span class="pre">'axes.facecolor':</span> <span class="pre">'white',</span> <span class="pre">'axes.grid':</span> <span class="pre">True,</span> <span class="pre">'axes.labelsize':</span> <span class="pre">'large',</span> <span class="pre">'axes.linewidth':</span> <span class="pre">3.0,</span> <span class="pre">'axes.prop_cycle':</span> <span class="pre">cycler('color',</span> <span class="pre">['#0267c1',</span> <span class="pre">'#efa00b',</span> <span class="pre">'#00af54',</span> <span class="pre">'#e2cfea',</span> <span class="pre">'#d65108',</span> <span class="pre">'#6915E0',</span> <span class="pre">'#3DA5D9',</span> <span class="pre">'#FEC601',</span> <span class="pre">'#097109',</span> <span class="pre">'#EA7317',</span> <span class="pre">'#AF0BA5']),</span> <span class="pre">'axes.spines.bottom':</span> <span class="pre">False,</span> <span class="pre">'axes.spines.left':</span> <span class="pre">False,</span> <span class="pre">'axes.spines.right':</span> <span class="pre">False,</span> <span class="pre">'axes.spines.top':</span> <span class="pre">False,</span> <span class="pre">'axes.titlesize':</span> <span class="pre">'x-large',</span> <span class="pre">'figure.facecolor':</span> <span class="pre">'white',</span> <span class="pre">'figure.subplot.bottom':</span> <span class="pre">0.07,</span> <span class="pre">'figure.subplot.left':</span> <span class="pre">0.08,</span> <span class="pre">'figure.subplot.right':</span> <span class="pre">0.95,</span> <span class="pre">'font.size':</span> <span class="pre">14.0,</span> <span class="pre">'grid.color':</span> <span class="pre">'#B0B0B0',</span> <span class="pre">'grid.linestyle':</span> <span class="pre">':',</span> <span class="pre">'grid.linewidth':</span> <span class="pre">1.0,</span> <span class="pre">'legend.fancybox':</span> <span class="pre">True,</span> <span class="pre">'lines.linewidth':</span> <span class="pre">4,</span> <span class="pre">'lines.solid_capstyle':</span> <span class="pre">'butt',</span> <span class="pre">'patch.edgecolor':</span> <span class="pre">'white',</span> <span class="pre">'patch.linewidth':</span> <span class="pre">0.5,</span> <span class="pre">'savefig.edgecolor':</span> <span class="pre">'white',</span> <span class="pre">'savefig.facecolor':</span> <span class="pre">'white',</span> <span class="pre">'svg.fonttype':</span> <span class="pre">'path',</span> <span class="pre">'xtick.major.size':</span> <span class="pre">0,</span> <span class="pre">'xtick.minor.size':</span> <span class="pre">0,</span> <span class="pre">'ytick.major.size':</span> <span class="pre">0,</span> <span class="pre">'ytick.minor.size':</span> <span class="pre">0}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lims_file</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">'_std'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_output</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><span class="sig-paren">)</span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace" title="Permalink to this definition">#</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A class describing PyFlowBAT workspaces. Workspaces
contain all the methods for operating on batches
of PyFlowBAT data and contain all samples and
statistics.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>stylesheet</strong> (<em>dict</em>) – the stylesheet for plotting
PyFlowBAT analyzed data,
defaults to the PyFlowBAT standard stylesheet</p></li>
<li><p><strong>lims_file</strong> (<em>str</em>) – the path to the CSV file defining
upper and lower limits for standard PyFlowBAT
gating functions</p></li>
<li><p><strong>full_output</strong> (<em>bool</em>) – whether or not to display all
output of PyFlowBAT operations;
it is HIGHLY recommended to leave this at the
default value:
True,
defaults to True</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.apply_compensation_matrix">
<span class="sig-name descname"><span class="pre">apply_compensation_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sample_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_sample_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.apply_compensation_matrix" title="Permalink to this definition">#</a></dt>
<dd><p>Applies the workspace compensation matrix to one sample collection creating another.
NOTE: the workspace’s <cite>calculate_compensation_matrix</cite> method must be run before this
method may be run.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sample_collection_name</strong> (<em>str</em>) – the name of the sample collection to compensate</p></li>
<li><p><strong>new_sample_collection_name</strong> (<em>str</em>) – the name of the new sample collection to create
for the compensated samples</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.apply_gate">
<span class="sig-name descname"><span class="pre">apply_gate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sample_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_sample_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gating_function</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Callable</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_plots</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gating_channel_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</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">['FSC-A',</span> <span class="pre">'SSC-A']</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_override</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">bool</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="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">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.apply_gate" title="Permalink to this definition">#</a></dt>
<dd><p>Applies a specified gate to a sample collection.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sample_collection_name</strong> (<em>str</em>) – the name of the sample collection to gate</p></li>
<li><p><strong>new_sample_collection_name</strong> (<em>str</em>) – the name of the new sample collection to create
for the gated samples</p></li>
<li><p><strong>gating_function</strong> (<em>function/Callable</em>) – the function defining the gate to apply</p></li>
<li><p><strong>output_plots</strong> (<em>int</em>) – the number of plots to visualize if full output is true,
defaults to 5</p></li>
<li><p><strong>gating_channel_names</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the channels to visualize,
if has more than one element, uses the first two
elements
if has one element, uses that value twice,
defaults to <cite>[“FSC-A”, “SSC-A”]</cite></p></li>
<li><p><strong>output_override</strong> (<em>Optional</em><em>[</em><em>bool</em><em>]</em>) – if not <cite>None</cite>, workspace will use this
instead of its <cite>full_output</cite> variable,
defaults to None</p></li>
<li><p><strong>**kwargs</strong> – keywords to pass to the gating function</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.apply_operation">
<span class="sig-name descname"><span class="pre">apply_operation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">statistics_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_statistics_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">statistic_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_statistic_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operation</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Callable</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">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.apply_operation" title="Permalink to this definition">#</a></dt>
<dd><p>Applies a specified operation to a statistic in a statistics collection.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>statistics_collection_name</strong> (<em>str</em>) – the name of the statistics collection to
operate on</p></li>
<li><p><strong>new_statistics_collection_name</strong> (<em>str</em>) – the name of the new statistics collection
to create for the post-operation statistics</p></li>
<li><p><strong>statistic_name</strong> (<em>Union</em><em>[</em><em>str</em><em>, </em><em>list</em><em>[</em><em>str</em><em>]</em><em>]</em>) – the name of the statistic to operate on;
can be a single statistic or multiple; only statistics specified
here will be used in the operation</p></li>
<li><p><strong>new_statistic_name</strong> (<em>str</em>) – the name of the statistic to be created from
the operation</p></li>
<li><p><strong>operation</strong> (<em>function/Callable</em>) – the function defining the opperation to apply</p></li>
<li><p><strong>**kwargs</strong> – keywords to pass to the operation</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.calculate_beads_factors">
<span class="sig-name descname"><span class="pre">calculate_beads_factors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">beads_file_file_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">beads_fluorescent_channels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">beads_num_pops</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">beads_conversions_file</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">'_std'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.calculate_beads_factors" title="Permalink to this definition">#</a></dt>
<dd><p>Calculates the conversion factors for this workspace
from a specified beads file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>beads_file_file_path</strong> (<em>str</em>) – the path to the beads file
to calculate conversion factors from</p></li>
<li><p><strong>beads_fluorescent_channels</strong> (<em>list</em><em>[</em><em>tuple</em><em>[</em><em>str</em><em>, </em><em>str</em><em>]</em><em>]</em>) – a list of tuples containing
the names of the fluorescent channels and the corresponding
MEFs;
follows the pattern of:
[(CHANNEL, MEF), (CHANNEL, MEF),…]</p></li>
<li><p><strong>beads_num_pops</strong> (<em>int</em>) – the number of beads populations in the
beads file to calculate conversion factors from</p></li>
<li><p><strong>beads_conversions_file</strong> (<em>str</em>) – the path to the file
specifying the manufacturers bead conversion values,
defaults to the PyFlowBAT standard beads values aka
Spherotech RCP-30-5 Rainbow Calibration Beads</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.calculate_compensation_matrix">
<span class="sig-name descname"><span class="pre">calculate_compensation_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sample_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compensation_sample_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compensation_channel_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">0.0001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compensation_rate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">0.1</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.calculate_compensation_matrix" title="Permalink to this definition">#</a></dt>
<dd><p>Calculates a compensation matrix by repeatedly flattening to zero
the best fit line through the specified compensation sample data.
Flattening stops once the best fit line has a slope under the provided
threshold.
NOTE: at present, only 2- and 3- sample compensation matrices can
be calculated.
NOTE: at present, flattening continues for all compensation samples
as long as any compensation sample has a best fit slope greater than
the threshold.
NOTE: this method must always be run before the workspace’s
<cite>apply_compensation_matrix</cite> method.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sample_collection_name</strong> (<em>str</em>) – the name of the collection from
which to find the samples for compensation matrix calculation</p></li>
<li><p><strong>compensation_sample_names</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the names of the samples used
for compensation</p></li>
<li><p><strong>compensation_channel_names</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the channel names to be
compensated</p></li>
<li><p><strong>threshold</strong> (<em>float</em>) – the threshold to flatten the best fit
lines to,
defaults to 10**4</p></li>
<li><p><strong>compensation_rate</strong> (<em>float</em>) – the rate at which to calculate the
compensation matrix,
defaults to 0.1</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.combine_replicates">
<span class="sig-name descname"><span class="pre">combine_replicates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">statistics_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combined_statistics_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_by</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combination_operations</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Callable</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sem_cols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.combine_replicates" title="Permalink to this definition">#</a></dt>
<dd><p>Combines replicates in a statistics collection.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>statistics_collection_name</strong> (<em>str</em>) – the name of the statistics collection
from which to combine replicates</p></li>
<li><p><strong>combined_statistics_collection_name</strong> (<em>str</em>) – the name of the new statistics
collection storing the combined statistics</p></li>
<li><p><strong>combine_by</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the statistics by which to combine replicates;
each set of statistics is combined if all statistics here are
equivalent</p></li>
<li><p><strong>combination_operations</strong> (<em>dict</em><em>[</em><em>str</em><em>, </em><em>Union</em><em>[</em><em>function/Callable</em><em>, </em><em>str</em><em>]</em><em>]</em>) – the functions defining the operation
by which to combine rows for each column;
may be a Pandas GroupBy function or a function;
follows the pattern:
{STATISTIC: OPERATION, STATISTIC: OPERATION…}</p></li>
<li><p><strong>sem_cols</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – list of statistics for which the standard error of the mean
of the combination should be calculated</p></li>
<li><p><strong>**kwargs</strong> – keywords to pass to the combination operation</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.create_statistic_extraction">
<span class="sig-name descname"><span class="pre">create_statistic_extraction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sample_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">statistics_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">not_include</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">statistic_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pyflowbat.pyflowbat.StatisticsExtraction" title="pyflowbat.pyflowbat.StatisticsExtraction"><span class="pre">pyflowbat.pyflowbat.StatisticsExtraction</span></a></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.create_statistic_extraction" title="Permalink to this definition">#</a></dt>
<dd><p>Creates a rule needed for extracting statistics from a sample collection</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sample_collection_name</strong> (<em>str</em>) – the name of the sample collection from which to extract</p></li>
<li><p><strong>statistics_collection_name</strong> (<em>str</em>) – the name of the statistics collection to create and extract statistics to</p></li>
<li><p><strong>include</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – a list of words that must be included in the samples from which to extract statistics</p></li>
<li><p><strong>not_include</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – a list of words that must NOT be included in the samples from which to extract statistics</p></li>
<li><p><strong>statistic_names</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – a list of the stastics that will be extracted using this rule</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the extraction rule to be used in <cite>extract_samples</cite></p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="#pyflowbat.pyflowbat.StatisticsExtraction" title="pyflowbat.pyflowbat.StatisticsExtraction">pyflowbat.pyflowbat.StatisticsExtraction</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.extract_statistic">
<span class="sig-name descname"><span class="pre">extract_statistic</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">extraction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pyflowbat.pyflowbat.StatisticsExtraction" title="pyflowbat.pyflowbat.StatisticsExtraction"><span class="pre">pyflowbat.pyflowbat.StatisticsExtraction</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">statistic_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operation</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Callable</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">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.extract_statistic" title="Permalink to this definition">#</a></dt>
<dd><p>Extracts a statistic for a StatisticExtraction rule.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>extraction</strong> (<a class="reference internal" href="#pyflowbat.pyflowbat.StatisticsExtraction" title="pyflowbat.pyflowbat.StatisticsExtraction"><em>pyflowbat.pyflowbat.StatisticsExtraction</em></a>) – the StatisticExtraction rule to use for the
extraction</p></li>
<li><p><strong>statistic_name</strong> (<em>str</em>) – the name of the statistic being created</p></li>
<li><p><strong>operation</strong> (<em>function/Callable</em>) – the function defining the operation defining
the extraction</p></li>
<li><p><strong>**kwargs</strong> – keywords to pass to the operation</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.graph_statistics">
<span class="sig-name descname"><span class="pre">graph_statistics</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">errors</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">bool</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">bool</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">(False,</span> <span class="pre">False)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">legend</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">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></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">title</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">str</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">labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></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 class="pre">None)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xlog</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">ylog</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">save</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">bool</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</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">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.graph_statistics" title="Permalink to this definition">#</a></dt>
<dd><p>Plots statistics from a collection.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data</strong> (<em>list</em><em>[</em><em>list</em><em>[</em><em>Union</em><em>[</em><em>str</em><em>, </em><em>tuple</em><em>[</em><em>str</em><em>, </em><em>str</em><em>]</em><em>]</em><em>]</em><em>]</em>) – the data to plot;
follows the pattern of a list of the following:
[STATISTIC_COLLECTION_NAME, X_STATISTIC_NAME, Y_STATISTIC_NAME, SPECIFICATION_TUPLEs…];
where each SPECIFICATION_TUPLE is follows the pattern of:
(STATISTIC, VALUE);
and only rows were STATISTIC=VALUE are included in this x,y plot;
an arbitrary number of SPECIFICATION_TUPLEs can be included;
an arbitrary number of these lists can be included to define different scatter
plots in one figure</p></li>
<li><p><strong>errors</strong> (<em>tuple</em><em>[</em><em>bool</em><em>, </em><em>bool</em><em>]</em>) – if x and y axis errors should be included; only
one tuple can be provided for the entire figure,
defaults to (False, False)</p></li>
<li><p><strong>legend</strong> (<em>Optional</em><em>[</em><em>list</em><em>[</em><em>str</em><em>]</em><em>]</em>) – the legend for the plot,
defaults to None</p></li>
<li><p><strong>title</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em>) – the title for the plot,
defaults to None</p></li>
<li><p><strong>labels</strong> (<em>tuple</em><em>[</em><em>Optional</em><em>[</em><em>str</em><em>]</em><em>, </em><em>Optional</em><em>[</em><em>str</em><em>]</em><em>]</em>) – the x and y labels for the plot,
defaults to (None, None)</p></li>
<li><p><strong>xlog</strong> (<em>bool</em>) – if the x axis should be in logarithmic scale,
defaults to False</p></li>
<li><p><strong>ylog</strong> (<em>bool</em>) – if the y axis should be in logarithmic scale,
defaults to False</p></li>
<li><p><strong>save</strong> (<em>Union</em><em>[</em><em>bool</em><em>, </em><em>str</em><em>]</em>) – if the plot should be saved;
can be a boolean or a string;
if a string, saves to the specified file;
if a boolean, saves to a file with the
name of the plot title if True;
does not save figure if set to False,
defaults to True</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.init_r">
<span class="sig-name descname"><span class="pre">init_r</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">check_R_installation</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">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.init_r" title="Permalink to this definition">#</a></dt>
<dd><p>Initialized R functionality for R language gating functions.
NOTE: this method and R gating functionality both require
the R programming language to be installed for features to
work properly.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>check_R_installation</strong> (<em>bool</em>) – whether or not to check if the R
language is installed
it is HIGHLY recommended to leave this at the
default value:
True,
defaults to True</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.load_samples">
<span class="sig-name descname"><span class="pre">load_samples</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sample_collection_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">samples_folder_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">not_include</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.load_samples" title="Permalink to this definition">#</a></dt>
<dd><p>Loads samples from a folder into a sample collection in the workspace.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sample_collection_name</strong> (<em>str</em>) – the name of the sample collection
into which to load samples</p></li>
<li><p><strong>samples_folder_path</strong> (<em>str</em>) – the path to the folder with the samples
to load</p></li>
<li><p><strong>include</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the list of keywords in the names of files
that must be present to load, all keywords must be
present in a file’s name to load as a sample</p></li>
<li><p><strong>not_include</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the list of keywords in the names of files
that must not be present to load, all keywords must not be
present in a file’s name to load as a sample</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.visualize_plot_change">
<span class="sig-name descname"><span class="pre">visualize_plot_change</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sample_collection_name_0</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sample_collection_name_f</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sample_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.visualize_plot_change" title="Permalink to this definition">#</a></dt>
<dd><p>Visualizes the change in a sample from one collection to another.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sample_collection_name_0</strong> (<em>str</em>) – the name of the initial sample collection</p></li>
<li><p><strong>sample_collection_name_f</strong> (<em>str</em>) – the name of the final sample collection</p></li>
<li><p><strong>sample_name</strong> (<em>str</em>) – the name of the sample to visualize</p></li>
<li><p><strong>channel_names</strong> (<em>tuple</em><em>[</em><em>str</em><em>, </em><em>str</em><em>]</em>) – the names of the channels to visualize change in</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pyflowbat.pyflowbat.Workspace.visualize_plot_overlay">
<span class="sig-name descname"><span class="pre">visualize_plot_overlay</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">plots</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colors</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sizes</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">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></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">markers</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">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></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">legend</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">list</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">title</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">str</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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#pyflowbat.pyflowbat.Workspace.visualize_plot_overlay" title="Permalink to this definition">#</a></dt>
<dd><p>Visualizes an overlay between samples.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>plots</strong> (<em>list</em><em>[</em><em>list</em><em>]</em>) – the data to plot</p></li>
<li><p><strong>colors</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the names of the colors for the overlayed plots</p></li>
<li><p><strong>channel_names</strong> (<em>tuple</em><em>[</em><em>str</em><em>, </em><em>str</em><em>]</em>) – the names of the channels to visualize change in</p></li>
<li><p><strong>sizes</strong> (<em>Optional</em><em>[</em><em>list</em><em>[</em><em>int</em><em>]</em><em>]</em>) – the sizes of the scatters to overlay</p></li>
<li><p><strong>markers</strong> (<em>Optional</em><em>[</em><em>list</em><em>[</em><em>str</em><em>]</em><em>]</em>) – the markers for the plot</p></li>
<li><p><strong>legend</strong> (<em>Optional</em><em>[</em><em>list</em><em>]</em>) – the legend for the plot</p></li>
<li><p><strong>title</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em>) – the title for the plot</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pyflowbat.r_gating">
<span id="pyflowbat-r-gating-module"></span><h2>pyflowbat.r_gating module<a class="headerlink" href="#module-pyflowbat.r_gating" title="Permalink to this headline">#</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.r_gating.clust_2d_gate">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.r_gating.</span></span><span class="sig-name descname"><span class="pre">clust_2d_gate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_to_gate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gating_channel_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">quantile</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">0.95</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">K</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">_r_ready</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="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">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pyflowbat.r_gating.clust_2d_gate" title="Permalink to this definition">#</a></dt>
<dd><p>PyFlowBAT wrapper for the <cite>flowClust.2d</cite> function from the R <cite>OpenCyto</cite> library.
For more, please see the OpenCyto documentation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data_to_gate</strong> (<em>pyflowbat.pyflowbat.SampleCollection</em>) – the PyFlowBAT sample collection to gate;
NOTE: this parameter is provided by the
<cite>pyflowbat.pyflowbat.Workspace.apply_gate</cite> method and should
NOT be specified by the user</p></li>
<li><p><strong>gating_channel_names</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the 2 channels to use for gating</p></li>
<li><p><strong>target</strong> (<em>list</em><em>[</em><em>float</em><em>]</em>) – the 2 dimenstional target around which to cluster</p></li>
<li><p><strong>quantile</strong> (<em>float</em>) – the quantile provided to <cite>flowClust.2d</cite> for gating,
defaults to 0.95</p></li>
<li><p><strong>K</strong> (<em>int</em>) – the K provided to <cite>flowClust.2d</cite> for gating,
defaults to 2</p></li>
<li><p><strong>_r_ready</strong> (<em>bool</em>) – a boolean describing whether or not R functionality
has been initialized forthis Workspace;
NOTE: this parameter is provided by the
<cite>pyflowbat.pyflowbat.Workspace.apply_gate</cite> method and should
NOT be specified by the user</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the gated PyFlowBAT sample collection</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>pyflowbat.pyflowbat.SampleCollection</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.r_gating.singlet_gate">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.r_gating.</span></span><span class="sig-name descname"><span class="pre">singlet_gate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_to_gate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gating_channel_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">_r_ready</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="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">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pyflowbat.r_gating.singlet_gate" title="Permalink to this definition">#</a></dt>
<dd><p>PyFlowBAT wrapper for the <cite>singletGate</cite> function from the R <cite>OpenCyto</cite> library.
For more, please see the OpenCyto documentation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data_to_gate</strong> (<em>pyflowbat.pyflowbat.SampleCollection</em>) – the PyFlowBAT sample collection to gate;
NOTE: this parameter is provided by the
<cite>pyflowbat.pyflowbat.Workspace.apply_gate</cite> method and should
NOT be specified by the user</p></li>
<li><p><strong>gating_channel_names</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the 2 channels to use for gating</p></li>
<li><p><strong>_r_ready</strong> (<em>bool</em>) – a boolean describing whether or not R functionality
has been initialized for this Workspace;
NOTE: this parameter is provided by the
<cite>pyflowbat.pyflowbat.Workspace.apply_gate</cite> method and should
NOT be specified by the user</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the gated PyFlowBAT sample collection</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>pyflowbat.pyflowbat.SampleCollection</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pyflowbat.r_gating.transitional_gate">
<span class="sig-prename descclassname"><span class="pre">pyflowbat.r_gating.</span></span><span class="sig-name descname"><span class="pre">transitional_gate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_to_gate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gating_channel_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">quantile</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">0.95</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">K</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">translation</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">0.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">_r_ready</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="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">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">FlowCal.io.FCSData</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pyflowbat.r_gating.transitional_gate" title="Permalink to this definition">#</a></dt>
<dd><p>PyFlowBAT wrapper for the <cite>flowClust.2d</cite> translational gate function from the R <cite>OpenCyto</cite> library.
For more, please see the OpenCyto documentation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data_to_gate</strong> (<em>pyflowbat.pyflowbat.SampleCollection</em>) – the PyFlowBAT sample collection to gate;
NOTE: this parameter is provided by the
<cite>pyflowbat.pyflowbat.Workspace.apply_gate</cite> method and should
NOT be specified by the user</p></li>
<li><p><strong>gating_channel_names</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – the 2 channel names to use for gating</p></li>
<li><p><strong>target</strong> (<em>list</em><em>[</em><em>float</em><em>]</em>) – the 2 dimenstional target around which to cluster</p></li>
<li><p><strong>quantile</strong> (<em>float</em>) – the quantile provided to <cite>flowClust.2d</cite> for gating,
defaults to 0.95</p></li>
<li><p><strong>K</strong> (<em>int</em>) – the K provided to <cite>flowClust.2d</cite> for gating,
defaults to 2</p></li>
<li><p><strong>translation</strong> (<em>float</em>) – the translation provided to <cite>flowClust.2d</cite> for gating,
defaults to 0.15</p></li>
<li><p><strong>_r_ready</strong> (<em>bool</em>) – a boolean describing whether or not R functionality
has been initialized forthis Workspace;
NOTE: this parameter is provided by the
<cite>pyflowbat.pyflowbat.Workspace.apply_gate</cite> method and should
NOT be specified by the user</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the gated PyFlowBAT sample collection</p>