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matsengrp · Feb 28, 2024 · e01ab9a · e01ab9a
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diff --git a/multidms.data.html b/multidms.data.html
@@ -56,7 +56,7 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="multidms.data.Data">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">multidms.data.</span></span><span class="sig-name descname"><span class="pre">Data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variants_df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.0)"><span class="pre">DataFrame</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">('A',</span> <span class="pre">'C',</span> <span class="pre">'D',</span> <span class="pre">'E',</span> <span class="pre">'F',</span> <span class="pre">'G',</span> <span class="pre">'H',</span> <span class="pre">'I',</span> <span class="pre">'K',</span> <span class="pre">'L',</span> <span class="pre">'M',</span> <span class="pre">'N',</span> <span class="pre">'P',</span> <span class="pre">'Q',</span> <span class="pre">'R',</span> <span class="pre">'S',</span> <span class="pre">'T',</span> <span class="pre">'V',</span> <span class="pre">'W',</span> <span class="pre">'Y')</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">collapse_identical_variants</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">condition_colors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">('#0072B2',</span> <span class="pre">'#CC79A7',</span> <span class="pre">'#009E73',</span> <span class="pre">'#17BECF',</span> <span class="pre">'#BCDB22')</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">letter_suffixed_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">assert_site_integrity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nb_workers</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#multidms.data.Data" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">multidms.data.</span></span><span class="sig-name descname"><span class="pre">Data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variants_df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.1)"><span class="pre">DataFrame</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">('A',</span> <span class="pre">'C',</span> <span class="pre">'D',</span> <span class="pre">'E',</span> <span class="pre">'F',</span> <span class="pre">'G',</span> <span class="pre">'H',</span> <span class="pre">'I',</span> <span class="pre">'K',</span> <span class="pre">'L',</span> <span class="pre">'M',</span> <span class="pre">'N',</span> <span class="pre">'P',</span> <span class="pre">'Q',</span> <span class="pre">'R',</span> <span class="pre">'S',</span> <span class="pre">'T',</span> <span class="pre">'V',</span> <span class="pre">'W',</span> <span class="pre">'Y')</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">collapse_identical_variants</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">condition_colors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">('#0072B2',</span> <span class="pre">'#CC79A7',</span> <span class="pre">'#009E73',</span> <span class="pre">'#17BECF',</span> <span class="pre">'#BCDB22')</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">letter_suffixed_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">assert_site_integrity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nb_workers</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#multidms.data.Data" title="Link to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <p>Prep and store one-hot encoding of
 variant substitutions data.
@@ -65,7 +65,7 @@
 for efficiently fitting various models to the same data.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>You can initialize a <a class="reference internal" href="#multidms.data.Data" title="multidms.data.Data"><code class="xref py py-class docutils literal notranslate"><span class="pre">Data</span></code></a> object with a <a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code></a>
+<p>You can initialize a <a class="reference internal" href="#multidms.data.Data" title="multidms.data.Data"><code class="xref py py-class docutils literal notranslate"><span class="pre">Data</span></code></a> object with a <a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code></a>
 with a row for each variant sampled and annotations
 provided in the required columns:</p>
 <ol class="arabic simple">
@@ -93,7 +93,7 @@
 <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>variants_df</strong> (<a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code></a> or None) – The variant level information from all experiments you
+<li><p><strong>variants_df</strong> (<a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code></a> or None) – The variant level information from all experiments you
 wish to analyze. Should have columns named <code class="docutils literal notranslate"><span class="pre">'condition'</span></code>,
 <code class="docutils literal notranslate"><span class="pre">'aa_substitutions'</span></code>, and <code class="docutils literal notranslate"><span class="pre">'func_score'</span></code>.
 See the class note for descriptions of each of the features.</p></li>
@@ -248,19 +248,19 @@
 
 <dl class="py property">
 <dt class="sig sig-object py" id="multidms.data.Data.mutations_df">
-<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mutations_df</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.0)"><span class="pre">DataFrame</span></a></em><a class="headerlink" href="#multidms.data.Data.mutations_df" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mutations_df</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.1)"><span class="pre">DataFrame</span></a></em><a class="headerlink" href="#multidms.data.Data.mutations_df" title="Link to this definition">¶</a></dt>
 <dd><p>A dataframe summarizing all single mutations</p>
 </dd></dl>
 
 <dl class="py property">
 <dt class="sig sig-object py" id="multidms.data.Data.variants_df">
-<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">variants_df</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.0)"><span class="pre">DataFrame</span></a></em><a class="headerlink" href="#multidms.data.Data.variants_df" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">variants_df</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.1)"><span class="pre">DataFrame</span></a></em><a class="headerlink" href="#multidms.data.Data.variants_df" title="Link to this definition">¶</a></dt>
 <dd><p>A dataframe summarizing all variants in the training data.</p>
 </dd></dl>
 
 <dl class="py property">
 <dt class="sig sig-object py" id="multidms.data.Data.site_map">
-<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">site_map</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.0)"><span class="pre">DataFrame</span></a></em><a class="headerlink" href="#multidms.data.Data.site_map" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">site_map</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.1)"><span class="pre">DataFrame</span></a></em><a class="headerlink" href="#multidms.data.Data.site_map" title="Link to this definition">¶</a></dt>
 <dd><p>A dataframe indexed by site, with columns
 for all conditions giving the wild type amino acid
 at each site.</p>
@@ -278,7 +278,7 @@
 <dt class="sig sig-object py" id="multidms.data.Data.non_identical_sites">
 <em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">non_identical_sites</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><span class="pre">dict</span></a></em><a class="headerlink" href="#multidms.data.Data.non_identical_sites" title="Link to this definition">¶</a></dt>
 <dd><p>A dictionary keyed by condition names with values
-being a <a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code></a> indexed by site,
+being a <a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code></a> indexed by site,
 with columns for the reference
 and non-reference amino acid at each site that differs.</p>
 </dd></dl>