update doc

docs/html/_modules/PyWGCNA/wgcna.html

@@ -132,6 +132,7 @@ <h1>Source code for PyWGCNA.wgcna</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">gseapy.plot</span> <span class="kn">import</span> <span class="n">dotplot</span>
 <span class="kn">from</span> <span class="nn">pyvis.network</span> <span class="kn">import</span> <span class="n">Network</span>
 <span class="kn">from</span> <span class="nn">reactome2py</span> <span class="kn">import</span> <span class="n">analysis</span>
+<span class="kn">from</span> <span class="nn">pandas.api.types</span> <span class="kn">import</span> <span class="n">is_numeric_dtype</span>
 
 <span class="kn">from</span> <span class="nn">PyWGCNA.geneExp</span> <span class="kn">import</span> <span class="o">*</span>
 
@@ -172,7 +173,6 @@ <h1>Source code for PyWGCNA.wgcna</h1><div class="highlight"><pre>
 <span class="n">BOLD</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\033</span><span class="s2">[1m&quot;</span>
 <span class="n">UNDERLINE</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\033</span><span class="s2">[4m&quot;</span>
 
-
 <div class="viewcode-block" id="WGCNA"><a class="viewcode-back" href="../../api.html#PyWGCNA.wgcna.WGCNA">[docs]</a><span class="k">class</span> <span class="nc">WGCNA</span><span class="p">(</span><span class="n">GeneExp</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    A class used to do weighted gene co-expression network analysis.</span>
@@ -2467,7 +2467,7 @@ <h1>Source code for PyWGCNA.wgcna</h1><div class="highlight"><pre>
 <span class="sd">        :param MEs: Module eigengenes in a multi-set format.</span>
 <span class="sd">        :type MEs: dict</span>
 <span class="sd">        :param greyLast: Normally the color grey is reserved for unassigned genes; hence the grey module is not a proper module and it is conventional to put it last. If this is not desired, set the parameter to FALSE. (default = True)</span>
-<span class="sd">        :type greyLast:bool</span>
+<span class="sd">        :type greyLast: bool</span>
 <span class="sd">        :param greyName: Name of the grey module eigengene. (default = &quot;MEgrey&quot;)</span>
 <span class="sd">        :type greyName: str</span>
 <span class="sd">        :param orderBy: Specifies the set by which the eigengenes are to be ordered (in all other sets as well). Defaults to the first set in useSets (or the first set, if useSets is not given). (defualt = 0)</span>
@@ -2842,6 +2842,9 @@ <h1>Source code for PyWGCNA.wgcna</h1><div class="highlight"><pre>
         <span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">datExpr</span><span class="o">.</span><span class="n">obs</span><span class="o">.</span><span class="n">copy</span><span class="p">()[</span><span class="n">metaData</span><span class="p">]</span>
         <span class="n">datTraits</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">index</span><span class="o">=</span><span class="n">data</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
         <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">data</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span>
+            <span class="k">if</span> <span class="n">is_numeric_dtype</span><span class="p">(</span><span class="n">data</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">dtypes</span><span class="p">):</span>
+                <span class="n">datTraits</span><span class="p">[</span><span class="n">data</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="n">i</span><span class="p">]</span>
+                <span class="k">continue</span>
             <span class="n">data</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span>
             <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">data</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="n">i</span><span class="p">]))</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
                 <span class="n">datTraits</span><span class="p">[</span><span class="n">data</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="n">i</span><span class="p">]</span>

docs/html/api.html

@@ -929,25 +929,18 @@
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>MEs</strong> (<em>dict</em>) – Module eigengenes in a multi-set format.</p></li>
-<li><p><strong>greyLast</strong> – Normally the color grey is reserved for unassigned genes; hence the grey module is not a proper module and it is conventional to put it last. If this is not desired, set the parameter to FALSE. (default = True)</p></li>
+<li><p><strong>greyLast</strong> (<em>bool</em>) – Normally the color grey is reserved for unassigned genes; hence the grey module is not a proper module and it is conventional to put it last. If this is not desired, set the parameter to FALSE. (default = True)</p></li>
+<li><p><strong>greyName</strong> (<em>str</em>) – Name of the grey module eigengene. (default = “MEgrey”)</p></li>
+<li><p><strong>orderBy</strong> (<em>int</em>) – Specifies the set by which the eigengenes are to be ordered (in all other sets as well). Defaults to the first set in useSets (or the first set, if useSets is not given). (defualt = 0)</p></li>
+<li><p><strong>order</strong> (<em>list</em>) – Allows the user to specify a custom ordering.</p></li>
+<li><p><strong>useSets</strong> (<em>list</em>) – Allows the user to specify for which sets the eigengene ordering is to be performed.</p></li>
 </ul>
 </dd>
-</dl>
-<p>:type greyLast:bool
-:param greyName: Name of the grey module eigengene. (default = “MEgrey”)
-:type greyName: str
-:param orderBy: Specifies the set by which the eigengenes are to be ordered (in all other sets as well). Defaults to the first set in useSets (or the first set, if useSets is not given). (defualt = 0)
-:type orderBy: int
-:param order: Allows the user to specify a custom ordering.
-:type order: list
-:param useSets: Allows the user to specify for which sets the eigengene ordering is to be performed.
-:type useSets: list</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>A dictionary of the same type as MEs containing the re-ordered eigengenes.</p>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A dictionary of the same type as MEs containing the re-ordered eigengenes.</p>
 </dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p>dict</p>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p>dict</p>
 </dd>
 </dl>
 </dd></dl>