deploy: 176bd94

_modules/ete4/smartview/renderer/nodestyle.html

@@ -91,7 +91,7 @@ <h1>Source code for ete4.smartview.renderer.nodestyle</h1><div class="highlight"
 <span class="sd">        :param 3 size: integer number</span>
 <span class="sd">        :param &quot;circle&quot; shape: &quot;circle&quot;, &quot;square&quot; or &quot;sphere&quot;</span>
 <span class="sd">        :param True draw_descendants: Mark an internal node as a leaf.</span>
-<span class="sd">                :param 0 hz_line_width: integer number representing the width</span>
+<span class="sd">        :param 0 hz_line_width: integer number representing the width</span>
 <span class="sd">            of the line in pixels. A line width of zero indicates a</span>
 <span class="sd">            cosmetic pen. This means that the pen width is always</span>
 <span class="sd">            drawn one pixel wide, independent of the transformation</span>

_sources/tutorial/tutorial_phylogeny.rst.txt

@@ -439,8 +439,6 @@ purpose.
 Working with duplicated gene families
 -------------------------------------
 
-.. _treeko_trees:
-
 TreeKO (splitting gene trees into species trees)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -544,8 +542,6 @@ Here is a basic example on how to use it::
   be processed or dumped into a file.
 
 
-.. _split_by_dup:
-
 Splitting gene trees by duplication events
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -602,8 +598,6 @@ Example::
   # ╴Yeast_1
 
 
-.. _collapse_expansions:
-
 Collapse species specific duplications
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

reference/reference_smartview.html

@@ -85,7 +85,7 @@ <h1><a class="toc-backref" href="#id1" role="doc-backlink">Smartview (web graphi
 </dl>
 <dl class="py class">
 <dt class="sig sig-object py" id="ete4.smartview.gui.server.AppTree">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">AppTree</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree:</span> <span class="pre">ete4.core.tree.Tree</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name:</span> <span class="pre">str</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">style:</span> <span class="pre">ete4.smartview.renderer.treestyle.TreeStyle</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nodestyles:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">layouts:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timer:</span> <span class="pre">float</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialized:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selected:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">active:</span> <span class="pre">&lt;function</span> <span class="pre">namedtuple</span> <span class="pre">at</span> <span class="pre">0x7fe86c71b2e0&gt;</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">searches:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/ete4/smartview/gui/server.html#AppTree"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ete4.smartview.gui.server.AppTree" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">AppTree</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree:</span> <span class="pre">ete4.core.tree.Tree</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name:</span> <span class="pre">str</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">style:</span> <span class="pre">ete4.smartview.renderer.treestyle.TreeStyle</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nodestyles:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">layouts:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timer:</span> <span class="pre">float</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialized:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selected:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">active:</span> <span class="pre">&lt;function</span> <span class="pre">namedtuple</span> <span class="pre">at</span> <span class="pre">0x7f2d0a51b2e0&gt;</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">searches:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/ete4/smartview/gui/server.html#AppTree"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ete4.smartview.gui.server.AppTree" title="Link to this definition">¶</a></dt>
 <dd><dl class="py method">
 <dt class="sig sig-object py" id="ete4.smartview.gui.server.AppTree.__init__">
 <span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="reference_tree.html#ete4.Tree" title="ete4.core.tree.Tree"><span class="pre">Tree</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <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><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">style</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#ete4.smartview.renderer.treestyle.TreeStyle" title="ete4.smartview.renderer.treestyle.TreeStyle"><span class="pre">TreeStyle</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nodestyles</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_props</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</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">exclude_props</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</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">layouts</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</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">timer</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialized</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">selected</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">active</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">namedtuple</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">searches</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">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#ete4.smartview.gui.server.AppTree.__init__" title="Link to this definition">¶</a></dt>
@@ -1639,19 +1639,12 @@ <h3><a class="toc-backref" href="#id8" role="doc-backlink">Nexus</a><a class="he
 <li><p><strong>vt_line_type</strong> (<em>0</em>) – integer number</p></li>
 <li><p><strong>size</strong> (<em>3</em>) – integer number</p></li>
 <li><p><strong>shape</strong> (<em>&quot;circle&quot;</em>) – “circle”, “square” or “sphere”</p></li>
-<li><p><strong>draw_descendants</strong> (<em>True</em>) – <dl class="simple">
-<dt>Mark an internal node as a leaf.</dt><dd><dl class="field-list simple">
-<dt class="field-odd">param 0 hz_line_width<span class="colon">:</span></dt>
-<dd class="field-odd"><p>integer number representing the width</p>
-</dd>
-</dl>
-</dd>
-</dl>
-<p>of the line in pixels. A line width of zero indicates a
+<li><p><strong>draw_descendants</strong> (<em>True</em>) – Mark an internal node as a leaf.</p></li>
+<li><p><strong>hz_line_width</strong> (<em>0</em>) – integer number representing the width
+of the line in pixels. A line width of zero indicates a
 cosmetic pen. This means that the pen width is always
 drawn one pixel wide, independent of the transformation
-set on the painter.</p>
-</p></li>
+set on the painter.</p></li>
 <li><p><strong>vt_line_width</strong> (<em>0</em>) – integer number representing the width
 of the line in pixels. A line width of zero indicates a
 cosmetic pen. This means that the pen width is always

tutorial/tutorial_phylogeny.html

@@ -784,7 +784,7 @@ <h2><a class="toc-backref" href="#id15" role="doc-backlink">Automatic rooting (o
 <section id="working-with-duplicated-gene-families">
 <h2><a class="toc-backref" href="#id16" role="doc-backlink">Working with duplicated gene families</a><a class="headerlink" href="#working-with-duplicated-gene-families" title="Link to this heading">¶</a></h2>
 <section id="treeko-splitting-gene-trees-into-species-trees">
-<span id="treeko-trees"></span><h3><a class="toc-backref" href="#id17" role="doc-backlink">TreeKO (splitting gene trees into species trees)</a><a class="headerlink" href="#treeko-splitting-gene-trees-into-species-trees" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id17" role="doc-backlink">TreeKO (splitting gene trees into species trees)</a><a class="headerlink" href="#treeko-splitting-gene-trees-into-species-trees" title="Link to this heading">¶</a></h3>
 <p>Comparisons between tree topologies provide important information for
 many evolutionary studies. <a class="reference external" href="http://treeko.cgenomics.org">TreeKO</a>
 (<a class="reference external" href="https://www.ncbi.nlm.nih.gov/pubmed/21335609">Marcet and Gabaldon, 2011</a>)
@@ -883,7 +883,7 @@ <h2><a class="toc-backref" href="#id16" role="doc-backlink">Working with duplica
 </div>
 </section>
 <section id="splitting-gene-trees-by-duplication-events">
-<span id="split-by-dup"></span><h3><a class="toc-backref" href="#id18" role="doc-backlink">Splitting gene trees by duplication events</a><a class="headerlink" href="#splitting-gene-trees-by-duplication-events" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id18" role="doc-backlink">Splitting gene trees by duplication events</a><a class="headerlink" href="#splitting-gene-trees-by-duplication-events" title="Link to this heading">¶</a></h3>
 <p>A much simpler approach to separate duplicates within the same gene
 family tree is to split the topology by their duplication nodes. For
 this, the method <a class="reference internal" href="../reference/reference_phylo.html#ete4.PhyloTree.split_by_dups" title="ete4.PhyloTree.split_by_dups"><code class="xref py py-func docutils literal notranslate"><span class="pre">PhyloTree.split_by_dups()</span></code></a> is provided.</p>
@@ -937,7 +937,7 @@ <h2><a class="toc-backref" href="#id16" role="doc-backlink">Working with duplica
 </div>
 </section>
 <section id="collapse-species-specific-duplications">
-<span id="collapse-expansions"></span><h3><a class="toc-backref" href="#id19" role="doc-backlink">Collapse species specific duplications</a><a class="headerlink" href="#collapse-species-specific-duplications" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id19" role="doc-backlink">Collapse species specific duplications</a><a class="headerlink" href="#collapse-species-specific-duplications" title="Link to this heading">¶</a></h3>
 <p>The method <a class="reference internal" href="../reference/reference_phylo.html#ete4.PhyloTree.collapse_lineage_specific_expansions" title="ete4.PhyloTree.collapse_lineage_specific_expansions"><code class="xref py py-func docutils literal notranslate"><span class="pre">PhyloTree.collapse_lineage_specific_expansions()</span></code></a>
 returns a pruned version of a tree, where nodes representing lineage
 specific expansions are converted into a single leaf node.</p>