deploy: 0fa2085

_sources/tutorial/tutorial_trees.rst.txt

@@ -1386,7 +1386,7 @@ Solving multifurcations
 
 When a tree contains a polytomy (a node with more than 2 children),
 the method :func:`resolve_polytomy` can be used to convert the node
-into a randomly bifurcated structure. This is really not a solution
+into an arbitrarily bifurcated structure. This is really not a solution
 for the polytomy but it allows to export the tree as a strictly
 bifurcated newick structure, which is a requirement for some external
 software.
@@ -1396,7 +1396,7 @@ of the tree intact by disabling the :attr:`recursive` flag.
 
 Example::
 
-  t = Tree('(((a,b,c),(d,e,f,g)),(f,i,h));')
+  t = Tree('(((a,b,c),(d,e,f,g)),(h,i,j));')
 
   print(t)
   #      ╭╴a
@@ -1406,38 +1406,38 @@ Example::
   #  │ ╰─┼╴e
   # ─┤   ├╴f
   #  │   ╰╴g
-  #  │ ╭╴f
+  #  │ ╭╴h
   #  ╰─┼╴i
-  #    ╰╴h
+  #    ╰╴j
 
   polynode = t.common_ancestor(['a', 'b'])
-  polynode.resolve_polytomy(recursive=False)
+  polynode.resolve_polytomy(descendants=False)
 
   print(t)
-  #      ╭─┬╴b
-  #    ╭─┤ ╰╴c
-  #  ╭─┤ ╰╴a
+  #      ╭─┬╴a
+  #    ╭─┤ ╰╴b
+  #  ╭─┤ ╰╴c
   #  │ │ ╭╴d
   #  │ ╰─┼╴e
   # ─┤   ├╴f
   #  │   ╰╴g
-  #  │ ╭╴f
+  #  │ ╭╴h
   #  ╰─┼╴i
-  #    ╰╴h
+  #    ╰╴j
 
-  t.resolve_polytomy(recursive=True)
+  t.resolve_polytomy(descendants=True)
 
   print(t)
-  #      ╭─┬╴b
-  #    ╭─┤ ╰╴c
-  #    │ ╰╴a
-  #  ╭─┤   ╭─┬╴f
-  #  │ │ ╭─┤ ╰╴g
-  # ─┤ ╰─┤ ╰╴e
-  #  │   ╰╴d
-  #  │ ╭─┬╴i
-  #  ╰─┤ ╰╴h
-  #    ╰╴f
+  #      ╭─┬╴a
+  #    ╭─┤ ╰╴b
+  #    │ ╰╴c
+  #  ╭─┤   ╭─┬╴d
+  #  │ │ ╭─┤ ╰╴e
+  # ─┤ ╰─┤ ╰╴f
+  #  │   ╰╴g
+  #  │ ╭─┬╴h
+  #  ╰─┤ ╰╴i
+  #    ╰╴j
 
 
 Tree rooting

reference/reference_smartview.html

@@ -92,7 +92,7 @@ <h1><a class="toc-backref" href="#id1" role="doc-backlink">Smartview (web graphi
 
 <dl class="py class">
 <dt class="sig sig-object py" id="ete4.smartview.gui.server.TreeData">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TreeData</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">ultrametric:</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">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">0x7f0749f42a20&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#TreeData"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ete4.smartview.gui.server.TreeData" 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">TreeData</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">ultrametric:</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">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">0x7f9fd8d42a20&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#TreeData"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ete4.smartview.gui.server.TreeData" title="Link to this definition">¶</a></dt>
 <dd><dl class="py method">
 <dt class="sig sig-object py" id="ete4.smartview.gui.server.TreeData.__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">ultrametric</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">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.TreeData.__init__" title="Link to this definition">¶</a></dt>

reference/reference_tree.html

@@ -901,22 +901,16 @@ <h1>Tree (main class)<a class="headerlink" href="#tree-main-class" title="Link t
 
 <dl class="py method">
 <dt class="sig sig-object py" id="ete4.Tree.resolve_polytomy">
-<span class="sig-name descname"><span class="pre">resolve_polytomy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">recursive</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">defaults</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="#ete4.Tree.resolve_polytomy" title="Link to this definition">¶</a></dt>
-<dd><p>Resolve all polytomies under the current node, randomly.</p>
+<span class="sig-name descname"><span class="pre">resolve_polytomy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">descendants</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.Tree.resolve_polytomy" title="Link to this definition">¶</a></dt>
+<dd><p>Convert node to a series of dicotomies if it is a polytomy.</p>
 <p>A polytomy is a node that has more than 2 children. This
-function resolves them by creating an arbitrary dicotomic
-structure among the affected nodes. It randomly modifies the
-current tree topology and should only be used for
-compatibility reasons (like to later use programs that reject
-multifurcated nodes).</p>
+function changes them to a ladderized series of dicotomic
+branches. The tree topology modification is arbitrary (no
+important results should depend on it!).</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>recursive</strong> – If True, resolve all polytomies under this
-node too. Otherwise, only the current node will be
-checked and fixed.</p></li>
-<li><p><strong>defaults</strong> – Dictionary of properties to use for new nodes.</p></li>
-</ul>
+<dd class="field-odd"><p><strong>descendants</strong> – If True, resolve all polytomies under this
+node too. Otherwise, do it only for the current node.</p>
 </dd>
 </dl>
 </dd></dl>