.. _sphx_glr_gallery_tree:

Trees
+++++



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to add a scale bar to an iplotx tree.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_scalebar_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_scalebar.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Scale bar</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example showcases the &quot;equal angle&quot; layout. This layout is inspired by the ggtree layout with the same name, which originally comes from Joseph Felsenstein&#x27;s book &quot;Inferring Phylogenies&quot;.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_equalangle_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_equalangle.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Equal angle layout</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot trees from skbio or scikit-bio.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_skbio_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_skbio_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">scikit-bio tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use leaf edges, dashed lines connecting each leaf to the deepest leaf and label.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_leafedges_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_leafedges.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Leaf edges</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This Biopython-inspired example shows how to style clade edges for a node and its descendants.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_cladeedges_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_cladeedges.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Subtrees and cascades</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This short example demonstrates how to combine leaf edges and cascades.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_leafedges_and_cascades_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_leafedges_and_cascades.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Leaf edges and cascades</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use split edges, i.e. how to apply different styles to tree edges that are composed of multiple segments. See also ../zero_dependency/plot_simpletreedataprovider for the basic example of how to plot a tree with iplotx&#x27;s internal tree representation.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_split_edges_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_split_edges.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Split edges</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a few elements from  iplotx&#x27;s style hierarchy.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_style_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_style_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Style hierarchy</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot trees from cogent3, the successor to pycogent.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_cogent3_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_cogent3_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Cogent3 tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to style tree clades - or subtrees - post rendering, similar of the equivalent option in cogent3.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_tree_style_clades_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_tree_style_clades.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Subtree styling</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to visualise support values for clades or branches.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_support_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_support.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Branch support</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot trees from dendropy.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_dendropy_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_dendropy.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Dendropy tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot trees from Biopython&#x27;s Phylo module.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_biopython_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_biopython_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Biopython tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot trees from ete4.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_ete4_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_ete4.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">ETE4 tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates iplotx&#x27;s capability to style tree appearance with an angular look, either for the whole tree or specific edges.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_angular_waypoints_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_angular_waypoints.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Angular layout and edge waypoints</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to reproduce cogent3 layouts using iplotx.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_cogent3_layouts_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_cogent3_layouts.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Cogent3 layouts</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example showcases plot elements for tree styling in iplotx.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_elements_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_elements_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Tree element showroom</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot two trees facing each other, which is typical in coevolutionary studies.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_double_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_double_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Double tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to plot trees at the leaf of a tree, using the iplotx library. Note that there are a few conceivable ways to do similar things as this in matplotlib and this is just one such approach, using inset axes.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_trees_of_trees_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_trees_of_trees.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Tree of trees</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to add cascading backgrounds to trees. &quot;Cascading&quot; here means that each patch (rectangle/wedge/etc.) will cover a node and all descendants, down to the leaves.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_tree_node_background_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_tree_node_background.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Tree cascades</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to plot trees from the phyloframe library, using Seaborn to overlay scatter points.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_phyloframe_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_phyloframe_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">phyloframe tree</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /gallery/tree/plot_scalebar
   /gallery/tree/plot_equalangle
   /gallery/tree/plot_skbio_tree
   /gallery/tree/plot_leafedges
   /gallery/tree/plot_cladeedges
   /gallery/tree/plot_leafedges_and_cascades
   /gallery/tree/plot_split_edges
   /gallery/tree/plot_style_tree
   /gallery/tree/plot_cogent3_tree
   /gallery/tree/plot_tree_style_clades
   /gallery/tree/plot_support
   /gallery/tree/plot_dendropy
   /gallery/tree/plot_biopython_tree
   /gallery/tree/plot_ete4
   /gallery/tree/plot_angular_waypoints
   /gallery/tree/plot_cogent3_layouts
   /gallery/tree/plot_elements_tree
   /gallery/tree/plot_double_tree
   /gallery/tree/plot_trees_of_trees
   /gallery/tree/plot_tree_node_background
   /gallery/tree/plot_phyloframe_tree