.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "gallery/tree/plot_cogent3_tree.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_gallery_tree_plot_cogent3_tree.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_gallery_tree_plot_cogent3_tree.py:


Cogent3 tree
==============

This example shows how to use `iplotx` to plot trees from `cogent3`, the successor to `pycogent`.

.. GENERATED FROM PYTHON SOURCE LINES 7-23

.. code-block:: Python


    from cogent3.phylo import nj
    import numpy as np
    import iplotx as ipx
    import matplotlib.pyplot as plt

    nleaves = 8
    distance_dict = {}
    for i in range(nleaves):
        for j in range(i):
            distance_dict[(str(i), str(j))] = np.random.rand()
    tree = nj.nj(distance_dict)
    ipx.plotting.tree(
        tree,
    )




.. image-sg:: /gallery/tree/images/sphx_glr_plot_cogent3_tree_001.png
   :alt: plot cogent3 tree
   :srcset: /gallery/tree/images/sphx_glr_plot_cogent3_tree_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    <iplotx.tree.TreeArtist object at 0x7af38ff22490>



.. GENERATED FROM PYTHON SOURCE LINES 24-27

To add labels to the leaves, you can use the `vertex_labels` argument as a dictionary.
Moreover, the plot can be customised further using hmargin (horizontal label margin)
and some `matplotlib` settings.

.. GENERATED FROM PYTHON SOURCE LINES 27-38

.. code-block:: Python


    leaf_labels = {leaf: f"Species {i + 1}" for i, leaf in enumerate(tree.tips())}
    fig, ax = plt.subplots(figsize=(5, 4))
    ipx.plotting.tree(
        tree,
        ax=ax,
        vertex_labels=leaf_labels,
        vertex_label_hmargin=10,
    )
    ax.set_xlim(-0.2, 1.5)




.. image-sg:: /gallery/tree/images/sphx_glr_plot_cogent3_tree_002.png
   :alt: plot cogent3 tree
   :srcset: /gallery/tree/images/sphx_glr_plot_cogent3_tree_002.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    (-0.2, 1.5)



.. GENERATED FROM PYTHON SOURCE LINES 39-41

`iplotx` can compute a radial tree layout as well, and usual style modifications
work for trees same as networks:

.. GENERATED FROM PYTHON SOURCE LINES 41-56

.. code-block:: Python


    ipx.plotting.tree(
        tree,
        layout="radial",
        style=[
            "tree",
            {
                "edge": {
                    "color": "deeppink",
                    "linewidth": 4,
                },
            },
        ],
        aspect=1,
    )



.. image-sg:: /gallery/tree/images/sphx_glr_plot_cogent3_tree_003.png
   :alt: plot cogent3 tree
   :srcset: /gallery/tree/images/sphx_glr_plot_cogent3_tree_003.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    <iplotx.tree.TreeArtist object at 0x7af390d9e0d0>




.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 0.114 seconds)


.. _sphx_glr_download_gallery_tree_plot_cogent3_tree.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_cogent3_tree.ipynb <plot_cogent3_tree.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_cogent3_tree.py <plot_cogent3_tree.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_cogent3_tree.zip <plot_cogent3_tree.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_