.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "gallery/tree/plot_biopython_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_biopython_tree.py>`
        to download the full example code.

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

.. _sphx_glr_gallery_tree_plot_biopython_tree.py:


Biopython tree
==============

This example shows how to use `iplotx` to plot trees from Biopython's Phylo module.

.. GENERATED FROM PYTHON SOURCE LINES 7-26

.. code-block:: Python


    from Bio import Phylo
    from io import StringIO
    import matplotlib.pyplot as plt
    import iplotx as ipx

    # Make a tree from a string in Newick format
    tree = next(
        Phylo.NewickIO.parse(
            StringIO(
                "(()(()((()())(()()))))",
            )
        )
    )

    ipx.plotting.tree(
        tree,
    )




.. image-sg:: /gallery/tree/images/sphx_glr_plot_biopython_tree_001.png
   :alt: plot biopython tree
   :srcset: /gallery/tree/images/sphx_glr_plot_biopython_tree_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


    <iplotx.tree.TreeArtist object at 0x7af382c1f610>



.. GENERATED FROM PYTHON SOURCE LINES 27-30

To add labels to the leaves, you can use the `leaf_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 30-44

.. code-block:: Python


    # sphinx_gallery_thumbnail_number = 2
    leaf_labels = {leaf: f"Species {i + 1}" for i, leaf in enumerate(tree.get_terminals())}
    fig, ax = plt.subplots(figsize=(4, 4))
    ipx.plotting.tree(
        tree,
        ax=ax,
        leaf_labels=leaf_labels,
        leaf_label_hmargin=10,
        leaf_deep=False,
    )
    ax.set_xlim(0, 8)
    ax.invert_yaxis()




.. image-sg:: /gallery/tree/images/sphx_glr_plot_biopython_tree_002.png
   :alt: plot biopython tree
   :srcset: /gallery/tree/images/sphx_glr_plot_biopython_tree_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 45-47

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

.. GENERATED FROM PYTHON SOURCE LINES 47-63

.. code-block:: Python


    ipx.plotting.tree(
        tree,
        layout="radial",
        style=[
            "tree",
            {
                "edge": {
                    "color": ["black", "pink"],
                    "linewidth": 4,
                },
            },
        ],
        aspect=1,
        title="Black pink in your area",
    )



.. image-sg:: /gallery/tree/images/sphx_glr_plot_biopython_tree_003.png
   :alt: Black pink in your area
   :srcset: /gallery/tree/images/sphx_glr_plot_biopython_tree_003.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


    <iplotx.tree.TreeArtist object at 0x7af382c30e10>




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

   **Total running time of the script:** (0 minutes 0.109 seconds)


.. _sphx_glr_download_gallery_tree_plot_biopython_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_biopython_tree.ipynb <plot_biopython_tree.ipynb>`

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

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

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

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


.. only:: html

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

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