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

.. only:: html

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

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

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

.. _sphx_glr_gallery_biology_plot_animal_phylogeny.py:


Animal phylogeny
================

This example from ``cogent3`` shows how to use ``iplotx`` to visualise a phylogenetic tree of many animals.

It also shows how to combine ``iplotx`` trees with other ``matplotlib`` artists such as annotations and
scatter plots.

.. GENERATED FROM PYTHON SOURCE LINES 10-82



.. image-sg:: /gallery/biology/images/sphx_glr_plot_animal_phylogeny_001.png
   :alt: plot animal phylogeny
   :srcset: /gallery/biology/images/sphx_glr_plot_animal_phylogeny_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    from collections import defaultdict
    import cogent3
    import matplotlib.pyplot as plt
    import iplotx as ipx

    reader = cogent3.get_app("load_json")

    ens_tree = reader("data/GN-tree.json")

    # Customise the figure as you like
    fig, ax = plt.subplots(figsize=(8, 14))

    # Inject plot into the figure/axes
    tree_artist = ipx.tree(
      ens_tree,
      layout="horizontal",
      ax=ax,
      leaf_labels=True,
      # Style options
      layout_angular=False,
      leaf_deep=True,
      margins=(0.2, 0),
      leafedge_color=defaultdict(lambda: "black", {
          "Human": "tomato",
          "Chimpanzee": "orange",
          "Orangutan": "gold",
          "Gorilla": "gold",
          "Rhesus": "yellow",
          "HowlerMon": "yellow",
      }),
      leafedge_linewidth=2,
    )

    # Add an annotation with an arrow towards the root
    layout = tree_artist.get_layout().values
    root_coords = layout[layout[:, 0] == 0][0]
    ax.annotate(
        "Tree root",
        root_coords,
        (-0.1, 55),
        xycoords="data",
        textcoords="data",
        arrowprops=dict(
          color="grey",
          arrowstyle="-|>",
          shrinkA=4,
          shrinkB=12,
          linewidth=2,
          connectionstyle="angle",
        ),
        bbox=dict(
            boxstyle="round,rounding_size=0.2,pad=0.5",
            facecolor="white",
            edgecolor="grey",
            linewidth=2,
        ),
        fontsize=12,
    )

    # Also add concentric circles at the root
    ax.scatter(
        [root_coords[0]] * 3,
        [root_coords[1]] * 3,
        s=[50, 200, 500],
        facecolor="none",
        edgecolor="orchid",
        linewidth=2,
    )

    # Ensure tight layout for minimal whitespace
    fig.tight_layout()


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

   **Total running time of the script:** (0 minutes 8.249 seconds)


.. _sphx_glr_download_gallery_biology_plot_animal_phylogeny.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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