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

.. only:: html

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

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

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

.. _sphx_glr_examples_gallery_sequence_misc_color_schemes.py:


Biotite color schemes
=====================

This script displays the available color schemes.

.. GENERATED FROM PYTHON SOURCE LINES 7-73



.. image-sg:: /examples/gallery/sequence/misc/images/sphx_glr_color_schemes_001.png
   :alt: Nucleotide color schemes, Protein color schemes, Protein block color schemes
   :srcset: /examples/gallery/sequence/misc/images/sphx_glr_color_schemes_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    # Code source: Patrick Kunzmann
    # License: BSD 3 clause

    import matplotlib.pyplot as plt
    import numpy as np
    from matplotlib.gridspec import GridSpec
    from matplotlib.patches import Rectangle
    import biotite.sequence as seq
    import biotite.sequence.graphics as graphics


    def plot_colors(ax, alphabet):
        x_space = 0.1
        y_space = 0.3
        scheme_names = sorted(graphics.list_color_scheme_names(alphabet))
        scheme_names.reverse()
        schemes = [graphics.get_color_scheme(name, alphabet) for name in scheme_names]
        for i, scheme in enumerate(schemes):
            for j, color in enumerate(scheme):
                box = Rectangle(
                    (j - 0.5 + x_space / 2, i - 0.5 + y_space / 2),
                    1 - x_space,
                    1 - y_space,
                    color=color,
                    linewidth=0,
                )
                ax.add_patch(box)
        ax.set_xticks(np.arange(len(alphabet)))
        ax.set_yticks(np.arange(len(schemes)))
        ax.set_xticklabels([symbol for symbol in alphabet])
        ax.set_yticklabels(scheme_names)
        ax.set_xlim(-0.5, len(alphabet) - 0.5)
        ax.set_ylim(-0.5, len(schemes) - 0.5)
        ax.spines["left"].set_visible(False)
        ax.spines["right"].set_visible(False)
        ax.spines["bottom"].set_visible(False)
        ax.spines["top"].set_visible(False)
        ax.xaxis.set_ticks_position("none")
        ax.yaxis.set_ticks_position("none")


    nuc_alphabet = seq.NucleotideSequence.alphabet_amb
    prot_alphabet = seq.ProteinSequence.alphabet
    pb_alphabet = seq.LetterAlphabet("abcdefghijklmnop")

    figure = plt.figure(figsize=(8.0, 5.0))
    gs = GridSpec(
        3,
        1,
        height_ratios=[
            len(graphics.list_color_scheme_names(alphabet))
            for alphabet in (nuc_alphabet, prot_alphabet, pb_alphabet)
        ],
    )
    ax = figure.add_subplot(gs[0, 0])
    ax.set_title("Nucleotide color schemes")
    plot_colors(ax, nuc_alphabet)
    ax = figure.add_subplot(gs[1, 0])
    ax.set_title("Protein color schemes")
    plot_colors(ax, prot_alphabet)
    ax = figure.add_subplot(gs[2, 0])
    ax.set_title("Protein block color schemes")
    plot_colors(ax, pb_alphabet)
    plt.tight_layout()
    plt.show()


.. _sphx_glr_download_examples_gallery_sequence_misc_color_schemes.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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