Biotite color schemes

This script displays the available color schemes.

# 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()