Biotite color schemes

This script displays the available color schemes for the different built-in alphabets.

# 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
import biotite.structure.alphabet as strucalph


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
i3d_alphabet = strucalph.I3DSequence.alphabet
pb_alphabet = strucalph.ProteinBlocksSequence.alphabet

figure = plt.figure(figsize=(8.0, 7.0))
gs = GridSpec(
    4,
    1,
    height_ratios=[
        len(graphics.list_color_scheme_names(alphabet))
        for alphabet in (nuc_alphabet, prot_alphabet, i3d_alphabet, pb_alphabet)
    ],
)

ax = figure.add_subplot(gs[0, 0])
ax.set_title("Nucleotide")
plot_colors(ax, nuc_alphabet)

ax = figure.add_subplot(gs[1, 0])
ax.set_title("Protein")
plot_colors(ax, prot_alphabet)

ax = figure.add_subplot(gs[2, 0])
ax.set_title("3Di")
plot_colors(ax, i3d_alphabet)

ax = figure.add_subplot(gs[3, 0])
ax.set_title("Protein Blocks")
plot_colors(ax, pb_alphabet)

plt.tight_layout()
plt.show()