ac052d8737d28287040445e119b1d8c8d8cd1519,doc/examples/scripts/sequence/pi3k_alignment.py,,,#,109

Before Change

alignment.trace = alignment.trace[start_index:stop_index]

matrix = align.SubstitutionMatrix.std_protein_matrix()
visualizer = graphics.AlignmentSimilarityVisualizer(alignment, matrix)
// The alignment is quite long
// -> Reduce font and box size to reduce figure size
visualizer.set_alignment_properties(
    box_size=(8,14), symbols_per_line=80, font_size=6
)
visualizer.add_labels(names, font_size=10, size=80)
visualizer.add_location_numbers(size=40, font_size=10)
visualizer.set_color(color=biotite.colors["orange"])
visualizer.set_margin(5.0)
figure = visualizer.generate()

plt.show()

After Change

alignment.trace = alignment.trace[start_index:stop_index]

matrix = align.SubstitutionMatrix.std_protein_matrix()
fig = plt.figure(figsize=(8.0, 15))
ax = fig.add_subplot(111)
// The alignment is quite long
// -> Reduce font size to reduce figure size
graphics.plot_alignment_similarity_based(
    ax, alignment, matrix=matrix, symbols_per_line=80, labels=names,
    show_numbers=True,
    label_size=10, number_size=10, symbol_size=6,
    color=biotite.colors["orange"]
)
fig.tight_layout()

plt.show()

Instances