chromosome-ideogram 0.0.3

A python package for drawing genome-wide data on idiograms.

ChromosomeIdeogram

A python package for drawing genome-wide data on ideograms.

Install

pip install chromosome-ideogram --upgrade

Usage example

import matplotlib.pyplot as plt
from matplotlib import gridspec
from chromosome_ideogram import ChromosomeIdeogram

plt.rcParams['font.size'] = 8
plt.rcParams['pdf.fonttype'] = 42

fig = plt.figure(figsize=(10, 8))
gs = gridspec.GridSpec(nrows=10, ncols=1)
axes1 = fig.add_subplot(gs[:8, :])
axes2 = fig.add_subplot(gs[8:, :])

ci1 = ChromosomeIdeogram(
    karyotype='example/karyotype.xls',
    radius=0.4,  # Radius of chromosome (it is not recommended to make any changes)
    space=3  # Chromosome center coordinate interval (radius x space, also not recommended for modification)
)
ci1.draw_chromh(axes=axes1, centromere_angle=60, color='lightgrey')
ci1.annotations(axes=axes1, annotations='example/satellite_DNA.bed')

# Create a second karyotype diagram object (containing only chromosome 14)
ci2 = ChromosomeIdeogram(
    karyotype='example/Chr14_karyotype.xls',
    radius=0.4,
    space=3
)
ci2.draw_chromh(axes=axes2, centromere_angle=60, color='lightgrey')
ci2.annotations(axes=axes2, annotations='example/Chr14_satellite_DNA.bed')

axes1.legend(loc=(0.85, 0.85))  # Set axes1 legend, you can also set axes2 legend
plt.subplots_adjust(hspace=6)  # Adjust the vertical distance between the two subgraphs

plt.savefig('example/satellite_DNA.pdf', bbox_inches='tight')
plt.savefig('example/satellite_DNA.png', bbox_inches='tight')