Square versus circular displays¶

import numpy as np

import matplotlib  # Need this to check the version

import matplotlib.pyplot as plt

from matplotlib import colors

from circhic import datasets
from circhic import CircHiCFigure
from circhic.utils import generate_circular_map
from circhic.utils import generate_borders

from iced.normalization import ICE_normalization

#load the data
data = datasets.load_ccrescentus()
counts = data["counts"]
lengths = data["nbins"]
counts, bias = ICE_normalization(counts, output_bias=True)

granularity = 0.5
inner_radius = 0.005
resolution = 9958
inner_gdis, outer_gdis = 2000000, 600000

Circ = generate_circular_map(counts, granularity=granularity,
                             inner_radius=inner_radius, resolution=resolution,
                             inner_gdis=inner_gdis, outer_gdis=outer_gdis,
                             mode='reflect', origin=1,
                             chromosome_type='circular')

Bord = generate_borders(counts, granularity=granularity,
                        inner_radius=inner_radius, resolution=resolution,
                        inner_gdis=inner_gdis, outer_gdis=outer_gdis, origin=1,
                        chromosome_type='circular', thick_r=0.006)

vmax = np.max([counts[i, (i+1) % lengths[0]] for i in range(lengths[0])])
vmin = 77

plt.figure(figsize=(15, 12))

plt.subplot(1, 2, 1)

if matplotlib.__version__ < "3.2.0":
    norm = colors.SymLogNorm(vmin, vmax=vmax)
else:
    norm = colors.SymLogNorm(vmin, vmax=vmax, base=np.e)

plt.imshow(counts, norm=norm, cmap='bone_r')
plt.xticks([])
plt.yticks([])
plt.title('square', pad=10, fontsize=20)

plt.subplot(1, 2, 2)

plt.imshow(Circ, norm=norm, cmap='bone_r',
           interpolation='None')
plt.imshow(vmax*Bord, norm=norm, cmap='Greys',
           interpolation='None')

plt.xticks([])
plt.yticks([])
plt.axis('off')

plt.title('circular\n inner gdis = 200 kb, outer gdis = 60 kb', pad=10,
          fontsize=20)