Macrodomain phenomenology¶

import numpy as np

import matplotlib.pyplot as plt

from circhic import datasets
from circhic import CircHiCFigure

from iced.normalization import ICE_normalization

# Load the data, compute the cumulative raw counts.
data = datasets.load_ecoli()
counts_raw = data["counts"]
lengths = data["nbins"]
log_cumul_raw_counts = np.log(counts_raw.sum(axis=0))

# Normalize the data using ICE, and keep the biases
counts, bias = ICE_normalization(counts_raw, output_bias=True)

# compute extreme values
vmax = np.max(
    [counts[i, (i+1) % counts.shape[0]] for i in range(counts.shape[0])])
vmin = np.min(counts[counts > 0])

granularity = 0.5
resolution = 9897

fig = plt.figure(figsize=(6, 6))

inner_radius, outer_radius = 0.15, 0.85
inner_gdis, outer_gdis = 1200000, 1200000

chrom_lengths = lengths * resolution
circhicfig = CircHiCFigure(chrom_lengths, figure=fig)
m, ax = circhicfig.plot_hic(
    counts, granularity=granularity, resolution=resolution,
    outer_radius=outer_radius, inner_radius=inner_radius,
    inner_gdis=inner_gdis, outer_gdis=outer_gdis,
    vmin=vmin*10, vmax=vmax/2, cmap="bone_r", border_thickness=0.005)

rax = circhicfig.plot_raxis()
rax.set_yticklabels(["120", "0", "120"], fontsize="small")
rax.set_ylabel(
    "Genomic distance (kb)", fontsize="small", color="0.3", position=(0, 1.03))
rax.tick_params(colors="0.3")

lines, _ = circhicfig.plot_lines(
    log_cumul_raw_counts, inner_radius=0.87, outer_radius=0.95,
    color="C0")

ticklabels = ["%d kb" % (i * 500) for i in range(8)]
tickpositions = [int(i*500000) for i in range(8)]
ticklabels.append("oriC")
tickpositions.append(3925589)
ax = circhicfig.set_genomic_ticklabels(
    tickpositions=tickpositions,
    ticklabels=ticklabels,
    outer_radius=0.96, fontdict={'fontsize': "small"})
ax.tick_params(colors="0.3")

inner_radius, outer_radius = 0.485, 0.515
band, _ = circhicfig.plot_bands(
    np.array([int(0.26*chrom_lengths[0])]),
    np.array([int(0.41*chrom_lengths[0])]), colors=('cyan',),
    inner_radius=inner_radius, outer_radius=outer_radius)

cab = circhicfig.set_colorbar(m, orientation="horizontal")
cab.set_label("Normalized contact counts", fontsize="small")

fig.legend((lines[0], band), ("Log-mappability", "Ter"), fontsize="small",
           bbox_to_anchor=(0.8, 0.1, 0.15, 0.15), frameon=False)