bio-hi-c-analysis-hic-visualization

Version Compatibility

Reference examples tested with: cooler 0.9+, cooltools 0.6+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Hi-C Visualization

"Plot my Hi-C contact matrix" → Create triangle heatmaps, virtual 4C profiles, and multi-track figures combining contact maps with genomic annotations.

• Python: matplotlib.pyplot.imshow() on cooler matrices, cooltools for aggregate plots
• CLI: hicPlotMatrix (HiCExplorer)

Visualize Hi-C contact matrices and genomic features.

Required Imports

import cooler
import cooltools
import cooltools.lib.plotting
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
import bioframe

Basic Contact Matrix Plot

clr = cooler.Cooler('matrix.mcool::resolutions/10000')

# Get matrix for a region
matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000')

fig, ax = plt.subplots(figsize=(8, 8))
im = ax.imshow(matrix, cmap='Reds', norm=LogNorm(vmin=0.001, vmax=0.1))
plt.colorbar(im, ax=ax, label='Balanced contacts')
ax.set_title('chr1:50-60Mb')
plt.savefig('contact_matrix.png', dpi=150)

Triangle (Upper Triangle) Plot

def plot_triangle(matrix, ax, cmap='Reds', vmin=None, vmax=None):
    '''Plot Hi-C matrix as triangle (rotated 45 degrees)'''
    n = matrix.shape[0]

    # Create rotated matrix
    rotated = np.zeros((n, 2*n))
    for i in range(n):
        for j in range(i, n):
            y = j - i
            x = i + j
            rotated[y, x] = matrix[i, j]

    # Plot
    im = ax.imshow(rotated[:n//2, :], cmap=cmap, aspect='auto',
                   norm=LogNorm(vmin=vmin, vmax=vmax) if vmin else None)
    ax.set_ylim(n//2, 0)
    return im

matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000')
fig, ax = plt.subplots(figsize=(12, 4))
im = plot_triangle(matrix, ax, vmin=0.001, vmax=0.1)
plt.colorbar(im, ax=ax)
plt.savefig('triangle_plot.png', dpi=150)