Extracting parts of a contact map¶

import numpy as np
import matplotlib.pyplot as plt
from matplotlib import colors

from iced import datasets
from iced.utils import get_intra_mask
from iced.utils import get_inter_mask


# Loading a sample dataset
counts, lengths = datasets.load_sample_yeast()
intra_mask = get_intra_mask(lengths)
inter_mask = get_inter_mask(lengths)

fig, axes = plt.subplots(ncols=2, figsize=(12, 6))
inter_counts = counts.copy()
inter_counts[intra_mask] = np.nan
intra_counts = counts.copy()
intra_counts[inter_mask] = np.nan

m = axes[0].matshow(intra_counts, cmap="Blues", norm=colors.SymLogNorm(1),
                    origin="bottom",
                    extent=(0, len(counts), 0, len(counts)))
m = axes[1].matshow(inter_counts, cmap="Blues", norm=colors.SymLogNorm(1),
                    origin="bottom",
                    extent=(0, len(counts), 0, len(counts)))

axes[0].set_title("Intra-chromosomal maps")
axes[1].set_title("Inter-chromosomal maps")

[axes[0].axhline(i, linewidth=1, color="#000000") for i in lengths.cumsum()]
[axes[0].axvline(i, linewidth=1, color="#000000") for i in lengths.cumsum()]
[axes[1].axhline(i, linewidth=1, color="#000000") for i in lengths.cumsum()]
[axes[1].axvline(i, linewidth=1, color="#000000") for i in lengths.cumsum()]