Smoothing matrix with gaussian filter

CoolBox support smoothing the Hi-C contact matrix with gaussian filter.

[1]:

import coolbox
from coolbox.api import *

[2]:

coolbox.__version__

[2]:

'0.3.0'

[3]:

test_hic = "../../../tests/test_data/dothic_chr9_4000000_6000000.hic"
test_interval = "chr9:4000000-6000000"

[4]:

with Feature(depth_ratio=0.5, color="RdYlBu_r"):
    raw = DotHiC(test_hic) + Title("Not smooth")
    with Feature(norm='log', transform=False):
        smo0 = DotHiC(test_hic, gaussian_sigma=0.5) + MinValue(1e-1) + Title("Smooth\nsigma=0.5")
        smo1 = DotHiC(test_hic, gaussian_sigma=1) + MinValue(1e-1) + Title("Smooth\nsigma=1.0")

frame = XAxis() + raw + smo0 + smo1
frame.plot(test_interval)

[4]:
../_images/_gallery_smoothing_5_0.png

CLI code

[5]:

%%bash

test_hic="../../../tests/test_data/dothic_chr9_4000000_6000000.hic"

coolbox add XAxis - \
    start_with Color "RdYlBu_r" - \
    start_with Feature --depth_ratio="0.5" - \
    add DotHiC $test_hic - add Title "Not smooth" - \
    add DotHiC $test_hic --gaussian_sigma "0.5" --min_value "1e-1" - \
    add Title 'Smooth sigma=0.5' - \
    add DotHiC $test_hic --gaussian_sigma "1.0" --min_value "1e-1" - \
    add Title 'Smooth sigma=1.0' - \
    end_with - \
    end_with - \
    goto "chr9:4000000-6000000" - \
    plot /tmp/test_coolbox_smooth.png