Calculating insulation score

test data

HFF_MicroC.mcool: https://files.osf.io/v1/resources/hjcxg/providers/osfstorage/5f73756d9e9a3d03ec6e3922?action=download&direct&version=1

import cooler
from cooltools import insulation

resolution = 10000
coolfile = f"./HFF_MicroC.mcool::resolutions/{resolution}"
clr = cooler.Cooler(coolfile)
windows = [3 * resolution, 5 * resolution, 10 * resolution, 25 * resolution]
insulation_table = insulation(clr, windows, verbose=True)

INFO:root:Processing region chr2
INFO:root:Processing region chr17

display(insulation_table.head(5))

	chrom	start	end	region	is_bad_bin	log2_insulation_score_30000	n_valid_pixels_30000	log2_insulation_score_50000	n_valid_pixels_50000	log2_insulation_score_100000	...	log2_insulation_score_250000	n_valid_pixels_250000	boundary_strength_30000	boundary_strength_50000	boundary_strength_250000	boundary_strength_100000	is_boundary_30000	is_boundary_50000	is_boundary_100000	is_boundary_250000
0	chr2	0	10000	chr2	True	NaN	0.0	NaN	0.0	NaN	...	NaN	0.0	NaN	NaN	NaN	NaN	False	False	False	False
1	chr2	10000	20000	chr2	False	0.431607	1.0	0.507928	3.0	0.682245	...	1.318723	23.0	NaN	NaN	NaN	NaN	False	False	False	False
2	chr2	20000	30000	chr2	False	0.227998	3.0	0.400041	7.0	0.750755	...	1.342230	47.0	NaN	NaN	NaN	NaN	False	False	False	False
3	chr2	30000	40000	chr2	False	0.055763	6.0	0.378382	12.0	0.756891	...	1.338815	72.0	NaN	NaN	NaN	NaN	False	False	False	False
4	chr2	40000	50000	chr2	False	0.095784	6.0	0.194656	17.0	0.665099	...	1.268551	97.0	NaN	NaN	NaN	NaN	False	False	False	False

5 rows × 21 columns

windows

[30000, 50000, 100000, 250000]

df = insulation_table[
    [
        "chrom",
        "start",
        "end",
        "log2_insulation_score_30000",
        "log2_insulation_score_50000",
        "log2_insulation_score_100000",
        "log2_insulation_score_250000",
    ]
]

visualization of insulation

import trackc as tc

regions = "chr2:10500000-13200000"
HFF = tc.tl.extractCisContact(clr=coolfile, region=regions, extend=150)

ten = tc.tenon(figsize=(6, 1))
ten.add(pos="bottom", height=1.5, hspace=0.05)
ten.add(pos="bottom", height=1, hspace=0.07)

tc.pl.mapC(ax=ten.axs(0), mat=HFF, label="HFF", map_type="rec", height=150)

tc.pl.bdgmat_track(
    ax=ten.axs(1), bed=df, regions=regions, style="line", label="insulation score"
)
tc.pl.scale_track(
    ax=ten.axs(1),
    region=regions,
    scale_adjust="Mb",
    tick_pos="bottom",
    ratio2ax=1,
    space=0,
)

# tc.savefig('outfile.pdf')

no max min range
maxrange: 201.0 minrange: 1.0
color sizes less than plots, use defaults
bdg_mat minrange:-1.9644833979871403 maxrange:0.8863030621507203