mapC

Get test data

you can get test data from the following url:

https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM4417639&format=file&file=GSM4417639%5FSK%2DN%2DDZ%5FC6BC81F2%5Fb38d5%2Emcool

plot all chrom contact heatmap

import warnings

import cooler

import trackc as tc

warnings.simplefilter("ignore")

clr = cooler.Cooler(
    "../../trackc_data/tutorials/mapC/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::resolutions/5120000"
)
fig, axs = tc.make_spec(figsize=(6, 6), width_ratios=[1], wspace=0.2)

mat = clr.matrix(balance=False)[:]
tc.pl.mapC(ax=axs[0], mat=mat, map_type="squ", symmetric=True)
chromstarts = [clr.extent(i)[0] for i in clr.chromnames]
_ = axs[0].set(yticks=chromstarts, yticklabels=clr.chromnames)
# tc.savefig('all_chrom_cmap.pdf')

no max min range
maxrange: 1141.0 minrange: 3.0

plot one chrom

fig, axs = tc.make_spec(figsize=(5, 2.5), width_ratios=[1], wspace=0.2)
mat = tc.tl.extractCisContact(
    clr="../../trackc_data/tutorials/mapC/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/2560000",
    region="chr8",
)
tc.pl.mapC(ax=axs[0], mat=mat, maxrange=3000)
# tc.savefig('chrom_cmap_tri.pdf')

maxrange: 3000 minrange: 3.0

plot one chrom region

fig, axs = tc.make_spec(figsize=(11, 5), width_ratios=[1, 1], wspace=0.2)
mat = tc.tl.extractCisContact(
    clr="../../trackc_data/tutorials/mapC/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/10000",
    region="chr8:124000000-127000000",
)
tc.pl.mapC(ax=axs[0], mat=mat, map_type="squ", symmetric=True)

mat2 = tc.tl.extractCisContact(
    clr="../../trackc_data/tutorials/mapC/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/20000",
    region="chr8:51000000-53000000",
)
tc.pl.mapC(ax=axs[1], mat=mat2, map_type="squ", symmetric=True)
# tc.savefig('chrom_cmap_region_squ.pdf')

no max min range
maxrange: 13.0 minrange: 1.0
no max min range
maxrange: 29.0 minrange: 1.0

plot interaction of partial chromosomes

fig, axs = tc.make_spec(figsize=(5, 5), width_ratios=[1], wspace=0.2)
mat = tc.tl.extractContactRegions(
    clr="../../trackc_data/tutorials/mapC/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000",
    row_regions=["chr6", "chr8"],
)
tc.pl.mapC(ax=axs[0], mat=mat.cmat, map_type="squ", symmetric=True, maxrange=10000)

maxrange: 10000 minrange: 10.0

ten = tc.tenon(figsize=(8, 1))
ten.add(pos="bottom", height=3.6)
ten.add(pos="bottom", height=1)

chr6_len = clr.chromsizes["chr6"]
chr8_len = clr.chromsizes["chr8"]

mat = tc.tl.extractContactRegions(
    clr="../../trackc_data/tutorials/mapC/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000",
    row_regions=["chr6", "chr8"],
)
tc.pl.mapC(ax=ten.axs(0), mat=mat.cmat, map_type="tri", maxrange=5000, cmap="plasma")

tc.pl.multi_scale_track(
    ax=ten.axs(1),
    regions=["chr6:0-{0}".format(chr6_len), "chr8:0-{0}".format(chr8_len)],
    scale_adjust="Mb",
    intervals=2,
    tick_rotation=0,
)

maxrange: 5000 minrange: 10.0

plot inter-chrom interaction

fig, axs = tc.make_spec(figsize=(5, 5), width_ratios=[1], wspace=0.2)
mat = tc.tl.extractContactRegions(
    clr="../../trackc_data/tutorials/mapC/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000",
    row_regions="chr6",
    col_regions="chr8",
)
tc.pl.mapC(
    ax=axs[0], mat=mat.cmat, map_type="squ", symmetric=True, maxrange=1000, aspect=1
)

axs[0].set_ylabel("chr6")
axs[0].set_xlabel("chr8")

maxrange: 1000 minrange: 10.0

Text(0.5, 0, 'chr8')

ten = tc.tenon(figsize=(8, 1))
ten.add(pos="bottom", height=3.5)
ten.add(pos="bottom", height=1)

regions = ["chr6:0-25600000", "chr8:122880000-143360000"]
mat = tc.tl.extractContactRegions(
    clr="../../trackc_data/tutorials/mapC/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000",
    row_regions=regions,
)
tc.pl.mapC(
    ax=ten.axs(0), mat=mat.cmat, map_type="triangle", symmetric=False, maxrange=10000
)

tc.pl.multi_scale_track(ax=ten.axs(1), regions=regions, scale_adjust="Mb", intervals=2)

maxrange: 10000 minrange: 77.0