inter-chrom interaction (only trans)#

CLI mode#

conf-hicmap_2.yml

trackc:
  - ax: t1
    height: 4
    track_type: hicmap
    track_para:
      mat:
        method: extractContactRegions
        clr: /path/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000
        row_regions: chr6
        col_regions: chr8
      mapC:
        cmap: Blues
        map_type: squ
        symmetric: True
        maxrange: 1000
        aspect: 1

trackc cli conf-hicmap_2.yml -s 4,1

API mode#

[9]:

import cooler

import trackc as tc

ten = tc.tenon(figsize=(4, 1))
ten.add(pos="bottom", height=4)


clr = "./GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000"

mat = tc.tl.extractContactRegions(clr=clr, row_regions=["chr6"], col_regions=["chr8"])

tc.pl.mapC(
    ax=ten.axs(0),
    mat=mat.cmat,
    map_type="squ",
    cmap="Blues",
    symmetric=True,
    maxrange=1000,
    aspect=1,
)
# tc.savefig('chr6_chr8_trans.pdf')

maxrange: 1000 minrange: 10.0