flexible adjustments with matplotlib

Long range interactions

Example figure from https://doi.org/10.1016/j.cell.2023.07.008

Get test data

# wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM7113nnn/GSM7113848/suppl/GSM7113848_larval_CNS1.cool.gz
# wget https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6614nnn/GSM6614565/suppl/GSM6614565_Dmel_w1118_larva_CNS_HiC_2.mcool
wget https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM6614565&format=file&file=GSM6614565%5FDmel%5Fw1118%5Flarva%5FCNS%5FHiC%5F2%2Emcool

import cooler

import trackc as tc

ten = tc.tenon(figsize=(5, 5))
ten.add(pos="bottom", height=1, hspace=0)

clr = cooler.Cooler("../../trackc_data/examples/GSM6614565_Dmel_w1118_larva_CNS.cool")
mat = tc.tl.extractCisContact(clr=clr, region="chr3L")
tc.pl.mapC(ax=ten.axs(0), mat=mat, label="chr3L", map_type="square", symmetric=True)

region = f'chr3L:0-{clr.chromsizes["chr3L"]}'

tc.pl.scale_track(
    ax=ten.axs(0), region=region, scale_adjust="Mb", tick_pos="bottom", ratio2ax=0
)

no max min range
maxrange: 117.0 minrange: 1.0

ten = tc.tenon(figsize=(6, 1))
ten.add(pos="bottom", height=2, hspace=0)
ten.add(pos="bottom", height=5, hspace=0)
axin_l = ten.axs(1).inset_axes([-0.35, 0, 0.35, 1])

region1 = "chr3L:6480000-6840000"
region2 = "chr3L:9380000-9100000"

clr = cooler.Cooler(
    "../../trackc_data/examples/GSM6614565_Dmel_w1118_larva_CNS.2k.cool"
)

mat_c = tc.tl.extractContactRegions(clr=clr, row_regions=region2, col_regions=region1)
mat_u = tc.tl.extractCisContact(clr=clr, region=region1, extend=150)
mat_l = tc.tl.extractCisContact(clr=clr, region=region2, extend=150)

tc.pl.mapC(ax=ten.axs(0), mat=mat_u, map_type="rectangle", height=150, logdata=True)
tc.pl.mapC(
    ax=ten.axs(1), mat=mat_c.cmat, map_type="square", symmetric=True, logdata=True
)
tc.pl.mapC(
    ax=axin_l,
    mat2=mat_l,
    map_type="rectangle",
    height=150,
    trans_ax=True,
    logdata=True,
    cmap=tc.pa.fruitpunch,
)
tc.pl.scale_track(
    ax=ten.axs(1), region=region1, scale_adjust="Mb", tick_pos="bottom", ratio2ax=0.15
)

no max min range
maxrange: 64.0 minrange: 1.0
no max min range
maxrange: 4.0 minrange: 1.0
no max min range
maxrange: 58.0 minrange: 1.0