Cis contact heatmap#

In this section, we demonstrate how to generate various types of Hi-C cis contact heatmaps

Get test data#

Test data were origin from https://doi.org/10.1002/advs.202200818

[1]:

import cooler
import matplotlib.pyplot as plt

import trackc as tc

HPDE6C7_chr18_25k = cooler.Cooler(
    "../../trackc_data/examples/HPDE6C7.chr18.mcool::/resolutions/25000"
)
BxPC3_chr18_25k = cooler.Cooler(
    "../../trackc_data/examples/BxPC3.chr18.mcool::/resolutions/25000"
)


HPDE6C7_chr18_50k = cooler.Cooler(
    "../../trackc_data/examples/HPDE6C7.chr18.mcool::/resolutions/50000"
)
BxPC3_chr18_50k = cooler.Cooler(
    "../../trackc_data/examples/BxPC3.chr18.mcool::/resolutions/50000"
)

[2]:

region = "18:10000000-14500000"

normal = tc.tl.extractCisContact(clr=HPDE6C7_chr18_25k, region=region, extend=0)
tumor = tc.tl.extractCisContact(clr=BxPC3_chr18_25k, region=region, extend=50)

[3]:

fig, axs = tc.make_spec(figsize=(6, 7), height_ratios=[1, 1, 2, 1, 1, 2], hspace=0.3)

tc.pl.mapC(ax=axs[0], mat=normal, label="triangle\nmat", map_type="tri", height=50)
tc.pl.mapC(ax=axs[1], mat2=normal, label="triangle\nmat2", map_type="tri", height=50)

tc.pl.mapC(
    ax=axs[2],
    mat=normal,
    label="triangle\nsymmetric=True",
    map_type="tri",
    height=50,
    symmetric=True,
)

tc.pl.mapC(
    ax=axs[3],
    mat=tumor,
    label="rectangle\nmat",
    map_type="rec",
    height=50,
    cmap="Blues",
)
tc.pl.mapC(
    ax=axs[4],
    mat2=tumor,
    label="rectangle\nmat2",
    map_type="rec",
    height=50,
    cmap="cividis",
)

tc.pl.mapC(
    ax=axs[5],
    mat=tumor,
    label="rectangle\nsymmetric=True\nlogdata",
    map_type="rec",
    height=50,
    symmetric=True,
    logdata=True,
    cmap="magma",
)


tc.pl.scale_track(
    axs[5], region=region, scale_adjust="Mb", tick_pos="bottom", ratio2ax=0.9
)
tc.pl.scale_track(axs[0], region=region, scale_adjust="Mb", tick_pos="top", ratio2ax=1)
# tc.savefig("trackc_mapc1.pdf")

no max min range
maxrange: 296.0 minrange: 1.0
no max min range
maxrange: 296.0 minrange: 1.0
no max min range
maxrange: 296.0 minrange: 1.0
no max min range
maxrange: 248.0 minrange: 1.0
no max min range
maxrange: 248.0 minrange: 1.0
no max min range
maxrange: 248.0 minrange: 1.0
../_images/gallery_mapc_eg_3_1.png 
[4]:

fig, axs = tc.make_spec(figsize=(12, 7), width_ratios=[1, 1, 1, 1, 2, 2, 2], wspace=0.6)

tc.pl.mapC(
    ax=axs[0],
    mat2=normal,
    label="triangle\ntrans_ax=True\nmat2",
    map_type="tri",
    height=50,
    trans_ax=True,
)
tc.pl.mapC(
    ax=axs[1],
    mat=normal,
    label="triangle\ntrans_ax=True\nmat",
    map_type="tri",
    height=50,
    trans_ax=True,
)

tc.pl.mapC(
    ax=axs[2],
    mat2=tumor,
    label="rectangle\ntrans_ax=True\nmat2",
    map_type="rec",
    height=50,
    trans_ax=True,
)
tc.pl.mapC(
    ax=axs[3],
    mat=tumor,
    label="rectangle\ntrans_ax=True\nmat",
    map_type="rec",
    height=50,
    trans_ax=True,
)

tc.pl.mapC(
    ax=axs[4],
    mat=normal,
    label="triangle\ntrans_ax=True\nsymmetric=True",
    map_type="tri",
    height=50,
    trans_ax=True,
    symmetric=True,
)
tc.pl.mapC(
    ax=axs[5],
    mat2=tumor,
    label="rectangle\ntrans_ax=True\nsymmetric=True",
    map_type="rec",
    height=50,
    trans_ax=True,
    symmetric=True,
)
tc.pl.mapC(
    ax=axs[6],
    mat=tumor,
    mat2=tumor,
    label=["normal", "tumor"],
    map_type="rec",
    height=50,
    trans_ax=True,
    symmetric=True,
)

no max min range
maxrange: 296.0 minrange: 1.0
no max min range
maxrange: 296.0 minrange: 1.0
no max min range
maxrange: 248.0 minrange: 1.0
no max min range
maxrange: 248.0 minrange: 1.0
no max min range
maxrange: 296.0 minrange: 1.0
no max min range
maxrange: 248.0 minrange: 1.0
no max min range
maxrange: 248.0 minrange: 1.0
no max min range
maxrange: 248.0 minrange: 1.0
../_images/gallery_mapc_eg_4_1.png 
[5]:

region = "18:64000000-71000000"
normal_2 = tc.tl.extractCisContact(clr=HPDE6C7_chr18_50k, region=region)
tumor_2 = tc.tl.extractCisContact(clr=BxPC3_chr18_50k, region=region)

[6]:

fig, axs = tc.make_spec(figsize=(10, 4), width_ratios=[1, 1, 1], wspace=0.3)

tc.pl.mapC(mat=normal_2, ax=axs[0], map_type="squ", label="S1", aspect=1)
tc.pl.mapC(
    mat2=tumor_2, ax=axs[1], map_type="squ", symmetric=True, aspect=1, logdata=True
)
tc.pl.mapC(
    mat=normal_2,
    mat2=tumor_2,
    ax=axs[2],
    map_type="squ",
    aspect=1,
    maxrange=500,
    label=["normal", "tumor"],
)

fig.tight_layout()

no max min range
maxrange: 857.0 minrange: 1.0
no max min range
maxrange: 772.0 minrange: 1.0
maxrange: 500 minrange: 1.0
maxrange: 500 minrange: 1.0
../_images/gallery_mapc_eg_6_1.png 
[7]:

fig, axs = plt.subplots(1, 3, figsize=(14, 2.5))

tc.pl.mapC(mat=normal_2, ax=axs[0], map_type="triangle", label="S1", maxrange=600)
tc.pl.mapC(mat2=tumor_2, ax=axs[1], map_type="triangle", logdata=False, maxrange=600)
tc.pl.mapC(
    mat=normal_2,
    mat2=tumor_2,
    ax=axs[2],
    map_type="triangle",
    cmap=["pink_r", "Blues"],
    height=70,
    maxrange=500,
    label=["normal", "tumor"],
)

fig.tight_layout()

maxrange: 600 minrange: 1.0
maxrange: 600 minrange: 1.0
maxrange: 500 minrange: 1.0
maxrange: 500 minrange: 1.0
../_images/gallery_mapc_eg_7_1.png 
[8]:

fig, axs = plt.subplots(1, 3, figsize=(7, 5))

tc.pl.mapC(
    mat2=normal_2, ax=axs[0], map_type="tri", label="S1", maxrange=600, trans_ax=True
)
tc.pl.mapC(
    mat=tumor_2, ax=axs[1], map_type="tri", logdata=False, maxrange=600, trans_ax=True
)
tc.pl.mapC(
    mat=normal_2,
    mat2=tumor_2,
    ax=axs[2],
    map_type="triangle",
    height=70,
    maxrange=500,
    label=["normal", "tumor"],
    trans_ax=True,
)

fig.tight_layout()

maxrange: 600 minrange: 1.0
maxrange: 600 minrange: 1.0
maxrange: 500 minrange: 1.0
maxrange: 500 minrange: 1.0
../_images/gallery_mapc_eg_8_1.png 
[9]:

fig, axs = plt.subplots(1, 1, figsize=(2.5, 4))
tc.pl.mapC(
    mat=normal_2,
    mat2=tumor_2,
    ax=axs,
    map_type="triangle",
    height=70,
    maxrange=500,
    cmap=[tc.pa.fruitpunch, "PuBu"],
    label=["normal", "tumor"],
    trans_ax=True,
)

maxrange: 500 minrange: 1.0
maxrange: 500 minrange: 1.0
../_images/gallery_mapc_eg_9_1.png