links#

Show interaction loop

Get test data#

Test loop is from ENCODE https://www.encodeproject.org/experiments/ENCSR968KAY/

Homo sapiens GM12878
GRCh38
Accession: ENCFF041XLP

!gunzip ENCFF041XLP.bedpe.gz

[1]:

import pandas as pd

import trackc as tc

[2]:

loops = pd.read_table(
    "../../trackc_data/tutorials/links/ENCFF041XLP.bedpe", comment="#", header=None
)
loops = loops[[0, 1, 2, 3, 4, 5]]
display(loops.head(2))

	0	1	2	3	4	5
0	chr10	62550000	62575000	chr10	63075000	63100000
1	chr10	38085000	38090000	chr10	42560000	42565000

[3]:

regions = ["chr7:153000000-151000000", "chr11:118500000-116500000"]

ten = tc.tenon(figsize=(8, 0.6))
ten.add(pos="bottom", height=1)
ten.add(pos="bottom", height=1, hspace=0.1)
ten.add(pos="bottom", height=0.8, hspace=0.1)

tc.pl.links_track(
    ax=ten.axs(0),
    data=loops,
    label="GM12878",
    regions=regions,
    color=["#66AC84", "tab:purple"],
    maxrange=3000000,
    anchor="inside",
)

tc.pl.links_track(
    ax=ten.axs(1),
    data="../../trackc_data/tutorials/links/ENCFF041XLP.bedpe",
    label="loops",
    regions=regions,
    color="tab:purple",
    invert_y=True,
    anchor="outside",
    ax_on=True,
)
tc.pl.multi_scale_track(
    ten.axs(2),
    regions=regions,
    scale_adjust="Mb",
    intervals=1,
    tick_rotation=0,
    tick_fontsize=10,
    colors=["#66AC84", "tab:purple"],
)
# tc.savefig('trackc_loops.pdf')