Hist track styles

[1]:

import coolbox
from coolbox.api import *

[2]:

coolbox.__version__

[2]:

'0.4.0'

Hist track include:

BigWig
BedGraph
1D hic-feature tracks, see this link

Basic hist styles:

line
fill
scatter

[3]:

bw = "../../../tests/test_data/bigwig_chr9_4000000_6000000.bw"

frame = XAxis() + \
    BigWig(bw, style='fill') + Color("#fc07be") + Title("fill") + \
    BigWig(bw, style='line') + Color("#fcbe07") + Title('line') + \
    BigWig(bw, style='scatter') + Color("#be07fc") + Title('scatter')

frame.plot("chr9:4700000-4950000")

[3]:

Based on these basic styles, you can use parameters to make some changes, for example use 'fmt' to change line style:

[4]:

frame = XAxis() +\
    BigWig(bw, style='line', fmt='--') + Color("#fcbe07") + Title('dashed line') + \
    BigWig(bw, style='line', fmt=':') + Color("#be07fc") + Title('dotted line') + \
    BigWig(bw, style='line', fmt='-.') + Color("#0007fc") + Title('dashdot line')

frame.plot("chr9:4700000-4950000")

[4]:

fmt can also used for change scatter marker style:

[5]:

frame = XAxis() +\
    BigWig(bw, style='scatter', fmt='.') + Color("#fcbe07") + Title('point') + \
    BigWig(bw, style='scatter', fmt='^') + Color("#be07fc") + Title('triangle_up') + \
    BigWig(bw, style='scatter', fmt='s') + Color("#0007fc") + Title('square')

frame.plot("chr9:4700000-4950000")

[5]:

Another useful prameter ‘threshold’ are used for highlight some region:

[6]:

frame = XAxis() +\
    BigWig(bw, style='fill', threshold=100, color="#0000ff", threshold_color="#ff0000") + Title("fill") + \
    BigWig(bw, style='stairsfilled', threshold=100, color="#0000ff", threshold_color="#ff0000") + Title("stairsfill") + \
    BigWig(bw, style='line', line_width=1, threshold=100, color="#0000ff", threshold_color="#ff0000") + Title("line") + \
    BigWig(bw, style='stairs', line_width=1, threshold=100, color="#0000ff", threshold_color="#ff0000") + Title("stairs") + \
    BigWig(bw, style='scatter', size=50.0, threshold=100, color="#0000ff", threshold_color="#ff0000") + Title("scatter")

frame.plot("chr9:4700000-4950000")

[6]:

This feature can be used for visualize AB compartment, it’s same to use ABCompartment track

[7]:

ab = "../../../tests/test_data/chr9.1.pc.bedGraph"
frame = XAxis() +\
    BedGraph(ab, style='stairfill', threshold=0, color="#0000ff", threshold_color="#ff0000") + \
    ABCompartment(ab)
frame.plot("chr9:1-80000000")

[7]: