Dear developers,
I’ve encountered an alignment issue with BigWig files in coolbox 0.4.0 where the peaks do not align correctly with the X axis (see attached picture).
After downgrading to version 0.3.8 and running the exact same code, the four BigWig files are correctly aligned (matching the reference output viewed in IGV)
Here is the code I am using to plot the region:
import coolbox
from coolbox.api import *
frame = XAxis() \
+ BigWig("ChIP_protein_1.bigWig",
max_value = 20,
color = '#af8dc3',
min_value = 0) + Title("ChIP_protein_1") + TrackHeight(1) \
+ Spacer(0.5) \
+ BigWig("ChIP_protein_2.bigWig",
max_value = 20,
color = '#e7d4e8',
min_value = 0) + Title("ChIP_protein_2") + TrackHeight(1) \
+ Spacer(0.5) \
+ BigWig("ChIP_protein_3.bigWig",
max_value = 20,
color = '#7fbf7b',
min_value = 0) + Title("ChIP_protein_3") + TrackHeight(1) \
+ Spacer(0.5) \
+ BigWig("ChIP_protein_4.bigWig",
max_value = 20,
color = '#d9f0d3',
min_value = 0) + Title("ChIP_protein_4") + TrackHeight(1) \
+ Spacer(0.5) \
+ BED("genes.bed",
gene_style = "normal",
labels = False,
display = "stacked",
color = "black",
border_color = "black",
fontsize = 10) + Feature(height=1) + Title("Genes")
frame.plot("Chr3:7623001-7677067")
Thanks for your help!
Dear developers,
I’ve encountered an alignment issue with BigWig files in
coolbox 0.4.0where the peaks do not align correctly with the X axis (see attached picture).After downgrading to version 0.3.8 and running the exact same code, the four BigWig files are correctly aligned (matching the reference output viewed in IGV)
Here is the code I am using to plot the region:
Thanks for your help!