compare two cool balance matrices

[BenxiaHu]

Hello,
is there any idea to calculate the difference between two cool balance matrices? I know hicCompareMatrices can (https://hicexplorer.readthedocs.io/en/latest/content/tools/hicCompareMatrices.html) can do that.

[sergpolly]

There is no such functionality built-in into cooler or cooltools by itself. However you can easily do this while viewing your data interactively in higlass (or using higlass-python locally):

note that "divide by" button in the menu - here is the result after the division by one of the available hg19 datasets and changing a colormap to "bwr":

You can also achieve that by scripting it in python , e.g.:

import cooler
clr1 = cooler.Cooler("cooler1.cool")
clr2 = cooler.Cooler("cooler2.cool")

region_of_interest = ("chr1", 10_000_000, 50_000_000)

mat1 = clr1.matrix(balance=True).fetch(region_of_interest)
mat2 = clr2.matrix(balance=True).fetch(region_of_interest)

ratio_mat = mat1 / mat2

now you have your ratio_mat - and can display it e.g. following this tutorial https://github.com/open2c/open2c_examples/blob/master/viz.ipynb or just plotting it using matplotlib e.g. like here: https://www.geeksforgeeks.org/imshow-with-two-colorbars-under-matplotlib/