how to draw two different Y-axes with deeptools?

Question

[edoardobertolini]

Hi all, I’m trying to plot the methylation distribution along a set of genes using a metagene approach including the two flanking upstream/downstream regions. In particular I would like to draw two different Y-axes: one for the symmetrical CG/CHG methylation context and a second one for the CHH, as shown in the picture below. Is it possible to specify A different Y-axis for each bigwig input FILE LOADED in deeptools? Thanks a lot.

Ed

Answer 1

[Devon Ryan]

I think you posted this to the deepTools google-group too. But regardless, there's no way to do this directly in deepTools. I suggest that you export the data (there's an option for that in plotProfile) and then tweak things to your liking in R.

[steve]

I have a workflow where I did this here. It was a bit of an iterative trial&error process, but there might be some useful code scraps mixed in there.