deepTools - change line colors in profile plots above a heatmap

Question

[mbk0asis]

Hi.

I've generated a heatmap with profile plots above it using 'deepTools'. The heatmap is clustered into 2 groups using '--kmeans' option. The heatmap looks OK, but lines in the profile plots, especially, cluster2 lines are too faint to see. Is there a option to change the colours?

Thank you!

[Bastien Hervé]

Note : How to add images to a Biostars post

Answer 1

[Devon Ryan]

There's no great way within plotHeatmap to change the profile colors. The simplest thing to do would be to save the output as a PDF and change this in Adobe Illustrator, since those lines should (hopefully) be distinct paths.

As an aside, please post the image somewhere, since with only 2 groups you shouldn't be getting light colors. Also please post your full command.