show the names of the genes on the Y axis on the heatmap Deeptools

Question

[Bioiris]

Hello, I made the heatmap of épégénétiques marks around TSS using Deeptools (ComputeMatrix then plotHeatmap) but the problem that the latest tools (plotHeatmap) gives me a heatmap with the region (+ -1kb TSS and 1KB) in X axis.

is there any way to show the names of the genes on the Y axis on the heatmap?

thank you

[Farbod]

Hi,

Is this helpful for you ?

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Navigating-Trinity-DE-features-Using-TM4-MeV

[yugen30]

Is there a way to just get the top 100 genes from the heatmap as a list?

Answer 1

[Devon Ryan]

There's no option in deepTools to display the gene/transcript/region names on the heatmap, normally there are so many of them that you wouldn't be able to see them. If you really want the names displayed then you'll need to tweak the code to do that (if you're interested in doing so, just mention that in a comment and I'll look through the code for where you'll likely need to modify things on Monday).

[Bioiris]

yes I'm very interested if you can do it I will be very grateful

[Devon Ryan]

This will take a bit of playing around to get things correct, but the following is roughly how it'll work:

1. You'll need to delete this line to be something more like ax.axes.set_yticks(sub_matrix['matrix'].shape[0])
2. You'll then need to add new ticks and labels, which is something like ax.axes.yticks(np.arange(sub_matrix['regions'].shape[0]), labels).
3. The labels will have to be created and is in hm.matrix.regions I think.

Hopefully you only have one group, since it'll be tougher to do correctly with more.

[yugen30]

Hello,

I tried this but I still do not get the gene names on the y-axis. Is there a way I can just obtain the list of the top 100 genes? I am interested in obtaining the top genes where the peaks are near the TSS. Thank you.