Question: show the names of the genes on the Y axis on the heatmap Deeptools
0
gravatar for Bioiris
2.6 years ago by
Bioiris0
Bioiris0 wrote:

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

rna-seq chip-seq deeptools • 902 views
ADD COMMENTlink modified 2.6 years ago by Devon Ryan89k • written 2.6 years ago by Bioiris0
1

Hi,

Is this helpful for you ?

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

ADD REPLYlink written 2.6 years ago by Farbod3.2k
1
gravatar for Devon Ryan
2.6 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

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).

ADD COMMENTlink written 2.6 years ago by Devon Ryan89k

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

ADD REPLYlink written 2.6 years ago by Bioiris0

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.

ADD REPLYlink written 2.6 years ago by Devon Ryan89k
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