Heatmap for ChIP-seq data

Question

[Marco Pannone]

Hello everybody!

I have some data from ChIP-seq analysis, I have performed peak calling and I have annotated the peaks to the nearby genes. So basically I have a .bed file with unique peaks, genomic coordinates of the peaks, and a final column with the gene name of the nearby annotated gene for each peak.

I look for a way to produce a heatmap (and a profile plot on top of it) where I can plot all the peaks accordingly to their distance to the TSS, while having the gene names on each row of the heatmap.

I have checked some functions such as plotHeatmap from deepTools, but it does not seem to provide me an option for keeping the gene names as row names of the heatmap when plotting.

Any help would be very appreciated!

Thanks in advance :)

Answer 1

[Papyrus]

I think you can use EnrichedHeatmap (R package) with the show_row_names = T argument, like in the example shown here by the author: example.

[Marco Pannone]

Thanks for the suggestion! I did not know the existence of this package and I will for sure give it a try! :)