Making heatmaps of ATACseq annotation data in R?

Question

[Ronin]

I am wanting to try to make a heatmap of some basic ATACseq annotation results using R. My dataset is a subset of a larger dataset, and contains some basic peak annotation data. For peaks between 100-300bp, we have the following results:

exon    2531
Intergenic  10554
intron  10794
promoter-TSS    1691
TTS 807

And we have more than one table like this, for larger peak files (say, 301-400bp; 401-500bp; etc.). As you can see, we have five categories presented in the table above. My idea is to calculate the percentage within each of the five categories, and then to plot the category on the y-axis, the peak sizes on the x-axis, and the percentage within each category as the color.

Does this idea make sense? To me it seems fairly straightforward, but I'm not certain. Any links or guides to do something similar would also be very appreciated.

[Ming Tommy Tang]

take a look at this package https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html

Answer 1

[rfran010]

Normally I would plot this data as a stacked bar plot, however I like your suggestion. For me, it took a second to adjust to seeing the data this way, but I think it is actually easier to distinguish differences in the heatmap form. This example is from Prism, but I'll probably try your idea out the next time I work with my annotation data!

One consideration is that you may also want to represent the peak count as well. Perhaps a separate bar graph to show the number of total peaks in each condition.

[Ronin]

This is great! I will definitely try this out. And you said this program is called Prism? I've never heard of this before, would you please provide any link so I can visit the site? I am very curious to know how you made that stacked barplot, I think that's a great visual. I went ahead and upvoted your comment.

edited to add a question

[rfran010]

It is by Graphpad, but it is subscription software.

Stacked barplots are handled well in R too though.