Help creating R plot for visualizing variant frequencies in multiple sample

Question

[pm2012]

Hello community,

I would like to create a plot similar to the one shown below in panel C (from PMID: 33444750) using information in my VCF file. I am assuming this is plotted in R. Could you please let me know what kind of plot this is and/or what package I can use to create a similar plot? Thanks!

Answer 1

[Florian]

Dear @pm2012, This is a typical heatmap used to plot the variant frequency. You can generate the plot via pheatmap (example here). But is also possible probably with ggplot and also in Python. Similar and a bit nicer plot can be found here using the following R code. The tool is specific for CIVD19 data, thus the tool is just for inspiration.

I hope that helps.

Kind regards, Florian

[pm2012]

Thanks Florian. This is helpful.