What Software Can Be Used To Make A Plot Of Abberations As Shown?

Question

[merajazizmeraj]

Does anyone know what software was used to make plots like the following:

[Neilfws]

Where did you obtain this figure? Got a reference?

[A. Domingues]

@merajazizmeraj did manage to make that plot? I am also interested. This package appears to be used to generate the report mentioned by @B. Arman Aksoy but I could not implement it.

Answer 1

[B. Arman Aksoy]

Aren't these Broad's signature "CoMut" plots? For example, on this Nozzle report, if you click on the "CoMut" link, you will get a similar plot:

http://gdac.broadinstitute.org/runs/analyses__latest/reports/cancer/GBM-TP/MutSigNozzleReport2.0/nozzle.html

I believe this plot is generated on the fly and depends on the MutSig output. Most publications have a customized version of it, as expected (similar to your example). I suggest you having a look at the MutSig package as part of GenePattern and as far as I know, the plot generation is part of that pipeline, too.

[merajazizmeraj]

yes you are correct...i will look into the documentation for further details...thanks..!

Answer 2

[Alex Reynolds]

Perhaps ggplot2 bins with stacked bar plots?