I am using the lastest MutSigCV v1.4, and trying to implement the ["CoMut plot"][1] to visualize the results. However, the [MutSigCv documenttation][2] only describes the content of one the results files (`my_results.sig_genes.txt`), but there are 5 files that MutSigCV outputs:

 - `my_results.categs.txt`
 - `my_results.coverage.txt`
 - `my_results.mutations.txt`
 - `my_results.mutcateg_discovery.txt`
 - `my_results.sig_genes.txt`

Yes, I did ask the developers but... *tumble-weed*

**Q1: Where can I find an explanation for the data in the other 4 files**?

As I mentioned, I am replicating some parts of [coMut][1], which has generated a couple of questions in Biostar ([here][3] and [here][4]). The plots representing the top mutated genes (left of coMut) and type of mutation per sample (bottom) were easy using data from MutSigCV - using data in the files `my_experiment.sig_genes.txt` and `my_experiment.mutations.txt`

However without having a precise explanation of the MutSigCV output, I cannot proceed further.

**Q2: Which data is used for the remaining components of the plot**?

I have a suspicion that the top bar plot (number of mutations/Mb) uses data from [MuTect][5], but no idea about the other 2 components. My guess is that some of that is buried in the MutSigCV output files but can't figure out where.

 [1]: http://www.broadinstitute.org/blog/visualizing-cancer-genome
 [2]: http://www.broadinstitute.org/cancer/software/genepattern/modules/docs/MutSigCV/1?print=true
 [3]: https://www.biostars.org/p/13226/
 [4]: https://www.biostars.org/p/87350/
 [5]: http://www.broadinstitute.org/cancer/cga/mutect
There is now an R package that reproduces this type of plot, and much more:

[GenVisR](https://github.com/griffithlab/GenVisR)

May thanks to the Griffith Lab. Other options listed [here](https://www.biostars.org/p/77286/).