Interpretation the percentage of top 10 mutated gene in plotmafSummary result

Question

[sugus]

Hi,

I am learning maftools, a R package, to analyze some mutation data but I am really confused about the percentage of top 10 mutated gene in plotmafSummary result when reading your delicate vignette. I made a screenshot and show it as the follows:

You could obviously see that 25% has a little bit longer than 27% regarding the bar length, or TET2 (9%) has longer bar length than that of IDH2 (10%). This is really confusing and how to interpret that? What does this percentage value mean?

Thank you.

Answer 1

[dsull]

See source code here: https://rdrr.io/bioc/maftools/src/R/dashboard.R

Seems like the length of the bars are based off of the total number of mutations in the gene while the percentage is based off of the fraction of samples with an alteration. This would mean that some samples may have multiple mutations (e.g. a single sample might have more than one mutation in DNMT3a), hence the discrepancy.

[dsull]

After searching around some more, seems like that is indeed the case: https://gitmemory.com/issue/PoisonAlien/maftools/339/501155132