Oncoplot omits samples

[rmnsimonyan]

Hello!:)

I am making oncoplots for a number of cancer patients, and I encounter the following issue all the time: some samples get automatically removed by the program, even when I set removeNonMutated=F, fill=T. Some of my annovar-annotated files are empty, because no mutations have been detected. Would that be reason or there is something else I am not taking into account? I am aiming for all the samples, even the ones without any mutations to be included in the plot. I would greatly appreciate any advice on this.

Thank you! Arman

[PoisonAlien]

Hello Arman,

The easiest fix would be adding a dummy synonymous variant to the empty annovar files. That should add them to the plot and wont affect much of the analysis.

[rmnsimonyan]

Thanks so much!

On a separate note - I was also trying to make oncoplots with specific variants instead of gene names as rows. I figured there is no parameter to adjust to that, so I tried to manually change the gene names in annovar files to variant IDs before parsing to maftools but it gives error

Error in data.table::tstrsplit(Gene.refGene, split = ";", keep = 1) :
  'keep' should contain integer values between 0 and 0.

Do you think it is something plausible to do with maftools' oncoplot?

[nuttynutmore]

Hi there,

Thanks for such a great and easy to use tool, with very visually appealing results.

I am also experiencing the issue of non-mutated samples being omitted from oncoplots, despite using removeNonMutated = FALSE, fill = TRUE. I have noted the use of dummy synonymous mutations as a workaround, however, as my pipeline is clinical grade, this is not professionally acceptable. I note this issue has been open for nearly 18 months now- do you have any solutions planned for future releases of maftools?

Kind regards, nuttynutmore

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This issue is stale because it has been open for 60 days with no activity.

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