maftools oncoplot samples

[WilliamPolar]

Dr. Wang, Thank you for your help.
Why is it that the Oncoplot is showing only 68 samples out of 73 samples from the maf?
It must be a simple answer but I cannot troubleshoot.

[ShixiangWang]

Hi @WilliamPolar , Please try setting removeNonMutated = FALSE in the plotting function, check https://rdrr.io/bioc/maftools/man/oncoplot.html

[WilliamPolar]

Is there a way to add continuous value annotation instead of categorical?
For example, If I have a score I generated that is a range of numbers, I want to show the spectrum, I guess I can give definition for each number too but I wonder if that is something this package has or I will just have to give each a definition.

[ShixiangWang]

Please see https://rdrr.io/bioc/maftools/f/vignettes/oncoplots.Rmd

I suggest you raise these questions in maftools GitHub repo https://github.com/PoisonAlien/maftools.

[WilliamPolar]

Thank you so much! this was so helpful~