How maftools oncoplot classifies variant classifications

Question

[lincaijin1994]

I've got a sequencing output dataframe. The summary of the variant classification is listed below

            3'UTR           5'Flank             5'UTR   Frame_Shift_Del 
              250                13               133               487 
  Frame_Shift_Ins               IGR      In_Frame_Del      In_Frame_Ins 
              354                 1               651                92 
           Intron Missense_Mutation Nonsense_Mutation  Nonstop_Mutation 
             8793              6385               517                 2 
              RNA            Silent       Splice_Site           Unknown 
              278              3062               225               181

I've created a oncoplot matrix and replaced the Intron, Silent, 3UTR, 5UTR, 5Flank, RNA, and Unknown with NULL using the following code.

maf_mat <- gsub('Silent;','',maf_mat)

Then I used the complexheatmap oncoprint to create a oncoplot and I got a oncoplot the same as maftools' one. So I just want to know if oncoplot presents Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, In_Frame_Ins, Missense_Mutation, Nonsense_Mutation, and Splice_Site only. And it will ignore the rest variant classification, 3'UTR and Silent for example, by default?

Answer 1

[MatthewP]

Hello, maftools oncoplot shows only non-synonymous mutation by default, you can see this issue.