How maftools oncoplot classify variant type?

Question

[MatthewP]

Hello, I need to draw oncoplot with ComplexHeatmap instead of use oncoplot function in maftools for some reason. So I first need to extract plot data from maftools.

pradMaf <- read.maf("/Work/Mutect2.maf")

# get top 20 genes
geneSummary <- getGeneSummary(pradMaf)[1:20,]
geneList <- geneSummary$Hugo_Symbol
geneSample <- genesToBarcodes(pradMaf, genes = geneList)

I need to know how maftools classify variant especially Multi_Hit. It's Multi_Hit means one gene has multiple types of variant in same sample? Below is variant type stats(same gene), each tibble presents one sample.

# A tibble: 1 x 6
  Frame_Shift_Del Frame_Shift_Ins In_Frame_Del Missense_Mutati… Nonsense_Mutati…
            <int>           <int>        <int>            <int>            <int>
1               4               3            1               46                3
# … with 1 more variable: Splice_Site <int>
# A tibble: 1 x 5
  Frame_Shift_Del Frame_Shift_Ins In_Frame_Del Missense_Mutati… Nonsense_Mutati…
            <int>           <int>        <int>            <int>            <int>
1               3               3            1               42                1
# A tibble: 1 x 4
  Frame_Shift_Del Frame_Shift_Ins Missense_Mutation Nonsense_Mutation
            <int>           <int>             <int>             <int>
1               6               1                37                 4
# A tibble: 1 x 5
  Frame_Shift_Del Frame_Shift_Ins Missense_Mutation Nonsense_Mutati… Splice_Site
            <int>           <int>             <int>            <int>       <int>
1               1               2                36                4           1

If I assign Multi_Hit for those sample my plot has too many Multi_Hit compare to plot generate by maftools::oncoplot()

[MatthewP]

Ok, set writeMatrix = TRUE when using maftools::oncoplot function will get oncoplot data, no need to extract byhand. But I will leave question in case some have same problem.