Oncoplot showing wrong mutations compared to orignal MAF file

[dhwani2410]

Describe the issue So, I have selected top genes using MutSig2CV. I am passing the top genes in the "genes" parameter of oncoplot.

But the color code generated in the plot is a mismatch from the actual maf file data. The last 4 rows are completely grey in color(which means there is no variations). But when I check maf file, it shows there is a mutation in all the samples.

SQCC.maf = file.path('/home/user/combined_passed.maf') SQCC = read.maf(maf = SQCC.maf)

SQCC_genes=c('LTA4H','DIDO1','EIF1AX','CCNE2','NES','CCDC75','C19orf46','ABI3BP','IRGQ','FAM189B','CROCC','LIMA1','KIAA1012','PI4K2B','HSD17B13','DTWD2','CCDC78','PIGF','SMEK1','KLHL2')

oncoplot(maf = SQCC, genes = SQCC_genes, rightBarData =NULL, keepGeneOrder, showTumorSampleBarcodes = T,cohortSize = 3)

Session info Run sessionInfo() and post the output below

R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8
[4] LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8
[7] LC_PAPER=en_IN.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] maftools_2.12.0

loaded via a namespace (and not attached): [1] lattice_0.20-45 R.methodsS3_1.8.1 grid_4.2.0 R6_2.5.1
[5] lifecycle_1.0.1 gtable_0.3.0 scales_1.2.0 rlang_1.0.2
[9] cli_3.3.0 data.table_1.14.2 R.oo_1.24.0 R.utils_2.11.0
[13] Matrix_1.4-1 splines_4.2.0 RColorBrewer_1.1-3 tools_4.2.0
[17] pheatmap_1.0.12 munsell_0.5.0 survival_3.3-1 compiler_4.2.0
[21] colorspace_2.0-3 DNAcopy_1.70.0

[PoisonAlien]

Is it possible to post the plot?

[dhwani2410]

@PoisonAlien, please suggest the error

[PoisonAlien]

Hi, Are you sure that these genes are indeed mutated? Could you please do the following for example,

maftools::genesToBarcodes(maf = SQCC, genes = c("SMEK1", "CCDC75"))

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