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takes output generated by read.maf and draws an oncoplot (aka waterfall plot).
oncoplot(maf, writeMatrix = FALSE, top = 20, drawRowBar = TRUE,
drawColBar = TRUE, showTumorSampleBarcodes = FALSE, annotation = NULL,
genesToIgnore = NULL, removeNonMutated = FALSE, colors = NULL)
writes oncomatrix to output file.
how many top genes to be drawn. defaults to 20.
logical plots barplot for each gene.
logical plots barplot for each sample.
logical to include sample names.
data.frame with first column containing Tumor_Sample_Barcodes and rest of columns with annotations.
do not show these genes in Oncoplot. Default NULL.
Logical. If TRUE
removes samples with no mutations in the oncoplot for better visualization. Default FALSE
.
named vector of colors for each Variant_Classification.
None.
Takes maf file as input and plots it as a matrix. Any desired annotations can be added at the bottom of the oncoplot by providing annotation
# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
oncoplot(maf = laml, top = 3)
# }
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