Creates a set of plot summarising a maf file.

maf_viz(maf, ...)

Arguments

maf

Raw maf dataframe containing alteration data

...

any argument belonging to the binmat method

Value

Returns a list of the following plots:

varclass Barplot of counts of each variant classification

vartype Barplot of counts of each variant type

snvclass Histogram of counts of each SNV class

samplevar Histogram of counts variants per patient

topgenes Barplot of counts of top variant genes

genecor Correlation heatmap of the top 10 genes

Examples

library(gnomeR) library(dplyr) library(dtplyr) patients <- as.character(unique(mut$Tumor_Sample_Barcode))[1:200] all.plots <- maf_viz(maf=mut %>% filter(Tumor_Sample_Barcode %in% patients))
#> Warning: All samples were sequenced on the same platform. #> The specify.plat argument has been overwritten to FALSE.
#> Warning: All samples were sequenced on the same platform. #> The specify.plat argument has been overwritten to FALSE.
all.plots <- maf_viz(maf=mut %>% filter(Tumor_Sample_Barcode %in% patients),specify.plat = TRUE)
#> Warning: All samples were sequenced on the same platform. #> The specify.plat argument has been overwritten to FALSE.
#> Warning: All samples were sequenced on the same platform. #> The specify.plat argument has been overwritten to FALSE.