Function to generate Burden plot

This function generates burden plot using the MAF data.

generateBurdenPlot(
  mymaf,
  plotType = "Dotplot",
  mb_covered = NULL,
  save_data_to_file = NULL
)

Arguments

mymaf

The MAF object

plotType

Type of plot (Either "Dotplot" or "Barplot")

mb_covered

Total covered bases for mutation count normalization

save_data_to_file

The name and path of the output file

Value

A ggplot object containing the burden plot

Author

Mayank Tandon, Ashish Jain

Examples

library(MAFDash)
library(maftools)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
generateBurdenPlot(read.maf(maf), plotType="Dotplot")
#> -Reading
#> -Validating
#> -Silent variants: 561 
#> -Summarizing
#> --Possible FLAGS among top ten genes:
#>   MACF1
#>   MUC16
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.208s elapsed (0.188s cpu) 

generateBurdenPlot(read.maf(maf), plotType="Barplot")
#> -Reading
#> -Validating
#> -Silent variants: 561 
#> -Summarizing
#> --Possible FLAGS among top ten genes:
#>   MACF1
#>   MUC16
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.332s elapsed (0.304s cpu)