MAFDash (version 0.2.1)

generateOverlapPlot: Function to generate Overlap plot

Description

This function generates an overlap plot using the MAF data.

Usage

generateOverlapPlot(
  mymaf,
  use_silent_mutations = FALSE,
  summarize_by = "gene",
  plotType = c("ribbon", "heatmap"),
  savename = NULL,
  savewidth = 8,
  saveheight = 8
)

Arguments

mymaf

The MAF object

use_silent_mutations

Flag to use the silent mutations in the plot

summarize_by

Paramter to summarize the data (Either 'gene' or 'mutation'")

plotType

The type of plot generated ("ribbon" or "heatmap" or both)

savename

The name and path of the output file

savewidth

Width of plot

saveheight

Height of plot

Value

No return value, the plot is saved as a pdf

Examples

# NOT RUN {
library(MAFDash)
library(maftools)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
# }
# NOT RUN {
generateOverlapPlot(read.maf(maf))
# }