generateRibbonPlot: Function to generate a ribbon plot depicting co-occurence and...

In MAFDash: Create an HTML Dashboard to Visualize Data from MAF File

Function to generate a ribbon plot depicting co-occurence and mutual exclusivity of gene mutations

Description

This function provides an alternate visualization for maftools::somaticInteractions()

Usage

generateRibbonPlot(
  maf,
  onco_genes = NULL,
  save_name = NULL,
  pval_high = 0.1,
  pval_low = 0.05,
  plot_type = "matrix",
  plot_frac_mut_axis = TRUE,
  rotate_plot_degrees = 0,
  shrink_factor = 1.3,
  scale_ribbon_to_fracmut = TRUE,
  sig_colors = NULL,
  gene_colors = NULL
)

Arguments

maf	A MAF object
onco_genes	A list of genes to restrict the analysis. Passed to maftools::somaticInteractions()
save_name	The name and path of the output PDF
pval_high	All interactions with less than this p-value will be shown
pval_low	Links with p-value less than this will be shown in a darker color
plot_type	'ribbon' returns a customized chord diagram, 'matrix' returns the default somaticInteractions() plot
plot_frac_mut_axis	Whether or not to draw a numerical axis on the perimeter
rotate_plot_degrees	Rotate default layout by this many degrees
shrink_factor	Higher values = more shrinkage; use to control whitespace (or lack thereof) around figure. Mostly useful in 0.5 - 1.5 range.
scale_ribbon_to_fracmut	Whether or not to scale ribbon widths to their frequency
sig_colors	Vector of 4 colors for coloring significance
gene_colors	Color(s) for gene segments. By default, they're colored randomly.

Value

No return value. If 'save_name' is not provided, then the plot is printed to the current graphics device, otherwise a PDF is created at the given path.

Author(s)

Mayank Tandon, Ashish Jain

Examples

library(MAFDash)
library(maftools)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
generateRibbonPlot(read.maf(maf),save_name=paste0(tempdir(),"/ribbonPlot.pdf"))

MAFDash documentation built on April 1, 2022, 9:05 a.m.