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

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

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

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"))
#> -Reading
#> -Validating
#> -Silent variants: 561 
#> -Summarizing
#> --Possible FLAGS among top ten genes:
#>   MACF1
#>   MUC16
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.218s elapsed (0.199s cpu)