Interactive, zoomable rainfall plots and kataegis in R

rainfallPlot() is the interactive counterpart of maftools::rainfallPlot(). It defaults to the most mutated sample and plots chromosome-local inter-event distances for SNPs, including synonymous variants. The zoomable genomic scale can move from a whole-genome overview into dense mutation clusters without generating a new plot.

The bundled BRCA example contains several potential kataegis loci. With detectChangePoints = TRUE, MutGlyph applies the same operational criterion as maftools—at least six consecutive mutations with an average intermutation distance no greater than 1,000 bp. Arrows point to the clusters and subtle shading shows their complete genomic spans.

library(MutGlyph)

brca <- maftools::read.maf(
  maf = system.file("extdata", "brca.maf.gz", package = "maftools"),
  verbose = FALSE
)

rainfallPlot(
  brca,
  detectChangePoints = TRUE,
  pointSize = 0.5,
  height = 360
)

Try the plot: Scroll or pinch to zoom, drag to pan across the genome, and hover over a mutation for its coordinates and intermutation distance.

Detected loci remain available in the returned specification without writing a TSV file:

rainfall <- rainfallPlot(brca, detectChangePoints = TRUE)
rainfall$x$spec$datasets$kataegis

Pass region to open the interactive plot directly at a locus of interest. Coordinate separators are optional, and the plot remains zoomable.

rainfallPlot(
  brca,
  detectChangePoints = TRUE,
  region = "chr8:98,000,000-98,500,000",
  height = 360
)