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Draw an interactive rainfall plot

Source: R/rainfall.R
rainfallPlot.Rd

Creates a GenomeSpy rainfall plot from a maftools MAF object. The API deliberately follows maftools::rainfallPlot() where practical, making the function an almost drop-in interactive replacement.

Usage

rainfallPlot(
  maf,
  tsb = NULL,
  detectChangePoints = FALSE,
  ref.build = "hg19",
  color = NULL,
  savePlot = FALSE,
  width = NULL,
  height = NULL,
  fontSize = 1.2,
  pointSize = 0.4,
  region = NULL,
  elementId = NULL
)

Arguments

maf

A maftools MAF object.

tsb

One tumor sample barcode. When NULL, the most mutated sample is selected.

detectChangePoints

Detect and annotate potential kataegis loci using the maftools criterion: at least six consecutive mutations with an average intermutation distance no greater than 1,000 bp.

ref.build

Reference assembly: "hg18", "hg19", or "hg38".

color

Optional named character vector overriding colors for the six pyrimidine substitution classes.

savePlot

Retained for maftools API familiarity. TRUE is unsupported; use the widget's Save as SVG button instead.

width, height

Widget dimensions. Unlike maftools, these do not describe a PDF device.

fontSize

Relative font-size multiplier.

pointSize

Relative mutation-point size.

region

Optional initial genomic region such as "chr8:98000000-98500000", or a chromosome such as "chr8". Commas and whitespace in coordinates are accepted. The endpoints may span chromosomes, for example "chr3:43393228-chr4:8534670". The plot remains zoomable.

elementId

Optional element ID.

Value

A MutGlyph htmlwidget.

Details

Only SNP records are plotted, including synonymous variants. Substitutions are normalized to the six pyrimidine classes. Inter-event distances are calculated independently within each chromosome, so chromosome boundaries do not create artificial distances.

With detectChangePoints = TRUE, detected kataegis intervals are shaded and marked with upward arrows. The complete locus table is retained in plot$x$spec$datasets$kataegis and no files are written as a side effect.

See also

oncoplot() and as_json().

Examples

if (interactive()) {
  brca <- maftools::read.maf(
    maf = system.file("extdata", "brca.maf.gz", package = "maftools"),
    verbose = FALSE
  )
  rainfallPlot(brca, detectChangePoints = TRUE)
}