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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,
  showTitle = TRUE,
  detectChangePoints = FALSE,
  ref.build = "hg19",
  color = NULL,
  savePlot = FALSE,
  width = NULL,
  height = NULL,
  fontSize = 1.2,
  pointSize = 0.4,
  region = NULL,
  elementId = NULL,
  annotationTracks = NULL
)

Arguments

maf

A maftools MAF object.

tsb

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

showTitle

Show the autogenerated sample title.

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.

annotationTracks

Optional named list of GRanges or data-frame interval tracks to show below the rainfall panel. Scores prioritize labels; the built-in mutglyph_gene_annotations() resource is one option.

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)
}