Draw an interactive oncoplot

Creates a GenomeSpy oncoplot from a maftools MAF object. oncoplot() deliberately imitates the layout, ordering rules, and commonly used argument names of maftools::oncoplot(), making it an almost drop-in interactive replacement for common workflows. It is not intended to provide complete API compatibility with every maftools option.

Usage

oncoplot(
  maf,
  top = 20,
  minMut = NULL,
  altered = FALSE,
  genes = NULL,
  genesToIgnore = NULL,
  colors = NULL,
  keepGeneOrder = FALSE,
  sampleOrder = NULL,
  removeNonMutated = FALSE,
  clinicalFeatures = NULL,
  annotationColor = NULL,
  sortByAnnotation = FALSE,
  annotationOrder = NULL,
  topBarData = NULL,
  topBarLims = NULL,
  leftBarData = NULL,
  leftBarLims = NULL,
  rightBarData = NULL,
  rightBarLims = NULL,
  draw_titv = FALSE,
  titv_col = NULL,
  includeColBarCN = TRUE,
  showTumorSampleBarcodes = FALSE,
  rowHeight = 24,
  drawRowBar = TRUE,
  drawColBar = TRUE,
  showPct = TRUE,
  showTitle = TRUE,
  titleText = NULL,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

maf

A maftools MAF object.

top

Number of genes to display when genes is NULL.

minMut

Optional minimum mutated/altered sample count or cohort fraction.

altered

Use altered rather than mutated sample counts for minMut.

genes

Optional gene symbols to display instead of selecting top genes.

genesToIgnore

Optional gene symbols removed after selection.

colors

Optional named character vector of mutation-class colors.

keepGeneOrder

Preserve the supplied/selected gene order.

sampleOrder

Optional sample barcodes to select and order.

removeNonMutated

Remove samples without events in the displayed genes.

clinicalFeatures

Optional categorical clinical fields to display.

annotationColor

Optional named list of per-feature categorical color mappings or GenomeSpy color-scheme names.

sortByAnnotation

Sort samples by the selected clinical features.

annotationOrder

Optional named list of partial categorical level orders.

topBarData

Optional two-column sample metric data or one clinical field.

topBarLims

Optional numeric limits for the custom top bar.

leftBarData, rightBarData

Optional two-column gene metric data.

leftBarLims, rightBarLims

Optional numeric limits for custom side bars.

draw_titv

Show a transition/transversion contribution track.

titv_col

Optional named character vector of Ti/Tv class colors.

includeColBarCN

Include Amp and Del gene-level copy-number calls in the top sample summary bars, matching maftools::oncoplot().

showTumorSampleBarcodes

Show rotated sample names below the matrix.

rowHeight

Preferred height in pixels of each gene row when height is not supplied. The matrix grows to use the resulting widget height.

drawRowBar

Show the stacked mutation-count bars to the right.

drawColBar

Show the stacked sample mutation-burden bars above.

showPct

Show altered-sample percentages beside the gene rows.

showTitle

Show the cohort summary above the plot.

titleText

Optional text that replaces the generated cohort summary.

width, height

Widget dimensions.

elementId

Optional element ID.

Value

A MutGlyph htmlwidget.

Details

The sample axis supports wheel or trackpad zooming and panning. Hover over mutation cells and summary bars for details, or use the widget's Save as SVG button to export the currently visible composition.

Categorical and numeric clinical annotations use independent color scales. Sample labels use ranged text and appear only when their bands are wide enough; zooming in reveals labels hidden in a dense overview. Custom summary bars accept one numeric metric keyed by sample or gene, and use the metric's column name as the axis title.

See also

as_json() to retrieve the rendered GenomeSpy specification.

Examples

if (interactive()) {
  laml <- maftools::read.maf(
    maf = system.file("extdata", "tcga_laml.maf.gz", package = "maftools"),
    clinicalData = system.file(
      "extdata",
      "tcga_laml_annot.tsv",
      package = "maftools"
    )
  )
  oncoplot(laml, top = 10)
}