Derive the data needed by an oncoplot

Usage

oncoplot_data(
  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
)

Arguments

maf: A maftools MAF object.
top: Number of genes to select 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.
genesToIgnore: Optional gene symbols removed after selection.
colors: Optional named character vector of mutation-class colors.
keepGeneOrder: Preserve the selected gene order.
sampleOrder: Optional sample barcodes to select and order.
removeNonMutated: Remove samples without displayed events.
clinicalFeatures: Optional categorical or numeric clinical fields.
annotationColor: Optional named list of per-feature color mappings or GenomeSpy color-scheme names.
sortByAnnotation: Sort samples by selected clinical features.
annotationOrder: Optional named list of categorical level orders.
topBarData: Optional two-column sample metric data or clinical field.
topBarLims: Optional custom top-bar limits.
leftBarData, rightBarData: Optional two-column gene metric data.
leftBarLims, rightBarLims: Optional custom side-bar limits.
draw_titv: Derive transition/transversion contribution data.
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.

Value

A named list of data frames, vectors, and title statistics.