Derive mutation and protein-domain data for a lollipop plot

Usage

lollipop_data(
  maf,
  gene = NULL,
  AACol = NULL,
  refSeqID = NULL,
  proteinID = NULL,
  domains = NULL,
  proteinLength = NULL,
  count = c("events", "samples"),
  colors = NULL,
  allowEmpty = FALSE
)

Arguments

maf: A maftools MAF object or a normalized mutation data frame.
gene: One gene symbol. Optional for a data frame containing one gene.
AACol: Optional MAF column containing protein changes.
refSeqID, proteinID: Optional RefSeq transcript or protein identifier. These select the domain model, as in maftools::lollipopPlot(). When the mutation input contains compatible RefSeq metadata, MutGlyph checks it against the selected model and warns about mixed or mismatching isoforms.
domains: Optional custom protein-domain data frame.
proteinLength: Optional protein length in amino acids.
count: Count mutation events or distinct samples.
colors: Optional mutation-class color overrides.
allowEmpty: Return an empty mutation table instead of failing. Used by two-cohort plots, where maftools permits one cohort to have no mutations.

Value

Prepared mutation, domain, transcript, and color data.