Constructor for igvAnnotationTrack

Usage

igvAnnotationTrack(
  trackName,
  annotation,
  fileFormat = c("bed"),
  color = "gray",
  displayMode = c("SQUISHED", "COLLAPSED", "EXPANDED"),
  sourceType = "file",
  trackHeight = 30,
  expandedRowHeight = 30,
  squishedRowHeight = 15,
  maxRows = 500,
  searchable = FALSE,
  visibilityWindow = 1e+05
)

Arguments

trackName: A character string, used as track label by igv, we recommend unique names per track.
annotation: An opague type, currently either a data.frame, GRanges, or UCSCBed object from rtracklayer.
fileFormat: Only "bed" is currently supported.
color: A CSS color name (e.g., "red" or "#FF0000")
displayMode: "COLLAPSED", "EXPANDED", or "SQUISHED"
sourceType: Only "file" sources are currently supported.
trackHeight: track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files)
expandedRowHeight: Height of each row of features in "EXPANDED" mode.
squishedRowHeight: Height of each row of features in "SQUISHED" mode, for compact viewing.
maxRows: of features to display
searchable: If TRUE, labels on annotation elements may be used in search
visibilityWindow: Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types.

Value

An igvAnnotationTrack object