igvAnnotationTrack-class: Constructor for igvAnnotationTrack
In paul-shannon/igvR: igvR: integrative genomics viewer

igvAnnotationTrack-class

R Documentation

Constructor for igvAnnotationTrack

Description

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.