UCSCBedAnnotationTrack-class: Constructor for UCSCBedAnnotationTrack
In igvR: igvR: integrative genomics viewer

Description Usage Arguments Details Value Examples

UCSCBedAnnotationTrack creates and IGV track for bed objects imported using rtracklayer

UCSCBedAnnotationTrack(
  trackName,
  annotation,
  color = "darkGrey",
  displayMode = "SQUISHED",
  trackHeight = 50,
  expandedRowHeight = 30,
  squishedRowHeight = 15,
  maxRows = 500,
  searchable = FALSE,
  visibilityWindow = 1e+05
)

`trackName`	A character string, used as track label by igv, we recommend unique names per track.
`annotation`	A UCSCData object imported by `rtracklayer`
`color`	A CSS color name (e.g., "red" or "#FF0000")
`displayMode`	"COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise.
`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.

Detailed description goes here

A UCSCBedAnnotationTrack object

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bed.filepath <- system.file(package = "rtracklayer", "tests", "test.bed")
gr.bed <- rtracklayer::import(bed.filepath)
track <- UCSCBedAnnotationTrack("UCSC bed", gr.bed,  color="blue", displayMode="SQUISHED")