Constructor for GRangesAnnotationTrack

GRangesAnnotationTrack creates and IGV track for bed-like objects expressed as GRanges

Usage

GRangesAnnotationTrack(
  trackName,
  annotationData,
  color = "darkGrey",
  displayMode = "SQUISHED",
  trackHeight = 50,
  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.

annotationData

A GRanges object with optional name metadata column

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.

Value

A GRangesAnnotationTrack object

Details

Detailed description goes here

Examples

base.loc <- 88883100
tbl <- data.frame(chrom=rep("chr5", 3),
                  start=c(base.loc, base.loc+100, base.loc + 250),
                  end=c(base.loc + 50, base.loc+120, base.loc+290),
                  name=c("a", "b", "c"),
                  strand=rep("*", 3),
                  stringsAsFactors=FALSE)

gr <- GRanges(tbl)
track <- GRangesAnnotationTrack("GRangesQTest", gr)