Constructor for GRangesQuantitativeTrack — GRangesQuantitativeTrack-class • igvR

GRangesQuantitativeTrack creates and IGV track for bed objects imported using rtracklayer

Usage

GRangesQuantitativeTrack(
  trackName,
  quantitativeData,
  color = "blue",
  trackHeight = 50,
  autoscale = TRUE,
  min = NA_real_,
  max = NA_real_,
  visibilityWindow = 1e+05
)

Arguments

trackName: A character string, used as track label by igv, we recommend unique names per track.
quantitativeData: A GRanges object with (at least) a "score" metadata column
color: A CSS color name (e.g., "red" or "#FF0000")
trackHeight: track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files)
autoscale: Autoscale track to maximum value in view
min: Sets the minimum value for the data (y-axis) scale. Usually zero.
max: Sets the maximum value for the data (y-axis) scale. This value is ignored if autoscale is TRUE
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 GRangesQuantitativeTrack 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"),
                  score=runif(3),
                  strand=rep("*", 3),
                  stringsAsFactors=FALSE)

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