Constructor for UCSCBedGraphQuantitativeTrack — UCSCBedGraphQuantitativeTrack-class • igvR

UCSCBedGraphQuantitativeTrack creates an IGV track for bedGraph objects imported with rtracklayer

Usage

UCSCBedGraphQuantitativeTrack(
  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 UCSCBedGraphQuantitativeTrack object

Details

Detailed description goes here

Examples

bedGraph.filepath <- system.file(package = "rtracklayer", "tests", "test.bedGraph")
gr.bedGraph <- rtracklayer::import(bedGraph.filepath)
track <- UCSCBedGraphQuantitativeTrack("UCSCBedGraphTest", gr.bedGraph)