UCSCBedGraphQuantitativeTrack-class: Constructor for UCSCBedGraphQuantitativeTrack

In paul-shannon/IGV: igvR: integrative genomics viewer

Constructor for UCSCBedGraphQuantitativeTrack

Description

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.

Details

Detailed description goes here

Value

A UCSCBedGraphQuantitativeTrack object

Examples

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

if(interactive()){
   igv <- igvR()
   setGenome(igv, "hg38")
   setBrowserWindowTitle(igv, "UCSC BedGraph demo")
   displayTrack(igv, track)
   Sys.sleep(1)  # pause before zoomin
   showGenomicRegion(igv, "chr18:59,103,373-59,105,673")
   }

paul-shannon/IGV documentation built on Nov. 5, 2023, 2:09 p.m.