BedpeInteractionsTrack-class: Constructor for BedpeInteractionsTrack

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

Constructor for BedpeInteractionsTrack

Description

BedpeInteractionsTrack creates an IGV track for two-location annotations

Usage

BedpeInteractionsTrack(
  trackName,
  table,
  color = "darkBlue",
  trackHeight = 50,
  displayMode = "EXPANDED",
  visibilityWindow = 1e+05
)

Arguments

trackName	A character string, used as track label by igv, we recommend unique names per track.
table	data.frame of 6 or more columns
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)
displayMode	"COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise.
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 BedpeInteractionsTrack object

Examples

    #----------------------------
    #  first, from a local file
    #----------------------------

  file <- system.file(package="igvR", "extdata", "sixColumn-demo1.bedpe")
  tbl.bedpe <- read.table(file, sep="\t", as.is=TRUE, header=TRUE)
  dim(tbl.bedpe)  #  32 6
  track <- BedpeInteractionsTrack("bedpe-6", tbl.bedpe)

    #------------------------------------------
    #  show the relevant portion of the genome
    #------------------------------------------

  shoulder <- 10000
  if(interactive()){
     igv <- igvR()
     setGenome(igv, "hg38")
     setBrowserWindowTitle(igv, "Paired End Demo")
     roi <- with(tbl.bedpe, sprintf("%s:%d-%d", chrom1[1], min(start1)-shoulder, max(end2) + shoulder))
     showGenomicRegion(igv, roi)
     displayTrack(igv, track)
     }

paul-shannon/igvR documentation built on Nov. 17, 2024, 9:36 p.m.