DataFrameQuantitativeTrack-class: Constructor for DataFrameQuantitativeTrack
In paul-shannon/IGV: igvR: integrative genomics viewer

DataFrameQuantitativeTrack-class

R Documentation

Constructor for DataFrameQuantitativeTrack

Description

DataFrameQuantitativeTrack creates and IGV track for bed objects imported using rtracklayer

Usage

DataFrameQuantitativeTrack(
  trackName,
  quantitativeData,
  color = "blue",
  trackHeight = 50,
  autoscale,
  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 base R `data.frame`
`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 DataFrameQuantitativeTrack object

Examples

base.loc <- 88883100
tbl.blocks <- 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),
                  score=runif(3),
                  stringsAsFactors=FALSE)

track.blocks <- DataFrameQuantitativeTrack("blocks", tbl.blocks, autoscale=TRUE)

locs <- seq(from=base.loc, length.out=1000)
tbl.wig <- data.frame(chrom=rep("chr5", 1000), start=locs-1, end=locs,
                      score=runif(n=1000, min=-1, max=1))
track.wig <- DataFrameQuantitativeTrack("wig", tbl.wig, autoscale=FALSE,
                                        min=min(tbl.wig$score), max=max(tbl.wig$score),
                                        color="random")
if(interactive()){
   igv <- igvR()
   setGenome(igv, "hg38")
   setBrowserWindowTitle(igv, "DataFrameQuantitativeTrack demo")
   displayTrack(igv, track.blocks)
   roi <- sprintf("%s:%d-%d", tbl.blocks$chrom[1],
                  min(tbl.blocks$start)-1000, max(tbl.blocks$end) + 1000)
   showGenomicRegion(igv, roi)
   displayTrack(igv, track.wig)
   }

paul-shannon/IGV documentation built on Nov. 17, 2024, 11:55 p.m.