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

QuantitativeTrack-class

R Documentation

Constructor for QuantitativeTrack

Description

QuantitativeTrack creates an IGV track for genomic tracks in which a numerical value is associated with each reported location.

Usage

QuantitativeTrack(
  trackName,
  quantitativeData,
  fileFormat = c("wig", "bigWig", "bedGraph", "gwas"),
  color = "gray",
  sourceType = c("file", "url"),
  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 polyvalent object, either a data.frame, GRanges, or UCSCBedGraphQuantitative object
`fileFormat`	only "bedGraph" supported at present; wig and bigWig support soon.
`color`	A CSS color name (e.g., "red" or "#FF0000")
`sourceType`	only "file" supported at present ("gcs" for Google Cloud Storage, and "ga4gh" for the Global Alliance API may come)
`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.