QuantitativeTrack-class: Constructor for QuantitativeTrack

QuantitativeTrack-classR 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.

Details

Detailed description will go here

Value

A QuantitativeTrack object


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