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

GRangesAnnotationTrack-class

R Documentation

Constructor for GRangesAnnotationTrack

Description

GRangesAnnotationTrack creates and IGV track for bed-like objects expressed as GRanges

Usage

GRangesAnnotationTrack(
  trackName,
  annotationData,
  color = "darkGrey",
  displayMode = "SQUISHED",
  trackHeight = 50,
  expandedRowHeight = 30,
  squishedRowHeight = 15,
  maxRows = 500,
  searchable = FALSE,
  visibilityWindow = 1e+05
)

Arguments

`trackName`	A character string, used as track label by igv, we recommend unique names per track.
`annotationData`	A GRanges object with optional name metadata column
`color`	A CSS color name (e.g., "red" or "#FF0000")
`displayMode`	"COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise.
`trackHeight`	track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files)
`expandedRowHeight`	Height of each row of features in "EXPANDED" mode.
`squishedRowHeight`	Height of each row of features in "SQUISHED" mode, for compact viewing.
`maxRows`	of features to display
`searchable`	If TRUE, labels on annotation elements may be used in search
`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 GRangesAnnotationTrack object

Examples

base.loc <- 88883100
tbl <- 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),
                  name=c("a", "b", "c"),
                  strand=rep("*", 3),
                  stringsAsFactors=FALSE)

gr <- GRanges(tbl)
track <- GRangesAnnotationTrack("GRangesQTest", gr)

paul-shannon/igvR documentation built on Nov. 11, 2023, 8:26 p.m.