GRangesAnnotationTrack-class: Constructor for GRangesAnnotationTrack

In PriceLab/igvR: igvR: integrative genomics viewer

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)

PriceLab/igvR documentation built on Sept. 6, 2022, 5:45 a.m.