DataFrameAnnotationTrack-class: Constructor for DataFrameAnnotationTrack

In paul-shannon/igvR: igvR: integrative genomics viewer

Constructor for DataFrameAnnotationTrack

Description

DataFrameAnnotationTrack creates an IGV track for bed objects imported using rtracklayer

Usage

DataFrameAnnotationTrack(
  trackName,
  annotation,
  color = "",
  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.
annotation	A base R data.frame
color	A CSS color name (e.g., "red" or "#FF0000"), leave as default empty string if supplying bed9 format with itemRgb.
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 DataFrameAnnotationTrack 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"),
                  score=runif(3),
                  strand=rep("*", 3),
                  stringsAsFactors=FALSE)

track <- DataFrameAnnotationTrack("data.frame demo", tbl)

if(interactive()){
   igv <- igvR()
   setGenome(igv, "hg38")
   setBrowserWindowTitle(igv, "DataFrameAnnotationTrack demo")
   displayTrack(igv, track)
   roi <- sprintf("%s:%d-%d", tbl$chrom[1], min(tbl$start)-100, max(tbl$start) + 100)
   showGenomicRegion(igv, roi)
   Sys.sleep(1)
   zoomOut(igv)
   }

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