Create an igvR object

The igvR class provides an R interface to igv.js, a rich, interactive, full-featured, javascript browser-based genome browser. One constructs an igvR instance on a specified port (default 9000), the browser code is loaded, and a websocket connection openend. After specifying the reference genome, any number of genome tracks may be created, displayed, and navigated.

Usage

igvR(
  portRange = 15000:15100,
  host = "localhost",
  title = "igvR",
  browserFile = igvBrowserFile,
  quiet = TRUE
)

Arguments

portRange

The constructor looks for a free websocket port in this range. 15000:15100 by default

host

character, often "localhost" but (as with RStudio Server deployment) can be a remote host

title

Used for the web browser window, "igvR" by default

browserFile

The full path to the bundled html, js and libraries, and css which constitute the browser app

quiet

A logical variable controlling verbosity during execution

Value

An object of the igvR class

Examples

if(interactive()){
   igv <- igvR(title="igv demo")
   setGenome(igv, "hg38")
   showGenomicRegion(igv, "MEF2C")
     #---------------------------------------------------------------
     # an easy transparent way to create a bed track
     #---------------------------------------------------------------
   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("dataframeTest", tbl, color="red", displayMode="EXPANDED")
   displayTrack(igv, track)
   showGenomicRegion(igv, sprintf("chr5:%d-%d", base.loc-100, base.loc+350))
   } # if interactive