igvR-class: Create an igvR object

In PriceLab/igvR: igvR: integrative genomics viewer

Create an igvR object

Description

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

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