1 Overview
2 Load the libraries we need
3 Display a list of the currently supported genomes
4 Display MYC
5 Create and display minimal 1-row data.frame centered below MYC on chr8
6 Create and display a simulated quantitative (bedGraph) track
7 Zoom out by direct manipulation of the currently displayed region
8 Zoom out and by function calls
9 Session Info

1 Overview

The igvR package provides easy programmatic access in R to the web-based javascript library igv.js to create and display genome tracks in its richly interactive web browser visual interface.

In this vignette we present a few very simple uses of igvR:

connect to the web browser
query the names (e.g., “mm10”) of the currently supported genoems
specify that we will use the hg38 genome
zoom to the MYC gene
construct a simple data.frame specifying a bed-like track
display that data.frame track in the browser using a random color
create and display a “quantitative” data.frame
zoom out for a wider view

Your display will look like this at the conclusion of this demo:

2 Load the libraries we need

library(igvR)

Create the igvR instance, with all default parameters (portRange, quiet, title). Javascript and HTML is loaded into your browser, igv.js is initialized, a websocket connection between your R process and that web page is constructed, over which subsequent commands and data will travel.

igv <- igvR()
setBrowserWindowTitle(igv, "simple igvR demo")
setGenome(igv, "hg38")

3 Display a list of the currently supported genomes

print(getSupportedGenomes(igv))

4 Display MYC

showGenomicRegion(igv, "MYC")

5 Create and display minimal 1-row data.frame centered below MYC on chr8

loc <- getGenomicRegion(igv)

tbl.bed <- data.frame(chrom = loc$chrom, start = loc$start + 2000, end = loc$end - 2000,
                      name = "simple.example", stringsAsFactors = FALSE)

track <- DataFrameAnnotationTrack("simple bed", tbl.bed, color = "random")
displayTrack(igv, track)

6 Create and display a simulated quantitative (bedGraph) track

loc <- getGenomicRegion(igv)
size <- with(loc, 1 + end - start)
starts <- seq(loc$start, loc$end, by = 5)
ends <- starts + 5
values <- sample(1:100, size = length(starts), replace = TRUE)

tbl.bedGraph <- data.frame(chrom = rep("chr8", length(starts)), start = starts, end = ends,
                           value = values, stringsAsFactors = FALSE)

track <- DataFrameQuantitativeTrack("bedGraph", tbl.bedGraph, color = "red", autoscale = FALSE,
                                    min = 80, max = 100)
displayTrack(igv, track)

7 Zoom out by direct manipulation of the currently displayed region

loc <- getGenomicRegion(igv)
half.span <- round((loc$end - loc$start) / 2)

new.region <- with(loc, sprintf("%s:%d-%d", chrom, start - half.span, end + half.span))
showGenomicRegion(igv, new.region)

8 Zoom out and by function calls

zoomOut(igv)
zoomIn(igv)

9 Session Info

sessionInfo()

Introduction: a simple demo

2026-05-01

Package

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