# Introduction: a simple demo

Paul Shannon

#### 2022-04-26

#### Package

igvR 1.16.0

# Contents

# 1 Overview

The igvR package provides easy programmatic access in R to the web-based javascript library igv.js in order to create and display genome tracks in its richly interactive web browser visual interface. I am grateful to Jim Robinson, Douglass Turner and colleagues for their fine work.

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

    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 Session Info

    sessionInfo()