After initialization, the browser can be controlled using the functions described below.
loadGenome#
async
Returns a promise to load a reference genome.
browser.loadGenome(config)
See the reference object description for details on configuration options.
Example
browser.loadGenome(
{
"id": "hg38",
"name": "Human (GRCh38/hg38)",
"fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
"indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
"cytobandURL": "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt",
"tracks": [
{
"name": "Refseq Genes",
"url": "https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz",
"order": 1000000,
"indexed": false
}
]
}
}
loadSessionObject#
async
Load a session object, also referred to as a browser configuration object. See Browser Creation for details.
Loading a session will clear the current reference genome and all tracks.
browser.loadSessionObject(config)
loadSession#
async
Load a session by url or a javascript File blob, which should point to a valid session json object. The json is a representation of a browser configuration object described in the Browser Creation section, but does not support parameter values not representable as json such as functions and promises.
The method takes an object with a single property, url, which can be a URL or a local File blob.
browser.loadSession({url})
loadTrack#
async
Load a track and return a promise for the track object. See the Tracks page for more detail on configuration options.
const track = await browser.loadTrack(config)
Example
browser.loadTrack({
url: 'http://data.broadinstitute.org/igvdata/1KG/b37/data/HG02450/alignment/HG02450.mapped.ILLUMINA.bwa.ACB.low_coverage.20120522.bam',
label: 'HG02450'
})
loadSampleInfo#
async
Load a sample information file.
The method takes an object with a single property, url, which can be a URL or a local File blob.
browser.loadSampleInfo({url})
findTracks#
Returns an array of tracks matching input critera. Criteria can be specified as either
- A property value pair
- A function taking the track object as an argument and returning true or false
const tracks = browser.findTracks(propertyOrFunction, value)
Examples
console.log("Find tracks by property 'id' with value 'T2':");
const tracksById = browser.findTracks("id", "T2");
for(let t of tracksById) {
console.log(` id=${t.id} name=${t.name}`);
}
console.log("Find tracks by type 'wig'");
const tracksByType = browser.findTracks("type", "wig");
for(let t of tracksByType) {
console.log(` id=${t.id} name=${t.name}`);
}
console.log("Find tracks by function function(track) {return track.name && track.name.startsWith('GM128')}");
const tracksByFunction = browser.findTracks(function(track) {
return track.name && track.name.startsWith('GM128');
});
removeTrack#
Remove a track object from the browser.
browser.removeTrack(track)
removeTrackByName#
Remove track(s) whose "name" property matches the given name.
browser.removeTrackByName(name)
loadROI#
async
Load an annotation file or array of annotation files to define regions of interest (ROIs). Regions of interest are overlaid on the genome view across all tracks. See Regions of Interest for more details.
browser.loadROI(trackConfig | arrayOfTrackConfigs )
Examples
browser.loadROI([
{
name: 'ROI set 1',
url: 'https://s3.amazonaws.com/igv.org.test/data/roi/roi_bed_1.bed',
format: bed,
color: "rgba(68, 134, 247, 0.25)"
},
{
name: 'ROI set 2',
url: 'https://s3.amazonaws.com/igv.org.test/data/roi/roi_bed_2.bed',
format: bed,
color: "rgba(0, 150, 50, 0.25)"
})
clearROIs#
Remove all regions of interest.
browser.clearROIs()
getUserDefinedROIs#
async
Returns a promise for an array containing all user-defined ROIs (regions of interest created interactively during an igv.js session).
const rois = await browser.getUserDefinedROIs()
search#
async
Search by a locus, and change browser locus to corresponding region.
By default the search function uses a webservice to query positions of RefSeq genes for genome "hg19".
This can be overriden during initialization by supplying a url to a custom webservice.
For details see Browser initialization.
browser.search(locus)
Examples
browser.search('EGFR')
browser.search('chr10:1000-2000')
Multiple loci can be passed as space delimited list. This will result in a multi-locus view.
browser.search('chr10:1000-2000 EGFR')
This function returns a promise which resolves to true if the symbol was found, false otherwise.
currentLoci#
Return the current genomic region as a locus string, or array of locus strings if in multi-locus view.
zoomIn#
Zoom in by a factor of 2
browser.zoomIn()
zoomOut#
Zoom out by a factor of 2
browser.zoomOut()
currentLoci#
Return the current genomic region as a locus string, or an array of locus strings if in multi-locus view
const locusStringOrArray = browser.currentLoci()
visibilityChange#
Signal a change in visibility, typically from hidden (e.g. display:none) to shown (e.g. display:block).
This is necessary because changes in display attribute do not trigger events.
browser.visibilityChange()
If multiple igv browsers are on a page, the function igv.visibilityChange can be used to signal all.
igv.visibilityChange();
toJSON#
Return the current state of the browser as a JSON style object. This object can be loaded with loadSessionObject. Note the returned value is a jsonifiable object, not a json string.
const json = browser.toJSON();
compressedSession#
Return a compressed, encoded, string representing the current browser state.
const sessionString = browser.compressedSession()
This string can be used to load the session on any page hosting an igv.js instance with a url of the form
https://myhost/mypage?sessionURL=blob:<compressed session string>
Note to reinstate the session queryParametersSupported must be set to true in the igv.js configuration.
toSVG#
Convert the browser contents to SVG format. This includes ideogram, ruler, and all tracks. The value returned by this function is a serialized SVG object.
const svg = browser.toSVG()
setCustomCursorGuideMouseHandler#
Pass genomic location and mouse location with respect to trackContainer to the provided handler. The data is transmitted as the cursor guide is manipulated across the track container.
The handler function will receive an object with the following properties * bp - cursor-guide location. base-pair units. * start - track start location. base-pair units. * end - track end location. base-pair units. * interpolant - cursor-guide location. 0 - 1 units.
Example
browser.setCustomCursorGuideMouseHandler(({ bp, start, end, interpolant }) => { });