Function reference • igvR

All functions

BedpeInteractionsTrack(): Constructor for BedpeInteractionsTrack

DataFrameAnnotationTrack(): Constructor for DataFrameAnnotationTrack

DataFrameQuantitativeTrack(): Constructor for DataFrameQuantitativeTrack

GFF3Track(): Constructor for GFF3Track

GRangesAnnotationTrack(): Constructor for GRangesAnnotationTrack

GRangesQuantitativeTrack(): Constructor for GRangesQuantitativeTrack

GWASTrack(): Constructor for GWASTrack

GWASUrlTrack(): Constructor for GWASUrlTrack

GenomicAlignmentTrack(): Constructor for GenomicAlignmentTrack

QuantitativeTrack(): Constructor for QuantitativeTrack

RemoteAlignmentTrack(): Constructor for RemoteAlignmentTrack

Track(): Constructor for Track

UCSCBedAnnotationTrack(): Constructor for UCSCBedAnnotationTrack

UCSCBedGraphQuantitativeTrack(): Constructor for UCSCBedGraphQuantitativeTrack

VariantTrack(): Constructor for VariantTrack

currently.supported.stock.genomes(): currently.supported.stock.genomes

displayTrack(<igvR>): display the specified track in igv

enableMotifLogoPopups(<igvR>): turn mottif log popups on or off

getGenomicRegion(<igvR>): Obtain the chromosome and coordiates of the currently displayed genomic region.

getSupportedGenomes(<igvR>): Get the shorthand codes (eg, "hg38") for the genomes currently supported by our use of igv.js

getTrackNames(<igvR>): Get the names of all the tracks currently displayed in igv

igvAnnotationTrack(): Constructor for igvAnnotationTrack

igvR(): Create an igvR object

parseAndValidateGenomeSpec(): parseAndValidateGenomeSpec

ping(<igvR>): Test the connection between your R session and the webapp

removeTracksByName(<igvR>): Remove named tracks

saveToSVG(<igvR>): Get entire igv browser image in svg

setCustomGenome(<igvR>): Specify the reference genome you wish to use, via full specification of all urls

setGenome(<igvR>): Specify the reference genome, currently limited to hg38, hg19, mm10, tair10.

setTrackClickFunction(<igvR>): Specify (supply) the javascript function run on track click event

setTrackHeight(<igvR>): Remove named tracks

showGenomicRegion(<igvR>): Set the visible region, by explicit chromLoc string, or by named features in any curently loaded annotation tracks

showTrackLabels(<igvR>): Hide or show igv track labels

trackInfo(<Track>): Get basic info about a track: its type, file format, source and S4 class name

trackSize(<BedpeInteractionsTrack>): Retrieve the size of the BedpeInteractionsTrack

trackSize(<DataFrameAnnotationTrack>): Retrieve the size of the DataFrameAnnotationTrack

trackSize(<DataFrameQuantitativeTrack>): Retrieve the size of the DataFrameQuantitativeTrack

trackSize(<GFF3Track>): Retrieve the size of the GFF3Track

trackSize(<GRangesAnnotationTrack>): Retrieve the size of the GRangesAnnotationTrack

trackSize(<GRangesQuantitativeTrack>): Retrieve the size of the GRangesQuantitativeTrack

trackSize(<GWASTrack>): Retrieve the size of the GWASTrack

trackSize(<GWASUrlTrack>): Retrieve the size of the GWASUrlTrack

trackSize(<GenomicAlignmentTrack>): Retrieve the size of the GenomicAlignmentTrack

trackSize(<UCSCBedAnnotationTrack>): Retrieve the size of theUCSCBedAnnotationTrack

trackSize(<UCSCBedGraphQuantitativeTrack>): Retrieve the size of the UCSCBedGraphQuantitativeTrack

trackSize(<VariantTrack>): Retrieve the size of the VariantTrack

trackSize(<QuantitativeTrack>): Retrieve the size of the QuantitativeTrack

url.exists() url.exists(): url.exists

zoomIn(<igvR>): zoom the genome view in by a factor of 2

zoomOut(<igvR>): zoom the genome view out by a factor of 2