Interact Track

The interact track (type = 'interact') visualizes pairwise interactions between genome regions as arcs.

File formats#

• bedpe
• interact
• bigInteract

Configuration Options#

General options

Property	Description	Default
arcType	See below	"nested"
arcOrientation	Direction of arcs ("UP" or "DOWN")	"UP"
alpha	Alpha transparency to apply to arcs that extend beyond viewport. Number between 0 and 1	0.5
thickness	Line thickness	2

Arc types#

• nested - Arc height is proportional to feature width.
• propotional - Arc height is proportional to feature score.
• inView - Proportional type, only arcs that are completely in view are drawn.
• partialInView - Proportional type, only arcs that are whole or partially in view are drawn.

Example#

    const options =
    {
        genome: "hg38",
        locus: "chr2:65,489,209-65,795,733",
        tracks: [
            {
                url: "https://s3.amazonaws.com/igv.org.demo/GSM1872886_GM12878_CTCF_PET.bedpe.txt",
                type: "interact",
                format: "bedpe",
                name: "CTCF PET - proportional",
                arcType: "proportional",
                arcOrientation: "UP",
                color: "rgb(0,200,0)",
                logScale: true,
                max: 80,
                visibilityWindow: 10000000
            },
            {
                url: "https://s3.amazonaws.com/igv.org.demo/GSM1872886_GM12878_CTCF_PET.bedpe.txt",
                type: "interact",
                format: "bedpe",
                name: "CTCF PET - nested",
                arcType: "nested",
                arcOrientation: "DOWN",
                color: "blue",
                alpha: 0.15,
                visibilityWindow: 10000000
            }
        ]
    }