Visualization Community | St. Jude Cloud

GenomePaint ARC track example

Zhou Lab

Jan 4, 2022

< 1k

Hi-C

The ARC track shows the interactions of each region mapped from Hi-C data. In this track, the arcs are drawn between the centers of each region regions. The intensity of each arc corresponds to the proximity score as the color legend scale indicates. Interactions must be a minimum distance apart to be displayed.

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runproteinpaint({
    host: "https://proteinpaint.stjude.org",
    holder: visualizationContainer[0],
    parseurl: true,
    block: true,
    nobox: 1,
    noheader: 1,
    genome: "hg19",
    position: "chr11:7839893-9165172",
    nativetracks: "RefGene",
    tracks: [
        {
            type: "hicstraw",
            bedfile: "proteinpaint_demo/hg19/arc/mango.gz",
            name: "Arc Track Demo",
            percentile_max: 99,
            mode_arc: true,
            mode_hm: false
        }
    ]
})

Visualization Code

runproteinpaint({
    host: "https://proteinpaint.stjude.org",
    holder: visualizationContainer[0],
    parseurl: true,
    block: true,
    nobox: 1,
    noheader: 1,
    genome: "hg19",
    position: "chr11:7839893-9165172",
    nativetracks: "RefGene",
    tracks: [
        {
            type: "hicstraw",
            bedfile: "proteinpaint_demo/hg19/arc/mango.gz",
            name: "Arc Track Demo",
            percentile_max: 99,
            mode_arc: true,
            mode_hm: false
        }
    ]
})

GenomePaint ARC track example

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Visualization Code