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Multi-quantitative track

TL;DR: a MultiQuantitativeTrack overlays many BigWig/bedGraph signals in one display. Use the bigWigs array for quick absolute-URL setups, or subadapters when you need relative URLs or per-subtrack color, group, and source.

{
  "type": "MultiQuantitativeTrack",
  "trackId": "microarray_multi",
  "name": "MultiWig",
  "category": ["ENCODE bigWigs"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "bigWigs": [
      "https://www.encodeproject.org/files/ENCFF055ZII/@@download/ENCFF055ZII.bigWig",
      "https://www.encodeproject.org/files/ENCFF826HEW/@@download/ENCFF826HEW.bigWig",
      "https://www.encodeproject.org/files/ENCFF858LIM/@@download/ENCFF858LIM.bigWig",
      "https://www.encodeproject.org/files/ENCFF425TNW/@@download/ENCFF425TNW.bigWig"
    ]
  }
}
jbrowse add-track-json '{
  "type": "MultiQuantitativeTrack",
  "trackId": "microarray_multi",
  "name": "MultiWig",
  "category": ["ENCODE bigWigs"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "bigWigs": [
      "https://www.encodeproject.org/files/ENCFF055ZII/@@download/ENCFF055ZII.bigWig",
      "https://www.encodeproject.org/files/ENCFF826HEW/@@download/ENCFF826HEW.bigWig",
      "https://www.encodeproject.org/files/ENCFF858LIM/@@download/ENCFF858LIM.bigWig",
      "https://www.encodeproject.org/files/ENCFF425TNW/@@download/ENCFF425TNW.bigWig"
    ]
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "MultiQuantitativeTrack",
  "trackId": "microarray_multi",
  "name": "MultiWig",
  "category": ["ENCODE bigWigs"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "bigWigs": [
      "https://www.encodeproject.org/files/ENCFF055ZII/@@download/ENCFF055ZII.bigWig",
      "https://www.encodeproject.org/files/ENCFF826HEW/@@download/ENCFF826HEW.bigWig",
      "https://www.encodeproject.org/files/ENCFF858LIM/@@download/ENCFF858LIM.bigWig",
      "https://www.encodeproject.org/files/ENCFF425TNW/@@download/ENCFF425TNW.bigWig"
    ]
  }
}
Gotcha

The bigWigs shorthand only accepts absolute URLs; a relative path there will not resolve against the config's location. Use the subadapters form for relative URLs, which is also what you need for per-subtrack color, group, and source.

The subadapters form

Each subtrack carries a source: its label in the UI, and feature.source in a jexl color callback (jexl:feature.source=='k1'?'red':'blue'). bigWigs derives it from the file name; subadapters sets it explicitly (name is an alias, and source wins when both are set), plus a default color and a group label (MultiWiggleAdapter):

{
  "type": "MultiQuantitativeTrack",
  "trackId": "microarray_multi_groups",
  "name": "MultiWig (groups)",
  "category": ["ENCODE bigWigs"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "subadapters": [
      {
        "type": "BigWigAdapter",
        "source": "k1",
        "color": "red",
        "uri": "https://www.encodeproject.org/files/ENCFF055ZII/@@download/ENCFF055ZII.bigWig",
        "group": "group1"
      },
      {
        "type": "BigWigAdapter",
        "source": "k2",
        "color": "blue",
        "uri": "https://www.encodeproject.org/files/ENCFF826HEW/@@download/ENCFF826HEW.bigWig",
        "group": "group2"
      }
    ]
  }
}
jbrowse add-track-json '{
  "type": "MultiQuantitativeTrack",
  "trackId": "microarray_multi_groups",
  "name": "MultiWig (groups)",
  "category": ["ENCODE bigWigs"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "subadapters": [
      {
        "type": "BigWigAdapter",
        "source": "k1",
        "color": "red",
        "uri": "https://www.encodeproject.org/files/ENCFF055ZII/@@download/ENCFF055ZII.bigWig",
        "group": "group1"
      },
      {
        "type": "BigWigAdapter",
        "source": "k2",
        "color": "blue",
        "uri": "https://www.encodeproject.org/files/ENCFF826HEW/@@download/ENCFF826HEW.bigWig",
        "group": "group2"
      }
    ]
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "MultiQuantitativeTrack",
  "trackId": "microarray_multi_groups",
  "name": "MultiWig (groups)",
  "category": ["ENCODE bigWigs"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "subadapters": [
      {
        "type": "BigWigAdapter",
        "source": "k1",
        "color": "red",
        "uri": "https://www.encodeproject.org/files/ENCFF055ZII/@@download/ENCFF055ZII.bigWig",
        "group": "group1"
      },
      {
        "type": "BigWigAdapter",
        "source": "k2",
        "color": "blue",
        "uri": "https://www.encodeproject.org/files/ENCFF826HEW/@@download/ENCFF826HEW.bigWig",
        "group": "group2"
      }
    ]
  }
}

subadapters is an array of objects, so it templates from a samplesheet such as an RNA-seq timecourse:

// rows: [{ timepoint: '0h', bigwig: 's3://.../t0.bw' }, ...]
const track = {
  type: 'MultiQuantitativeTrack',
  trackId: 'rnaseq-timecourse', // keep this stable across rebuilds
  name: 'RNA-seq timecourse',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'MultiWiggleAdapter',
    subadapters: rows.map(row => ({
      type: 'BigWigAdapter',
      source: row.timepoint,
      uri: row.bigwig,
    })),
  },
}

Deploying JBrowse Web generates a whole config.json this way in a CI/CD pipeline.

Loading bedMethyl as a multi-quantitative track

A bedMethyl from modkit pileup reports the methylation fraction at each CpG, one row per modification type. Bgzipped and tabix-indexed (the methylation tutorial has the commands), it loads through BedTabixAdapter as a MultiQuantitativeTrack with one subtrack per modification type, which is also what a .bedmethyl.gz auto-detects as in the Add track form:

{
  "type": "MultiQuantitativeTrack",
  "trackId": "sample_modkit",
  "name": "CpG methylation (modkit)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://yourhost/sample_modkit.bedmethyl.gz"
  }
}
jbrowse add-track-json '{
  "type": "MultiQuantitativeTrack",
  "trackId": "sample_modkit",
  "name": "CpG methylation (modkit)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://yourhost/sample_modkit.bedmethyl.gz"
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "MultiQuantitativeTrack",
  "trackId": "sample_modkit",
  "name": "CpG methylation (modkit)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://yourhost/sample_modkit.bedmethyl.gz"
  }
}

JBrowse reads two columns: score (column 11), the percent methylation from 0 to 100, and name (column 4), the modification code (m for 5mC, h for 5hmC) used as the subtrack label.

See also