Quantitative track

A QuantitativeTrack shows a single BigWig or bedGraph signal; a MultiQuantitativeTrack carries several of them in one display. Both draw through LinearWiggleDisplay, so the scale, colour and layout settings below apply to either, through displayDefaults.

Config file

{
  "type": "QuantitativeTrack",
  "trackId": "my_wiggle_track",
  "name": "My Wiggle Track",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://yourhost/file.bw"
  },
  "displayDefaults": {
    "defaultRendering": "line",
    "scales": { "y": { "type": "log" } }
  }
}

CLI (add-track)

jbrowse add-track https://yourhost/file.bw \
  --trackId my_wiggle_track \
  --name "My Wiggle Track" \
  --assemblyNames hg19 \
  --displayDefaults '{"defaultRendering":"line","scales":{"y":{"type":"log"}}}'

JBrowse Desktop

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": "QuantitativeTrack",
  "trackId": "my_wiggle_track",
  "name": "My Wiggle Track",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://yourhost/file.bw"
  },
  "displayDefaults": {
    "defaultRendering": "line",
    "scales": { "y": { "type": "log" } }
  }
}

Display options

The axis is one object, scales.y, the colour is one object, color, and facet decides the layout; all three are LinearWiggleDisplay slots and all three go through displayDefaults.

defaultRendering picks xyplot, density, line, linecenter or scatter. Those five say what a signal is drawn as; facet says how many rows there are, so the two can be set independently.

Reference lines belong to the axis object too. scales.y.rules draws a dashed line across the plot at each value, a bare number or { value, color, label }, in every row of a faceted track:

Config file

{
  "type": "QuantitativeTrack",
  "trackId": "tumor_depth",
  "name": "Tumor depth",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://yourhost/tumor_depth.bw"
  },
  "displayDefaults": {
    "scales": {
      "y": { "rules": [{ "value": 30, "label": "2 copies" }, 15] }
    }
  }
}

CLI (add-track)

jbrowse add-track https://yourhost/tumor_depth.bw \
  --trackId tumor_depth \
  --name "Tumor depth" \
  --assemblyNames hg19 \
  --displayDefaults '{"scales":{"y":{"rules":[{"value":30,"label":"2 copies"},15]}}}'

JBrowse Desktop

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": "QuantitativeTrack",
  "trackId": "tumor_depth",
  "name": "Tumor depth",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://yourhost/tumor_depth.bw"
  },
  "displayDefaults": {
    "scales": {
      "y": { "rules": [{ "value": 30, "label": "2 copies" }, 15] }
    }
  }
}

An autoscaled end of the axis widens to keep every rule on it, so a rule stays drawn over a deletion the coverage never climbs out of, and a pinned domainMin or domainMax that excludes a rule drops it. A label is free text: JBrowse assumes no ploidy, so "2 copies" is the author's claim. The density rendering draws no rules, having no axis to rule.

A reader adds the same lines without a config file: the track menu's score submenu opens Reference lines, which writes this list.

Colors

color is a CSS color string, or an object naming the field it reads and the scale it reads through:

the picture	the value
one solid colour	`"#8b0000"`
a colour each side of a cut	`{ "field": "score", "scale": "threshold", "domain": [5], "range": ["#aaa", "#f00"] }`
a ramp, which density fades through	`{ "field": "score", "scale": "linear", "scheme": "viridis" }`
a colour per source	`{ "field": "source", "scale": "categorical" }`

A threshold with an empty domain cuts at origin, the value the bars also grow from. A ramp takes a named scheme or a range of CSS stops, runs straight across the y domain unless domainMid places its middle stop, and with one colour runs from white to it. The cookbook has worked recipes.

Adapters

BigWigAdapter, BedGraphTabixAdapter (bgzip plus tabix, for large data) and BedGraphAdapter (a small plain .bedGraph) all take the uri shorthand; supported file types lists them with their config pages.

Any numeric column of a feature file

The wiggle display also draws on a FeatureTrack: name it in the track's displays, and scoreField picks the column it plots. The default score reads the BED score column, or whatever the adapter's scoreColumn rewrote it to; an explicit field name reaches a raw column of the file instead, so a BED with a coverage column plots as a signal without a conversion to bedGraph:

Config file

{
  "type": "FeatureTrack",
  "trackId": "coverage_bed",
  "name": "Coverage",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://yourhost/coverage.bed.gz"
  },
  "displays": [{ "type": "LinearWiggleDisplay", "scoreField": "coverage" }]
}

CLI (add-track-json)

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "coverage_bed",
  "name": "Coverage",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://yourhost/coverage.bed.gz"
  },
  "displays": [{ "type": "LinearWiggleDisplay", "scoreField": "coverage" }]
}'

JBrowse Desktop

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": "FeatureTrack",
  "trackId": "coverage_bed",
  "name": "Coverage",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://yourhost/coverage.bed.gz"
  },
  "displays": [{ "type": "LinearWiggleDisplay", "scoreField": "coverage" }]
}

This FeatureTrack also offers the Manhattan plot under the track menu's Display types; the GWAS track guide covers it.

Many signals in one track

A MultiQuantitativeTrack puts many BigWig/bedGraph signals in one display. Use the bigWigs array for a plain list of URLs, or subadapters when you need per-subtrack color, group, and source.

Config file

{
  "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"
    ]
  }
}

CLI (add-track-json)

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"
    ]
  }
}'

JBrowse Desktop

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"
    ]
  }
}

The track type seeds facet: "source", summaryScoreMode: "avg" and a 200px height into its displayDefaults, so it opens as one row per source without saying so; a key the config spells wins over the seed. facet: "" puts every source back in one shared plot box, and facet: { "field": "source", "domain": […] } names the sources that lead the row order.

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):

Config file

{
  "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"
      }
    ]
  }
}

CLI (add-track-json)

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"
      }
    ]
  }
}'

JBrowse Desktop

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; a .bedmethyl.gz also auto-detects as this in the Add track form:

Config file

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

CLI (add-track-json)

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"
  }
}'

JBrowse Desktop

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.

Quantitative track

Display options#

Colors#

Adapters#

Any numeric column of a feature file#

Many signals in one track#

The subadapters form#

Loading bedMethyl as a multi-quantitative track#

See also#

Display options

Colors

Adapters

Any numeric column of a feature file

Many signals in one track

The subadapters form

Loading bedMethyl as a multi-quantitative track

See also