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Quantitative track

A QuantitativeTrack shows a single BigWig or bedGraph signal. Scale and color options (scaleType, autoscale, defaultRendering, color, etc.) go in displayDefaults.

{
  "type": "QuantitativeTrack",
  "trackId": "my_wiggle_track",
  "name": "My Wiggle Track",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://yourhost/file.bw"
  },
  "displayDefaults": { "defaultRendering": "line", "scaleType": "log" }
}
jbrowse add-track https://yourhost/file.bw \
  --trackId my_wiggle_track \
  --name "My Wiggle Track" \
  --assemblyNames hg19 \
  --displayDefaults '{"defaultRendering":"line","scaleType":"log"}'

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", "scaleType": "log" }
}

Display options

Scale and color settings (scaleType, autoscale, minScore, maxScore, color, bicolorPivot) are LinearWiggleDisplay slots, set through displayDefaults. defaultRendering picks xyplot, density, line or scatter. The cookbook has the single-color and bicolor 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:

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

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" }]
}

The same track offers the Manhattan plot under the track menu's Display types; the GWAS track guide covers it.

See also