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Quantitative track

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

Example QuantitativeTrack config:

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

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"
  }
}

Display options

Scale, autoscale, and color options (scaleType, autoscale, minScore, maxScore, defaultRendering, color, bicolorPivot, etc.) go in the displayDefaults shorthand. defaultRendering picks the plot style and accepts xyplot, density, line, or scatter:

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

See the LinearWiggleDisplay config docs for the full list of display slots and their defaults.

Adapters

The examples above use the reduced uri form. See the BigWigAdapter, BedGraphTabixAdapter, and BedGraphAdapter config docs for all options.

See also