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Quantitative tracks

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

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"}'

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