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Quantitative tracks

QuantitativeTrack config​

Example QuantitativeTrack config:

{
  "trackId": "my_wiggle_track",
  "name": "My Wiggle Track",
  "assemblyNames": ["hg19"],
  "type": "QuantitativeTrack",
  "adapter": {
    "type": "BigWig",
    "bigWigLocation": {
      "uri": "http://yourhost/file.bw",
      "locationType": "UriLocation"
    }
  }
}

General QuantitativeTrack options​

  • scaleType - options: linear, log, to display the coverage data. default: linear
  • adapter - an adapter that returns numeric signal data, e.g. feature.get('score')

Autoscale options for QuantitativeTrack​

Options for autoscale:

  • local - min/max values of what is visible on the screen
  • global - min/max values in the entire dataset
  • localsd - mean value +- N stddevs of what is visible on screen
  • globalsd - mean value +/- N stddevs of everything in the dataset

Score min/max for QuantitativeTrack​

These options overrides the autoscale options and provides a minimum or maximum value for the autoscale bar:

  • minScore
  • maxScore

QuantitativeTrack drawing options​

  • inverted - draws upside down
  • defaultRendering - can be density, xyplot, or line
  • summaryScoreMode - options: min, max, whiskers

QuantitativeTrack renderer options​

  • filled - fills in the XYPlot histogram
  • bicolorPivot - options: numeric, mean, none. default: numeric
  • bicolorPivotValue - number at which the color switches from posColor to negColor. default: 0
  • color - color or color callback for drawing the values. overrides posColor/negColor. default: none
  • posColor - color to draw "positive" values. default: red
  • negColor - color to draw "negative" values. default: blue
  • clipColor - color to draw "clip" indicator. default: red

BigWigAdapter options​

  • bigWigLocation - a 'file location' for the bigwig

Example BigWig adapter config:

{
  "type": "BigWig",
  "bigWigLocation": {
    "uri": "http://yourhost/file.bw",
    "locationType": "UriLocation"
  }
}