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LinearWiggleDisplay

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the wiggle plugin. View source.

Example usage

Minimal QuantitativeTrack config. See the quantitative track guide for all adapter and display options:

{
  type: 'QuantitativeTrack',
  trackId: 'coverage',
  name: 'Coverage',
  assemblyNames: ['hg38'],
  adapter: { type: 'BigWigAdapter', uri: 'https://example.com/coverage.bw' },
}

Several bigWigs, which a MultiQuantitativeTrack stacks one per row:

{
  type: 'MultiQuantitativeTrack',
  trackId: 'coverage_by_sample',
  name: 'Coverage by sample',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'MultiWiggleAdapter',
    bigWigs: [
      'https://example.com/sample1.bw',
      'https://example.com/sample2.bw',
    ],
  },
}

Taller track, log scale, custom color:

{
  type: 'QuantitativeTrack',
  trackId: 'coverage',
  name: 'Coverage',
  assemblyNames: ['hg38'],
  adapter: { type: 'BigWigAdapter', uri: 'https://example.com/coverage.bw' },
  displayDefaults: {
    height: 200,
    scales: { y: { type: 'log' } },
    color: 'darkgreen',
  },
}

See the Config slots section below for all available configuration fields.

configuration for the quantitative display: an XY plot, density, line or scatter rendering of one source or of many, with rows: 'source' giving each source a row of its own

Per-source metadata (a name, color and group for each) is preloaded on the adapter rather than here — see MultiWiggleAdapter's subadapters slot, where group drives the sidebar clustering tree and color sets each source's line or fill.

These are display-level slots: set them inside a track's displays to change its defaults (setting them at the track top level has no effect). The object shorthand displayDefaults: { key: value } is equivalent to the full displays: [{ type: 'LinearWiggleDisplay', displayId: '...', key: value }] array form — see configuring displays.

Config slots

These slots go on a display entry: "displays": [{ "type": "LinearWiggleDisplay", ... }], or in the track's displayDefaults when this is its default display. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
mark
stringEnum (bar, point, line, heatmap) = 'bar'		What each score is drawn as, in the mark display's words: bar, a bar from the origin to the score; point, a point at it; line, a line through the scores; heatmap, a strip whose colour is the score. The track menu's Plot type writes it. v4's defaultRendering loads as its mark: xyplot a bar, scatter a point, density a heatmap, and line and linecenter a line.
{
  "type": "LinearWiggleDisplay",
  "mark": "heatmap"
}
interpolate
stringEnum (step, linear) = 'step'		How a line joins its scores: step holds each across its bin, as the data says; linear runs from one bin's centre to the next, smoother where the bins are few. Read by a line alone.
rows
Rows		One row per value of a field, stacked down the track with a label, a separator and the clustering sidebar, and the arrangement a reader gives them. source — one row per subtrack — is the only field this display reads; leave it unset and every source is drawn in one shared plot. domain is the row order: the subtracks it names lead, the rest keep the adapter's order, and a clustering run rotates its dendrogram towards it rather than discarding it. labels, tree, treeProvenance and kept are what the arrangement dialog, a clustering run and a focus write, each as a session edit to this object.
{
  "type": "LinearWiggleDisplay",
  "rows": "source"
}
rowColor
RowColor		The colour a reader set on a named subtrack, as domain/range pairs: its plot, or under a score gradient the tint beside its label, ahead of the adapter's colour and the palette.
{
  "type": "LinearWiggleDisplay",
  "rowColor": { "domain": ["tumor"], "range": ["#b2182b"] }
}
color
WiggleColor		One CSS colour, or score through a scale — threshold for the bicolor plot, linear for the density ramp. Unset, it is the pos/neg pair about the origin, and several sources in one plot box each paint their row colour.
{
  "type": "LinearWiggleDisplay",
  "color": { "field": "score", "scale": "threshold", "domain": [2] }
}
scales
ValueScale		The y scale the plot is drawn through: type, domainMin, domainMax, domainQuantile, symlogConstant and rules, the reference lines drawn across it. The density rendering draws no rule and does not widen to one: it spends colour on the score and has no axis to rule.
{
  "type": "LinearWiggleDisplay",
  "scales": { "y": { "rules": [{ "value": 30, "label": "2 copies" }, 15] } }
}
showLegend
boolean = true		Draw the key: density's score color ramp, or the source colors where several share one plot. Defaults to on
height
number = 100		default height for the track
scoreField
string = 'score'		Feature field plotted on the score axis, read natively off each feature. The default score is the field every adapter serves — including the value a BED adapter's scoreColumn rewrote it to — so an explicit name here reaches a raw column the adapter left alone (a BED extra column, a GFF attribute) and takes precedence over that adapter-tier rewrite. The Manhattan plot skips a feature with no finite value in the field; the wiggle renderings plot it at 0
resolution
number = 1		how many points per pixel the fetch asks a tiered file for: 1 is one per pixel, larger is finer and smaller is coarser. Clamped to the range the Resolution menu offers, so a value outside it reads as the nearest end
origin
number = 0		The value bars grow from, and the cut a threshold color scale with an empty domain uses. The same slot, with the same meaning, as the mark display's origin
size
number = 2		Point diameter in px for the point mark, the display's constant for what the mark display spells encoding.size
advanced
lineWidth
number = 1		Line thickness in px for line rendering. Defaults to 1
advanced
maxGapMultiple
number = 0		Interpolated line only: break the line where consecutive points sit further apart than this multiple of the track's own mean point spacing, instead of drawing one long chord across the hole. Scaled to the data rather than a fixed bp distance so it holds at every zoom. 0 keeps one connected line
advanced
summaryScoreMode
stringEnum (max, min, avg, whiskers) = 'whiskers'		choose whether to use max/min/average or whiskers which combines all three into the same rendering
showTree
boolean = true		Show the subtrack clustering tree in the sidebar
showBranchLength
boolean = true		position tree nodes by branch length (dendrogram) rather than evenly by topology (cladogram)
showRowLabels
boolean = true		Name each subtrack row down the left edge
treeAreaWidth
number = 80		width in px of the tree sidebar, which a drag on its edge also writes
showRowSeparators
boolean = false		draw a hairline between adjacent rows; off by default, because a painting whose neighbouring rows differ in color already separates itself and the line only earns its pixel where they do not — a run of same-colored rows reads as one block without it, with no way to recover the row count by eye. Drawn only once rows are at least 4px tall: below that the line is as thick as the row it borders, turning a dense painting into a grid of hairlines with a little color between them