ChordVariantDisplay

Auto-generated from the @jbrowse/mobx-state-tree model in the source — see the developer guide for concepts. Provided by the circular-view plugin. View source.

Draws the structural variants of a VariantTrack in a CircularView, each translocation as a chord across the circle.

Example usage

The circular-view display for a VariantTrack of structural variants; translocations are drawn as chords across the circle. The track config below is what creates it; its colors are the config slots on ChordVariantDisplay:

{
  type: 'VariantTrack',
  trackId: 'sv',
  name: 'Structural variants',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfTabixAdapter',
    uri: 'https://example.com/sv.vcf.gz',
  },
  displays: [
    {
      type: 'ChordVariantDisplay',
      displayId: 'sv-ChordVariantDisplay',
    },
  ],
}

The configuration slots for this model are documented on its config schema page.

Each section ends with the members a composed model contributes, linked to the page that documents them.

Properties

Member	Description
type `type: types.literal('ChordVariantDisplay')`
configuration `configuration: ConfigurationReference(configSchema)`

2 inherited properties from 2 models

From ParkedColorMixin: parkedColors

From BaseDisplay: id

Volatiles

Member	Description
highlightedFeatureIds `string[] \| undefined`	ids of the records to keep at full strength while the rest dim; undefined dims nothing. The SV inspector writes the selected record's event here
visibleFeatureIds `string[] \| undefined`	ids of the records to draw; undefined draws them all. The SV inspector writes the rows its sheet's filters leave here, so a filter change is a redraw and no refetch

5 inherited volatiles from 2 models

From BaseChordDisplay: features, reloadCounter

From BaseDisplay: error, statusMessage, statusProgress

Getters

Member	Description
visibleIdSet `Set<string> \| undefined`
drawnFeatures `Feature[] \| undefined`	the held records `visibleFeatureIds` leaves
featureWidgetType `{ type: string; id: string; }`	the panel the linear variant displays open for the same record
chordFeet `{ x: Float32Array<ArrayBuffer>; x2: Float32Array<ArrayBuffer>; xGaps: Uint32Array<ArrayBuffer>; x2Gaps: Uint32Array<ArrayBuffer>; placed: Uint8Array<ArrayBuffer>; junction: string[]; }`	every held record's two ends on the circle's unrolled axis, by the record's place in `features`: its start, and its mate's position where it has one, else its end. `junction` is the two ends unordered, which a breakend pair's two records share.
colorSetting `ColorSetting`	`encoding.color` as written
paintedColorField `CategoricalField \| undefined`	the field the chords paint by, undefined for a constant or callback
chordStrokes `Map<Feature, string>`	each chord's record's color: its field's value through the scale, or the `value` the color channel answers for it
chordPicks `{ picked: number[]; features: Feature[]; laneOfId: Map<string, number>; }`	the drawn records a chord stands for, one per junction: the first record of a breakend pair draws it, and `laneOfId` sends both records' ids to that lane
dimmedFeatureIds `ReadonlySet<string> \| undefined`	the drawn records whose chords dim while the SV inspector highlights some: every lane but those a highlighted record, or its breakend twin, draws
chordLanes `ChordLanes`	the drawn records as the chord mark's lanes, each in its color with the alpha the SV inspector's dimming leaves it
drawnLanes `ChordLanes`	the chord lanes, the ones whose ends are under a pixel apart included
laneIndexById `ReadonlyMap<string, number>`	each drawn record's lane by id, a breakend pair's twin included
shapeAlpha `number`	`encoding.opacity`, over each chord's color's own alpha
chordCell `ChordCell \| undefined`	what the view's canvas draws for this display: its lanes while it is ready, nothing while its loading or error ring covers the circle
legendColor `string \| undefined`	the chord color the circle's key shows, when every chord shares one
colorScales `ColorScale[]`	the key of the values the drawn chords paint, while they paint a field
legendSpec `LegendSpec`
shapesTestId `string`	the test id on the chord paths' group, on screen and in the export
solidColor `string \| undefined`	the constant `color.value` holds as written, undefined for none or a `jexl:` one

33 inherited getters from 4 models

From ColorWritesMixin: writtenColor

From ParkedColorMixin: parkedColor

From BaseChordDisplay: view, trackAssemblyNames, fetchInert, loaded, ready, displayError, svgReady, displayPhase, radiusPx, curveDepth, bezierRadius, selectedFeatureId, hoveredFeatureId, figureStage, drawnCount, shapes

From BaseDisplay: parentTrack, RenderingComponent, DisplayBlurb, adapterConfig, isMinimized, hoveredFeature, featureNoun, liveNotices, plotKeys, plot, configNotices, notices, cornerNotices, plotExamples, configDocsUrl

Methods

Member	Description
isVisible `(feature: Feature) => boolean`	whether `visibleFeatureIds` leaves a record drawn
shapeAt `(i: number) => ChordShape \| undefined`	lane `i` as the SVG side draws it, on the unrotated figure; undefined for a chord whose ends are under a pixel apart
laneAt `(x: number, y: number) => number \| undefined`	the chord passing nearest a figure point, within `CHORD_HIT_PX`
shapeLabel `(feature: Feature) => string`
swatchColor `(color: string) => string`	a key swatch for `encoding.color`, faded as the chords draw it
renderSvg `() => Promise<Element \| null>`
trackMenuItems `() => MenuItem[]`	Color by and Advanced → Edit plot..., which the circular view shows under its Tracks menu

13 inherited methods from 3 models

From ParkedColorMixin: parkedColorOf

From BaseChordDisplay: shapeFor, shapePathFor, hitAt, assemblyOf, canonicalRefName, placeEnd, axisSlice

From BaseDisplay: renderingProps, configProblemsOf, liftPlot, plotProblems, plotWrites

Actions

Member	Description
onChordClick `(feature: Feature) => void`	the `onChordClick` callback when the config sets one, else the record's details
clickFeature `(feature: Feature) => void`	what a click on the canvas reaches
setHighlightedFeatureIds `(ids: string[] \| undefined) => void`
setVisibleFeatureIds `(ids: string[] \| undefined) => void`
openSolidColorDialog `() => void`	the picker Color by's Solid color... opens