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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.

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',
    },
  ],
}

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

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

MemberDescription
type
type: types.literal('ChordVariantDisplay')
configuration
configuration: ConfigurationReference(configSchema)
1 inherited property from one model

From BaseDisplay: id

Volatiles

MemberDescription
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

MemberDescription
drawnFeatures
Feature[] | undefined		the held records visibleFeatureIds leaves
highlightedFeatureIdSet
Set<string> | undefined
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[]; index: Map<Feature, number>; }
every held record's two ends on the circle's unrolled axis, by the record's place in features: its own start, and its mate's position where it names one, else its own end. junction is the two ends unordered, which a breakend pair's two records share.
colorSetting
ColorSetting		the color object as written
paintedColorField
CategoricalField | undefined		the field the chords paint by, undefined for a constant or callback
chordStrokes
Map<Feature, string>		each drawn record's color: its field's value through the scale, or the value the color object 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
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
drawnCount
number		how many records the chord lanes hold, the ones whose ends are under a pixel apart included
laneIndexById
Map<string, number>		each drawn record's place in the lanes, by id
shapes
ChordShape[]		every drawn chord as the export draws it
shapeAlpha
number		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
27 inherited getters from 2 models

From BaseChordDisplay: view, trackAssemblyNames, fetchInert, loaded, ready, displayError, svgReady, displayPhase, radiusPx, bezierRadiusRatio, bezierRadius, sliceIndex, selectedFeatureId, hoveredFeatureId, chordStage, figureStage

From BaseDisplay: parentTrack, RenderingComponent, DisplayBlurb, adapterConfig, isMinimized, hoveredFeature, featureNoun, plotKeys, plot, plotExamples, configDocsUrl

Methods

MemberDescription
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
shapeFor
(featureId: string) => ChordShape | undefined		the chord a drawn record's id names, as the SVG side draws it; undefined for an id the lanes do not hold, and for a chord whose ends are under a pixel apart
hitAt
(dx: number, dy: number) => Feature | undefined		the record whose chord passes nearest a point CSS px from the circle's centre in the screen frame, within CHORD_HIT_PX
shapeLabel
(feature: Feature) => string
shapePathFor
(feature: Feature) => string | undefined		a drawn feature's outline as an SVG path on the unrotated figure, for anything that has to find a chord on screen without a DOM node to find
renderSvg
(_opts: ViewExportSvgOptions & { theme?: ThemeOptions | undefined; }) => Promise<Element | null>
9 inherited methods from 2 models

From BaseChordDisplay: assemblyOf, canonicalRefName, sliceFor, axisSlice

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

Actions

MemberDescription
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
8 inherited actions from 2 models

From BaseChordDisplay: openErrorDialog, setFeatures, reload

From BaseDisplay: setStatusMessage, setError, clearHoveredFeature, applyDisplaySettings, applyPlot