LDTrackDisplay

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

A linkage disequilibrium matrix read from a pre-computed file, drawn as a triangle over the view.

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 `types.literal('LDTrackDisplay')`
configuration `ConfigurationReference(configSchema)`

2 inherited properties from 2 models

From ParkedColorMixin: parkedColors

From BaseDisplay: id

Volatiles

Member	Description
indexSnpLocus `string \| undefined`	Key (`refName:start:id`) of the SNP whose row and column are emphasized. A key rather than an index, so it survives a refetch.

24 inherited volatiles from 7 models

From TriangleMatrixMixin: rpcData

From LegendMixin: dismissedLegendSections

From KeyedFetchMixin: loadedFetchKey

From FetchMixin: activeSignal, fetchGeneration, reloadCounter, statusWindow, error, statusMessage, statusProgress, fetchCanceled, fetchRotation

From RenderLifecycleMixin: canvasDrawn, paintCount, currentRenderingBackend, renderTick, autorunsInstalled, renderError, offScreen

From RegionTooLargeMixin: forceLoadTrack, byteEstimate, gateMeasuredViewportKey

From TrackHeightMixin: scrollTop, hostHeight

Getters

Member	Description
view `LinearGenomeView`
prefersOffset `boolean`
colorField `LDMetric`	`encoding.color.field`, the statistic the fetch asks the file for.
showNames `boolean`
variantLayout `"columns" \| "genomic"`
snps `LDSnp[]`	The loaded SNPs in screen order along the column axis.
cellWidth `number`	The column width the payload was laid out at.
viewSignature `string \| undefined`	The dynamic blocks: the SNP set is the viewport's, so a pan refetches while the stale triangle draws under the live transform.
atGenomicPositions `boolean`	Whether the loaded matrix is at genomic positions: a multi-region view falls back to uniform columns.
r2Available `boolean`
dprimeAvailable `boolean`
indexSnpColumn `number`	Index of the index SNP in `snps`, or -1.
paintedColorField `LDMetric`	The loaded metric, so a stale triangle during a metric switch keeps its hue.
colorExtent `readonly [number, number]`	What an open end of the color domain follows: the statistic's own 0 to 1, not the loaded values, so one r² paints one color on every track.
colorScales `ColorScale[]`	The ramp the cells paint through, titled by the loaded metric. An end pinned inside the statistic's 0 to 1 reads `≤` or `≥`.
renderState `LDRenderState`
connectorsStack `BandStack<"connectors">`	The `connectors` band above the matrix: the connector lines in columns, the labels at genomic positions when they are on, else nothing; taken from the display's height so the triangle keeps its floor.
connectorsHeight `number`
drawsLabels `boolean`	Whether the SNP labels draw: on, in a `connectors` band that reserves room for them, so they never paint over the triangle.
matrixTop `number`	Where the triangle begins, under the `connectors` band.
depthFraction `number`	A file listing only nearby pairs draws a strip of the triangle's depth, so fit mode stretches that strip over the display.
gateEnabled `boolean`	Opt into RegionTooLargeMixin's byte gate: a tabix LD file's index says how much a region reads before any of it is downloaded.
connectorLineCoords `ConnectorCoord[]`	Each column tied to its SNP's genomic x, for the connector lines.
paintedCells `ReadonlyMap<number, LDDataResult>`	The payload as the painters read it: under a threshold scale each value at its interval's centre (`binnedColorValues`), while the hit test and the tooltip read the file's own.

94 inherited getters from 12 models

From TriangleMatrixMixin: heightMode, canvasWidth, viewTransform, matrixRegions, matrixHeight, matrixBlocks, yScalar, triangleTransform, triangleFrame

From ColorWritesMixin: writtenColor

From ParkedColorMixin: parkedColor, parkedIdentity

From MatrixRampMixin: paintedColorSetting, colorEncoding, colorScaleType, colorScheme, colorReverse, schemeRamp, colorBins, colorRamp, colorScale, colorDomain, colorMidNorm, matrixColor, colorFieldTitle

From LegendMixin: showLegend, legendRight, legendTop, legendSpec, hasLegendKey

From GlobalFetchMixin: host, canvasWidthPx, staticBlockSignature, dynamicBlockSignature, viewportEmpty, canRender, rendersCanvas, paintInert, svgReady, displayPhase

From KeyedFetchMixin: dataSuperseded, currentFetchKey, dataCurrent

From FetchMixin: isLoading, isLoadingOrCanceled, fetchInert, awaitingPrerequisite, awaitingDependentData, settingsFetchInputs

From RenderLifecycleMixin: paintSuperseded, painted

From RegionTooLargeMixin: byteGateAdapterConfig, configuredFetchSizeLimit, densityTooLarge, byteGateAdapterPath, adapterFetchSizeLimit, configForceLoad, gateViewportSpanBp, gateViewport, aboveForceLoadFloor, gateExempt, estimatedFetchBytes, gateMeasurementStale, gateByteLimit, gateActive, densityGateActive, tooLargeStatus, regionTooLarge, regionTooLargeReason, zoomCanReleaseGate, gateSkipsMeasuredViewport

From TrackHeightMixin: configuredHeight, allottedHeight, height, resizing, scrollContentHeight, scrollViewportHeight, scrollableHeight

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

Methods

Member	Description
rpcProps `() => LDRpcProps`
columnX `(column: number) => number`	Viewport x of a fractional column index: `i + 0.5` is column i's apex. Uses the payload's own column width, so it follows the live transform through a zoom's refetch.
locusViewportX `(refName: string, coord: number) => number \| undefined`	Viewport x of a locus, or undefined when it has none.
viewRefName `(refName: string) => string`	A file's refName as the view names it: PLINK writes `1` where the assembly says `chr1`.
hitTest `(mouseX: number, mouseY: number) => LDCellHit \| undefined`	The computed cell under a display-px point: a pair outside the band, or one no estimator filled, is not drawn and not hit.
configProblemsOf `(conf: AnyConfigurationModel) => string[]`	The schema's rules, then names asked for with no band to draw in.
trackMenuItems `() => MenuItem[]`
renderSvg `(opts: ExportSvgDisplayOptions) => Promise<ReactNode>`

13 inherited methods from 6 models

From TriangleMatrixMixin: cellToScreen, screenToCell

From ParkedColorMixin: parkedColorOf

From MatrixRampMixin: rampColorScales

From LegendMixin: colorScalesIn, legendSpecIn

From RegionTooLargeMixin: resolvedByteLimit, gateFetchState

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

Actions

Member	Description
setIndexSnp `(snp: LDSnp \| undefined) => void`
setConnectorsHeight `(n: number) => void`
setShowNames `(show: boolean) => void`
setVariantLayout `(value: "columns" \| "genomic") => void`
startRenderingBackend `(backend: LDRenderingBackend) => void`