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 |
|---|---|
typetype: types.literal('LDTrackDisplay') | |
configurationconfiguration: ConfigurationReference(configSchema) |
1 inherited property from one model
From BaseDisplay: id
Volatiles
| Member | Description |
|---|---|
focalSnpLocusstring | 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 8 models
From BaseDisplay: error, statusMessage, statusProgress
From TrackHeightMixin: scrollTop, hostHeight
From RegionTooLargeMixin: forceLoadTrack, byteEstimate, gateMeasuredViewportKey
From RenderLifecycleMixin: canvasDrawn, paintCount, currentRenderingBackend, renderTick, autorunsInstalled, renderError, offScreen
From KeyedFetchMixin: loadedFetchKey
From FetchMixin: activeSignal, fetchGeneration, reloadCounter, statusWindow, fetchCanceled, fetchRotation
From LegendMixin: dismissedLegendSections
From TriangleMatrixMixin: rpcData
Getters
| Member | Description |
|---|---|
| view | |
prefersOffsetboolean | |
lineZoneHeightnumber | |
colorFieldLDMetric | color.field, the statistic the fetch asks the file for. |
maxVariantSeparationnumber | |
showVerticalGuidesboolean | |
showLabelsboolean | |
tickHeightnumber | |
variantLayout"columns" | "genomic" | |
snpsLDSnp[] | The loaded SNPs in screen order along the column axis. |
cellWidthnumber | The column width the payload was laid out at. |
viewSignaturestring | undefined | The dynamic blocks: the SNP set is the viewport's, so a pan refetches while the stale triangle draws under the live transform. |
effectiveLdMetricLDMetric | The metric the loaded values are: a file with one column serves it whichever is asked for. |
effectiveUseGenomicPositionsboolean | Whether the loaded matrix is at genomic positions: a multi-region view falls back to uniform columns. |
r2Availableboolean | |
dprimeAvailableboolean | |
loadedLDWindownumber | undefined | The pair window the loaded matrix was computed at, or undefined for the whole triangle. The status bar names it, since a pair past it is not drawn and reads as no linkage. |
focalSnpIndexnumber | Index of the focal SNP in snps, or -1. |
| colorEncoding | The color object under the preset of the loaded metric, so a stale triangle during a metric switch keeps its hue. Both presets name a scheme, so the encoding always carries one. |
noticesstring[] | What the corner notice lists. |
| colorScheme | |
colorReverseboolean | color.reverse, or where unset whether the scheme runs dark at its low end. |
colorDomain[number, number] | The domain the statistic is colored over: each pinned end holds, and an open one is the statistic's own 0 or 1. |
colorRampUint8Array<ArrayBufferLike> | The ramp's 256 entries, read by the GPU texture, the Canvas2D fill and the legend. Reads colorScheme and colorReverse rather than the encoding, so a domain edit re-uploads no texture. |
colorScalesColorScale[] | The ramp the cells paint through, titled by the loaded metric. An end pinned inside the statistic's 0 to 1 reads ≤ or ≥. |
renderStateLDRenderState | |
matrixTopnumber | The band above the matrix: the connector lines in columns, the labels at genomic positions when they are on, else nothing. |
connectorLineCoordsConnectorCoord[] | Each column tied to its SNP's genomic x, for the connector lines. |
75 inherited getters from 9 models
From BaseDisplay: parentTrack, RenderingComponent, DisplayBlurb, adapterConfig, isMinimized, hoveredFeature, featureNoun, featureWidgetType, plotKeys, plot, schemaNotices, plotExamples, configDocsUrl
From TrackHeightMixin: configuredHeight, allottedHeight, height, resizing, scrollContentHeight, scrollViewportHeight, scrollableHeight
From GlobalFetchMixin: host, staticBlockSignature, dynamicBlockSignature, viewportEmpty, canRender, rendersCanvas, paintInert, svgReady, displayPhase
From RegionTooLargeMixin: gateEnabled, byteGateAdapterConfig, configuredFetchSizeLimit, densityTooLarge, byteGateAdapterPath, adapterFetchSizeLimit, configForceLoad, gateViewportSpanBp, gateViewport, aboveForceLoadFloor, gateExempt, estimatedFetchBytes, gateMeasurementStale, gateByteLimit, gateActive, densityGateActive, tooLargeStatus, regionTooLarge, regionTooLargeReason, zoomCanReleaseGate, gateSkipsMeasuredViewport
From RenderLifecycleMixin: paintSuperseded, painted
From KeyedFetchMixin: dataSuperseded, currentFetchKey, dataCurrent
From FetchMixin: isLoading, isLoadingOrCanceled, fetchInert, awaitingPrerequisite, awaitingDependentData, settingsFetchInputs
From LegendMixin: showLegend, legendTop, legendRight, legendSpec, hasLegendKey
From TriangleMatrixMixin: squashToHeight, canvasWidth, viewTransform, matrixRegions, matrixHeight, matrixBlocks, yScalar, triangleTransform, triangleFrame
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. |
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. |
() => MenuItem[] | |
renderSvg(opts: ExportSvgDisplayOptions) => Promise<ReactNode> |
11 inherited methods from 4 models
From BaseDisplay: renderingProps, liftPlot, plotProblems, plotWrites
From RegionTooLargeMixin: resolvedByteLimit, gateFetchState
From LegendMixin: svgLegendWidth, colorScalesIn, legendSpecIn
Actions
| Member | Description |
|---|---|
setFocalSnp(snp: LDSnp | undefined) => void | |
setLineZoneHeight(n: number) => void | |
setLDMetric(metric: LDMetric) => void | color.field, the statistic the cells are, which refetches. |
setShowVerticalGuides(show: boolean) => void | |
setShowLabels(show: boolean) => void | |
setVariantLayout(value: "columns" | "genomic") => void | |
| setColorScheme | The scheme, with reverse back to unset so it follows the scheme. The painted metric's own preset writes scheme unset, so it keeps following the metric. |
startRenderingBackend(backend: LDRenderingBackend) => void |
36 inherited actions from 8 models
From BaseDisplay: setStatusMessage, setError, clearHoveredFeature, reload, applyDisplaySettings, applyPlot
From TrackHeightMixin: setScrollTop, setHostHeight, setHeight, resizeHeight, expandToContentHeight
From RegionTooLargeMixin: clearByteEstimate, clearGateMeasurements, setForceLoadTrack, commitFetchBytes, forceLoad
From RenderLifecycleMixin: markCanvasDrawn, resetCanvasDrawn, stopRenderingBackend, renderNow, setOffScreen, setRenderError, attachRenderingBackend
From KeyedFetchMixin: commitFetchResult
From FetchMixin: stopActiveFetch, openStatusStream, cancelFetch, cancelFetchByUser, beforeDestroy, beginFetch, endFetch, runFetch