# LDTrackDisplay
Auto-generated from the @jbrowse/mobx-state-tree model in the source — see the [developer guide](https://jbrowse.org/jb2/docs/developer_guide/) for concepts. Provided by the `variants` plugin. [View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/variants/src/LDDisplay/model.ts).
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](../../config/ldtrackdisplay).
Each section ends with the members a composed model contributes, linked to the page that documents them.
## Properties
| Member | Description |
| --- | --- |
| **type**
type: types.literal('LDTrackDisplay') | |
| **configuration**
configuration: ConfigurationReference(configSchema) | |
1 inherited property from one model:
From [BaseDisplay](../basedisplay): [`id`](../basedisplay#property-id)
## Volatiles
| Member | Description |
| --- | --- |
| **focalSnpLocus**
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 8 models:
From [BaseDisplay](../basedisplay): [`error`](../basedisplay#volatile-error), [`statusMessage`](../basedisplay#volatile-statusmessage), [`statusProgress`](../basedisplay#volatile-statusprogress)
From [TrackHeightMixin](../trackheightmixin): [`scrollTop`](../trackheightmixin#volatile-scrolltop), [`hostHeight`](../trackheightmixin#volatile-hostheight)
From [RegionTooLargeMixin](../regiontoolargemixin): [`forceLoadTrack`](../regiontoolargemixin#volatile-forceloadtrack), [`byteEstimate`](../regiontoolargemixin#volatile-byteestimate), [`gateMeasuredViewportKey`](../regiontoolargemixin#volatile-gatemeasuredviewportkey)
From [RenderLifecycleMixin](../renderlifecyclemixin): [`canvasDrawn`](../renderlifecyclemixin#volatile-canvasdrawn), [`paintCount`](../renderlifecyclemixin#volatile-paintcount), [`currentRenderingBackend`](../renderlifecyclemixin#volatile-currentrenderingbackend), [`renderTick`](../renderlifecyclemixin#volatile-rendertick), [`autorunsInstalled`](../renderlifecyclemixin#volatile-autorunsinstalled), [`renderError`](../renderlifecyclemixin#volatile-rendererror), [`offScreen`](../renderlifecyclemixin#volatile-offscreen)
From [KeyedFetchMixin](../keyedfetchmixin): [`loadedFetchKey`](../keyedfetchmixin#volatile-loadedfetchkey)
From [FetchMixin](../fetchmixin): [`activeSignal`](../fetchmixin#volatile-activesignal), [`fetchGeneration`](../fetchmixin#volatile-fetchgeneration), [`reloadCounter`](../fetchmixin#volatile-reloadcounter), [`statusWindow`](../fetchmixin#volatile-statuswindow), [`fetchCanceled`](../fetchmixin#volatile-fetchcanceled), [`fetchRotation`](../fetchmixin#volatile-fetchrotation)
From [LegendMixin](../legendmixin): [`dismissedLegendSections`](../legendmixin#volatile-dismissedlegendsections)
From [TriangleMatrixMixin](../trianglematrixmixin): [`rpcData`](../trianglematrixmixin#volatile-rpcdata)
## Getters
| Member | Description |
| --- | --- |
| **view**
ModelInstanceTypeProps<…> & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & { rubberbandClickMenuItems(clickOffset: BpOffset): MenuItem[]; highlightMenuItems(_highlight: HighlightType): MenuItem[]; } & { flyTo: (centerBp: number, windowWidthBp: number) => void; flyToCenter(coord: number, refName: string, displayedRegionIndex?: number | undefined): void; flyToFit(centerBp: number, fitWidthBp: number): void; } & { afterCreate(): void; afterAttach(): void; } & IStateTreeNode<…> | |
| **prefersOffset**
boolean | |
| **lineZoneHeight**
number | |
| **colorField**
LDMetric | `color.field`, the statistic the fetch asks the file for. |
| **maxVariantSeparation**
number | |
| **showVerticalGuides**
boolean | |
| **showLabels**
boolean | |
| **tickHeight**
number | |
| **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. |
| **effectiveLdMetric**
LDMetric | The metric the loaded values are: a file with one column serves it whichever is asked for. |
| **effectiveUseGenomicPositions**
boolean | Whether the loaded matrix is at genomic positions: a multi-region view falls back to uniform columns. |
| **r2Available**
boolean | |
| **dprimeAvailable**
boolean | |
| **loadedLDWindow**
number | 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. |
| **focalSnpIndex**
number | Index of the focal SNP in `snps`, or -1. |
| **colorEncoding**
ContinuousRef & { scheme: "blues" | "blueyellowred" | "cividis" | "fall" | "inferno" | "juicebox" | "magma" | "purpleorange" | "redblue" | "redgreyblue" | "reds" | "viridis"; } | 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. |
| **notices**
string[] | What the corner notice lists. |
| **colorScheme**
"blues" | "blueyellowred" | "cividis" | "fall" | "inferno" | "juicebox" | "magma" | "purpleorange" | "redblue" | "redgreyblue" | "reds" | "viridis" | |
| **colorReverse**
boolean | `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. |
| **colorRamp**
Uint8Array<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. |
| **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 | |
| **matrixTop**
number | The band above the matrix: the connector lines in columns, the labels at genomic positions when they are on, else nothing. |
| **connectorLineCoords**
ConnectorCoord[] | Each column tied to its SNP's genomic x, for the connector lines. |
75 inherited getters from 9 models:
From [BaseDisplay](../basedisplay): [`parentTrack`](../basedisplay#getter-parenttrack), [`RenderingComponent`](../basedisplay#getter-renderingcomponent), [`DisplayBlurb`](../basedisplay#getter-displayblurb), [`adapterConfig`](../basedisplay#getter-adapterconfig), [`isMinimized`](../basedisplay#getter-isminimized), [`hoveredFeature`](../basedisplay#getter-hoveredfeature), [`featureNoun`](../basedisplay#getter-featurenoun), [`featureWidgetType`](../basedisplay#getter-featurewidgettype), [`plotKeys`](../basedisplay#getter-plotkeys), [`plot`](../basedisplay#getter-plot), [`schemaNotices`](../basedisplay#getter-schemanotices), [`plotExamples`](../basedisplay#getter-plotexamples), [`configDocsUrl`](../basedisplay#getter-configdocsurl)
From [TrackHeightMixin](../trackheightmixin): [`configuredHeight`](../trackheightmixin#getter-configuredheight), [`allottedHeight`](../trackheightmixin#getter-allottedheight), [`height`](../trackheightmixin#getter-height), [`resizing`](../trackheightmixin#getter-resizing), [`scrollContentHeight`](../trackheightmixin#getter-scrollcontentheight), [`scrollViewportHeight`](../trackheightmixin#getter-scrollviewportheight), [`scrollableHeight`](../trackheightmixin#getter-scrollableheight)
From [GlobalFetchMixin](../globalfetchmixin): [`host`](../globalfetchmixin#getter-host), [`staticBlockSignature`](../globalfetchmixin#getter-staticblocksignature), [`dynamicBlockSignature`](../globalfetchmixin#getter-dynamicblocksignature), [`viewportEmpty`](../globalfetchmixin#getter-viewportempty), [`canRender`](../globalfetchmixin#getter-canrender), [`rendersCanvas`](../globalfetchmixin#getter-renderscanvas), [`paintInert`](../globalfetchmixin#getter-paintinert), [`svgReady`](../globalfetchmixin#getter-svgready), [`displayPhase`](../globalfetchmixin#getter-displayphase)
From [RegionTooLargeMixin](../regiontoolargemixin): [`gateEnabled`](../regiontoolargemixin#getter-gateenabled), [`byteGateAdapterConfig`](../regiontoolargemixin#getter-bytegateadapterconfig), [`configuredFetchSizeLimit`](../regiontoolargemixin#getter-configuredfetchsizelimit), [`densityTooLarge`](../regiontoolargemixin#getter-densitytoolarge), [`byteGateAdapterPath`](../regiontoolargemixin#getter-bytegateadapterpath), [`adapterFetchSizeLimit`](../regiontoolargemixin#getter-adapterfetchsizelimit), [`configForceLoad`](../regiontoolargemixin#getter-configforceload), [`gateViewportSpanBp`](../regiontoolargemixin#getter-gateviewportspanbp), [`gateViewport`](../regiontoolargemixin#getter-gateviewport), [`aboveForceLoadFloor`](../regiontoolargemixin#getter-aboveforceloadfloor), [`gateExempt`](../regiontoolargemixin#getter-gateexempt), [`estimatedFetchBytes`](../regiontoolargemixin#getter-estimatedfetchbytes), [`gateMeasurementStale`](../regiontoolargemixin#getter-gatemeasurementstale), [`gateByteLimit`](../regiontoolargemixin#getter-gatebytelimit), [`gateActive`](../regiontoolargemixin#getter-gateactive), [`densityGateActive`](../regiontoolargemixin#getter-densitygateactive), [`tooLargeStatus`](../regiontoolargemixin#getter-toolargestatus), [`regionTooLarge`](../regiontoolargemixin#getter-regiontoolarge), [`regionTooLargeReason`](../regiontoolargemixin#getter-regiontoolargereason), [`zoomCanReleaseGate`](../regiontoolargemixin#getter-zoomcanreleasegate), [`gateSkipsMeasuredViewport`](../regiontoolargemixin#getter-gateskipsmeasuredviewport)
From [RenderLifecycleMixin](../renderlifecyclemixin): [`paintSuperseded`](../renderlifecyclemixin#getter-paintsuperseded), [`painted`](../renderlifecyclemixin#getter-painted)
From [KeyedFetchMixin](../keyedfetchmixin): [`dataSuperseded`](../keyedfetchmixin#getter-datasuperseded), [`currentFetchKey`](../keyedfetchmixin#getter-currentfetchkey), [`dataCurrent`](../keyedfetchmixin#getter-datacurrent)
From [FetchMixin](../fetchmixin): [`isLoading`](../fetchmixin#getter-isloading), [`isLoadingOrCanceled`](../fetchmixin#getter-isloadingorcanceled), [`fetchInert`](../fetchmixin#getter-fetchinert), [`awaitingPrerequisite`](../fetchmixin#getter-awaitingprerequisite), [`awaitingDependentData`](../fetchmixin#getter-awaitingdependentdata), [`settingsFetchInputs`](../fetchmixin#getter-settingsfetchinputs)
From [LegendMixin](../legendmixin): [`showLegend`](../legendmixin#getter-showlegend), [`legendTop`](../legendmixin#getter-legendtop), [`legendRight`](../legendmixin#getter-legendright), [`legendSpec`](../legendmixin#getter-legendspec), [`hasLegendKey`](../legendmixin#getter-haslegendkey)
From [TriangleMatrixMixin](../trianglematrixmixin): [`squashToHeight`](../trianglematrixmixin#getter-squashtoheight), [`canvasWidth`](../trianglematrixmixin#getter-canvaswidth), [`viewTransform`](../trianglematrixmixin#getter-viewtransform), [`matrixRegions`](../trianglematrixmixin#getter-matrixregions), [`matrixHeight`](../trianglematrixmixin#getter-matrixheight), [`matrixBlocks`](../trianglematrixmixin#getter-matrixblocks), [`yScalar`](../trianglematrixmixin#getter-yscalar), [`triangleTransform`](../trianglematrixmixin#getter-triangletransform), [`triangleFrame`](../trianglematrixmixin#getter-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. |
| **trackMenuItems**
() => MenuItem[] | |
| **renderSvg**
(opts: ExportSvgDisplayOptions) => Promise<ReactNode> | |
11 inherited methods from 4 models:
From [BaseDisplay](../basedisplay): [`renderingProps`](../basedisplay#method-renderingprops), [`liftPlot`](../basedisplay#method-liftplot), [`plotProblems`](../basedisplay#method-plotproblems), [`plotWrites`](../basedisplay#method-plotwrites)
From [RegionTooLargeMixin](../regiontoolargemixin): [`resolvedByteLimit`](../regiontoolargemixin#method-resolvedbytelimit), [`gateFetchState`](../regiontoolargemixin#method-gatefetchstate)
From [LegendMixin](../legendmixin): [`svgLegendWidth`](../legendmixin#method-svglegendwidth), [`colorScalesIn`](../legendmixin#method-colorscalesin), [`legendSpecIn`](../legendmixin#method-legendspecin)
From [TriangleMatrixMixin](../trianglematrixmixin): [`cellToScreen`](../trianglematrixmixin#method-celltoscreen), [`screenToCell`](../trianglematrixmixin#method-screentocell)
## 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**
(scheme: "blues" | "blueyellowred" | "cividis" | "fall" | "inferno" | "juicebox" | "magma" | "purpleorange" | "redblue" | "redgreyblue" | "reds" | "viridis") => void | 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](../basedisplay): [`setStatusMessage`](../basedisplay#action-setstatusmessage), [`setError`](../basedisplay#action-seterror), [`clearHoveredFeature`](../basedisplay#action-clearhoveredfeature), [`reload`](../basedisplay#action-reload), [`applyDisplaySettings`](../basedisplay#action-applydisplaysettings), [`applyPlot`](../basedisplay#action-applyplot)
From [TrackHeightMixin](../trackheightmixin): [`setScrollTop`](../trackheightmixin#action-setscrolltop), [`setHostHeight`](../trackheightmixin#action-sethostheight), [`setHeight`](../trackheightmixin#action-setheight), [`resizeHeight`](../trackheightmixin#action-resizeheight), [`expandToContentHeight`](../trackheightmixin#action-expandtocontentheight)
From [RegionTooLargeMixin](../regiontoolargemixin): [`clearByteEstimate`](../regiontoolargemixin#action-clearbyteestimate), [`clearGateMeasurements`](../regiontoolargemixin#action-cleargatemeasurements), [`setForceLoadTrack`](../regiontoolargemixin#action-setforceloadtrack), [`commitFetchBytes`](../regiontoolargemixin#action-commitfetchbytes), [`forceLoad`](../regiontoolargemixin#action-forceload)
From [RenderLifecycleMixin](../renderlifecyclemixin): [`markCanvasDrawn`](../renderlifecyclemixin#action-markcanvasdrawn), [`resetCanvasDrawn`](../renderlifecyclemixin#action-resetcanvasdrawn), [`stopRenderingBackend`](../renderlifecyclemixin#action-stoprenderingbackend), [`renderNow`](../renderlifecyclemixin#action-rendernow), [`setOffScreen`](../renderlifecyclemixin#action-setoffscreen), [`setRenderError`](../renderlifecyclemixin#action-setrendererror), [`attachRenderingBackend`](../renderlifecyclemixin#action-attachrenderingbackend)
From [KeyedFetchMixin](../keyedfetchmixin): [`commitFetchResult`](../keyedfetchmixin#action-commitfetchresult)
From [FetchMixin](../fetchmixin): [`stopActiveFetch`](../fetchmixin#action-stopactivefetch), [`openStatusStream`](../fetchmixin#action-openstatusstream), [`cancelFetch`](../fetchmixin#action-cancelfetch), [`cancelFetchByUser`](../fetchmixin#action-cancelfetchbyuser), [`beforeDestroy`](../fetchmixin#action-beforedestroy), [`beginFetch`](../fetchmixin#action-beginfetch), [`endFetch`](../fetchmixin#action-endfetch), [`runFetch`](../fetchmixin#action-runfetch)
From [LegendMixin](../legendmixin): [`setShowLegend`](../legendmixin#action-setshowlegend), [`dismissLegendSection`](../legendmixin#action-dismisslegendsection)
From [TriangleMatrixMixin](../trianglematrixmixin): [`setRpcData`](../trianglematrixmixin#action-setrpcdata), [`setSquashToHeight`](../trianglematrixmixin#action-setsquashtoheight)