LinearManhattanDisplay

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

The mark display with the LD join: an index SNP each fetch joins r² to, which follows the top hit until the user pins one, and the menus that color the points by it.

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('LinearManhattanDisplay')`
configuration `configuration: ConfigurationReference(configSchema)`
indexSnp `indexSnp: types.maybe(types.string)`	The index SNP the LD join reads r² to, as a 1-based `chr:bp`. It follows the highest-scoring loaded SNP until the user pins one.
indexSnpPinned `indexSnpPinned: types.stripDefault(types.boolean, false)`	True once the user pins an index SNP by right-clicking a point.

4 inherited properties from 2 models

From BaseDisplay: id

From TreeSidebarMixin: runClustering, clusterRegion, sortRowsBy

Volatiles

37 inherited volatiles from 12 models

From LinearMarkDisplay: sourceListing, plotFields, plotFieldsError, plotDefaultChecked, plotFieldsPromise, plotScanned, detailsRotation, plotScanRotation

From ScoreScaleMixin: unclippedQuantile

From LegendMixin: dismissedLegendSections

From ContextMenuMixin: contextMenuInfo

From StoredHoverMixin: storedHoveredFeature

From BaseDisplay: error, statusMessage, statusProgress

From TrackHeightMixin: scrollTop, hostHeight

From MultiRegionDisplayMixin: loadedRegions

From RegionTooLargeMixin: forceLoadTrack, byteEstimate, gateMeasuredViewportKey

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

From FetchMixin: activeSignal, fetchGeneration, reloadCounter, statusWindow, fetchCanceled, fetchRotation

From TreeSidebarMixin: hoveredTreeNode, treeCanvas, mouseoverCanvas

Getters

Member	Description
gateEnabled `boolean`	No byte gate: a Manhattan plot's case is a genome-wide view of summary statistics, which a region budget would refuse.
ldAdapterConfig `Record<string, unknown> \| undefined`	The `ldAdapter` on the track's `GWASAdapter`, or undefined for none. Read off the live track, since `self.adapterConfig` is a snapshot, which leaves out a slot at its default.
hasLdData `boolean`
joinsLd `boolean`	Whether a fetch joins r² to the index: the plot names `r2` or `ld_role` anywhere the worker reads, an expression or a filter included, and the adapter has an LD file to read them from. Without one, a plot reads `r2` off the features like any other field.
ldColored `boolean`	Whether "Color by LD to index SNP" is on: a mark's encoding names an LD field, which is what the item writes and takes off.
joinedPlotFields `{ numeric: string[]; categorical: string[]; }`	The two fields the LD join writes, for Edit plot to offer.
sharedSteps UnionNode<{ filter: ConfigurationSchemaType<…>; formula: ConfigurationSchemaType<…>; bin: ConfigurationSchemaType<…>; aggregate: ConfigurationSchemaType<…>; coverage: ConfigurationSchemaType<…>; flatten: ConfigurationSchemaType<…>; cells: ConfigurationSchemaType<…>; pileup: ConfigurationSchemaType<…>; mate: ConfigurationSchemaType<{ type: { type: "string"; } & { defaultValue: string; }; }, ConfigurationSchemaOptions<undefined, undefined, true, ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>; }>[]	The steps every mark runs before its own: the display's, then the facet's.
ldColorable `boolean`	Whether "Color by LD to index SNP" has a point mark to color.
topSnp `string \| undefined`	The highest-scoring loaded SNP as a 1-based `chr:bp`, the index the join follows while none is pinned. `GWASAdapter` reports each region's top hit off the file, so no filter, zoom gate or mark of the plot moves it. A tie goes to the lowest region index, then the lowest position, never to arrival order: adopting the index refetches, so a tie broken by arrival would flip between the tied SNPs and never paint (`ldAutoIndex.test.ts`).
adapterOptions `{ ld: string; } \| undefined`	The index the fetch joins r² to, a fetch input, so adopting or pinning one refetches. None before the first load names a top hit.
dataSuperseded `boolean`	The loaded data was joined under an index other than the top hit, so adopting it will clear the data and refetch: `MultiRegionDisplayMixin`'s supersession hook, and the auto-pick's trigger.

223 inherited getters from 14 models

From LinearMarkDisplay: conf, prefersOffset, markTypes, facet, groupKeySpace, markEntries, textMarkEntries, markView, markSizes, markRowProportions, rowProportion, hasLinkMark, pointSize, encodings, markStepLists, markChannels, markColors, facetSteps, layerRequests, origin, minWidthPx, configuredFilters, baseFilters, rowsField, drawsRows, splitField, rowColorFields, featurePayloads, rowListing, adapterSources, guideTreeNewick, discoveredRows, rowKeys, facetLayout, rpcDataMap, rowTable, drawnKeys, scaleDataMap, markList, hasPointMark, drawingMarkIndices, autoscaleRange, domain, sidebarPanel, valueInsetPx, valueScales, rowCount, nrow, autoRowHeight, rowsHeaderHeight, plotBox, paintScales, sizeScales, linkRegions, renderState, highlightedHit, highlightStyle, hoverInk, configProblems, dataNotices, sharedKeys, cornerNotices, notices, skippedFeatures, legendSections, colorScales, effectiveRowHeight, scrollContentHeight, scrollViewportHeight, valueMarkIndex, svgSidebar, plotScanLocus

From ScoreScaleMixin: scaleType, scaleZero, domainQuantile, clipQuantile, symlogConstant, manualMinScore, manualMaxScore, valueScaleNotices, autoscaleGroup, scaleTitle, grid, minimalTicks, scoreRulesDrawn, scoreRules

From ScoreAxisMixin: defaultScoreDomain, axisReachesZero, autoscaledDomain, minScoreBound, maxScoreBound, hasManualScoreBounds, axes

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

From StoredHoverMixin: hoveredFeature

From HiddenGroupsMixin: displayHiddenGroupKeys, ownGroupState, hiddenGroups, hiddenGroupKeys, groupStateKey

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

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

From MultiRegionDisplayMixin: host, canvasWidthPx, settledSubPixelBinBp, canRender, rendersCanvas, trackVisibleRegions, viewportWithinLoadedData, viewportEmpty, fetchSuspended, layoutReady, renderBlocks, fetchInputs, regionPayloads, hasRegionData, staleSettingsDrawn, dataCurrent, loadedAssembly, phaseViewportCurrent, svgReady, paintInert, paintSuperseded, displayPhase

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

From RenderLifecycleMixin: painted

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

From TreeSidebarMixin: showTree, showBranchLength, showRowLabels, treeAreaWidth, rowDomain, rowLabels, rowTreeProvenance, rowFocus, rowColorSetting, baseRowColor, baseRowDomain, rowAlias, unlistedRowsSort, rowBanding, rowFocusLineHeight, rowsTopOffset, guideTree, guideTreeHonoursDomain, rowTree, rowOrder, expandedRows, sharesPanel, rowColorPaintsMarks, rowNoun, internalRowFields, rowBandingNotices, rowPaletteDeals, rowColorDealRows, rowStylingIsCustom, rowColorChoice, rowColorAttribute, dealtRowColors, rowColorAttributesOffered, resolvedRowColors, rowArrangementIsCustom, editableSources, rowColorKeyInputs, rowColorScales, clusterableSources, parsedTree, root, bandedRows, bandedSources, rowBands, sources, treeRoot, drawsTree, rowsContentHeight, hierarchy, spatialIndex, clusterPartition, treelessBandCount, treeHasBranchLengths

From RowHeightMixin: rowHeight

Methods

Member	Description
resolveAdapterOptions `({ ld }: { ld: string; }, region: Region, signal: AbortSignal) => Promise<{ ld: LdJoin; } \| undefined>`	The LD join as one region's fetch asks the adapter for it.
trackMenuItems `() => MenuItem[]`
contextMenuItems `() => MenuItem[]`

21 inherited methods from 6 models

From LinearMarkDisplay: plotRequest, rpcProps, floatingLabels, plotProblems, liftMarkPlot

From LegendMixin: svgLegendWidth, colorScalesIn, legendSpecIn

From BaseDisplay: renderingProps, liftPlot, plotWrites

From MultiRegionDisplayMixin: regionHasData, isCacheValid

From RegionTooLargeMixin: resolvedByteLimit, gateFetchState

From TreeSidebarMixin: expandRows, svgSidebarWidth, rowBand, dealtRowColorsFor, rowColorFor, rowOrderWillDropTree

Actions

Member	Description
setIndexSnp `(snp?: string \| undefined) => void`
setLdColoring `(on: boolean) => void`	Color each point by its r² to the index SNP, the index a pink diamond over them, or take that coloring off, leaving every other member and mark of the plot as it was (`withLd`, `withoutLd`).
colorByLdToHit `(hit: { refName: string; start: number; }) => void`	Right-click "Color by LD to this SNP": color by r² to the clicked point and pin it as the index, in one action so the fetch inputs settle once.
useTopHitAsIndex `() => void`	Release a pinned index back to following the top hit.