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, picked once from the top hit, 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`. The display picks the top hit on screen once, when a plot first joins LD or LD coloring is turned on; after that only the user moves it.

4 inherited properties from 2 models

From TreeSidebarMixin: runClustering, clusterRegion, sortRowsBy

From BaseDisplay: id

Volatiles

37 inherited volatiles from 11 models

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

From StoredHoverMixin: storedHoveredFeature

From ContextMenuMixin: contextMenuInfo

From LegendMixin: dismissedLegendSections

From ScoreScaleMixin: unclippedFenceQuantile

From TreeSidebarMixin: hoveredTreeNode, treeCanvas, mouseoverCanvas

From MultiRegionDisplayMixin: loadedRegions

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
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.
ldColorable `boolean`	Whether "Color by LD to index SNP" has a point mark to color.
topSnp `string \| undefined`	The highest-scoring SNP on screen, as a 1-based `chr:bp`. `GWASAdapter` reports each region's top hits off the file, so no filter, zoom gate or mark of the plot moves it. A fetch reaches past the screen and a region scrolled off screen stays loaded, so only a hit inside a visible block counts. A tie goes to the lowest region index, then the lowest position, never to arrival order, so one load picks the same SNP however its regions land (`ldAutoIndex.test.ts`).
settledTopSnp `string \| undefined`	`topSnp` once the load covering the screen is complete, or undefined: mid-batch, `topSnp` is the best of what has arrived.
adapterOptions `{ ld: string; } \| undefined`	The index the fetch joins r² to, a fetch input, so picking one refetches. No index exists until the first load provides a top hit.
indexPending `boolean`	The plot joins LD and no index is picked yet, though the loaded data names a top hit: the one-time pick is due, and its refetch with it.
dataSuperseded `boolean`	`MultiRegionDisplayMixin`'s supersession hook, true while the mark display's row listing is unsettled or the index pick is due.
displayNotices `string[]`	The notices the display shows. Where the plot joins LD, it shows one when no point on screen lies in the LD window of the index, so none can be colored by it.

228 inherited getters from 15 models

From LinearMarkDisplay: conf, prefersOffset, markTypes, facet, groupKeySpace, markEntries, textMarkEntries, markView, markSizes, markRowProportions, rowProportion, hasLinkMark, pointSize, encodings, sharedSteps, markStepLists, markChannels, markColors, facetSteps, layerRequests, origin, minWidthPx, configuredFilters, filterSteps, baseFilters, rowsField, drawsRows, splitField, rowColorFields, featurePayloads, rowListing, rowListingSettled, adapterSources, guideTreeNewick, discoveredRows, rowKeySpace, 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, liveNotices, skippedFeatures, legendSections, colorScales, effectiveRowHeight, scrollContentHeight, scrollViewportHeight, valueMarkIndex, autoClusterReady, svgSidebar, plotScanLocus

From FacetWritesMixin: writtenFacet

From HiddenGroupsMixin: ownGroupState, hiddenGroups, hiddenGroupKeys, groupStateKey

From StoredHoverMixin: hoveredFeature

From LegendMixin: showLegend, legendRight, legendSpec, hasLegendKey

From ScoreScaleMixin: scaleType, scaleZero, fenceQuantile, clipFenceQuantile, symlogConstant, manualMinScore, manualMaxScore, autoscaleGroup, scaleTitle, grid, scoreRulesDrawn, scoreRules

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

From RowHeightMixin: rowHeight

From TreeSidebarMixin: showTree, showBranchLength, showRowLabels, treeAreaWidth, rowSort, rowLabels, rowTreeProvenance, rowFocus, rowColorSetting, baseRowColorSetting, baseRowSort, rowAlias, unlistedRowsSort, rowBanding, rowFocusLineHeight, rowsTopOffset, guideTree, guideTreeHonoursDomain, rowTree, rowOrder, expandedRows, sharesPanel, rowColorPaintsMarks, rowNoun, internalRowFields, rowBandingNotices, rowPaletteDeals, rowColorDealRows, rowColorIsCustom, rowColorChoice, rowColorField, dealtValueColors, rowColorFieldsOffered, resolvedRowColors, rowArrangementIsCustom, editableSources, rowColorKeyInputs, rowColorScales, clusterableSources, parsedTree, rotatableRowTree, root, bandedRows, bandedSources, rowBands, sources, treeRoot, drawsTree, awaitingDependentData, rowsContentHeight, hierarchy, spatialIndex, clusterPartition, treelessBandCount, treeHasBranchLengths

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 FetchMixin: isLoading, isLoadingOrCanceled, fetchInert, awaitingPrerequisite, settingsFetchInputs

From RenderLifecycleMixin: 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, scrollableHeight

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

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[]`

23 inherited methods from 6 models

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

From LegendMixin: colorScalesIn, legendSpecIn

From TreeSidebarMixin: expandRows, svgSidebarWidth, rowBand, rowColorDeclaredValues, dealtValueColorsFor, rowColorFor, orderDropsRowTree, rowOrderWillDropTree

From MultiRegionDisplayMixin: regionHasData, isCacheValid

From RegionTooLargeMixin: resolvedByteLimit, gateFetchState

From BaseDisplay: renderingProps, liftPlot, plotProblems, plotWrites

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`). Turning it on picks the top hit on screen as the index, or leaves the pick for the load in flight to make.
colorByLdToHit `(hit: { refName: string; start: number; }) => void`	Right-click "Color by LD to this SNP": color by r² to the clicked point as the index, in one action so the fetch inputs settle once.
setIndexSnpToTopHit `() => void`	Make the top hit on screen the index.