LinearHicDisplay

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

Example usage

A HicTrack whose display pins the color scale's top, so two tracks set alike share one scale, and runs one binsize coarser than the zoom picks:

{
  type: 'HicTrack',
  trackId: 'hic',
  name: 'Hi-C',
  assemblyNames: ['hg38'],
  adapter: { type: 'HicAdapter', uri: 'https://example.com/contacts.hic' },
  displays: [
    {
      type: 'LinearHicDisplay',
      displayId: 'hic-LinearHicDisplay',
      color: { scale: 'log', domainMax: 500 },
      resolutionBias: 1,
    },
  ],
}

The Hi-C contact matrix 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 `type: types.literal('LinearHicDisplay')`
configuration `configuration: ConfigurationReference(configSchema)`

1 inherited property from one model

From BaseDisplay: id

Volatiles

Member	Description
fileInfo `AdapterRead<HicFileInfo> \| undefined`	The file's normalizations and binsizes, stamped with the adapter config they answer.

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
availableNormalizations `string[] \| undefined`
availableResolutions `number[] \| undefined`	Smallest first, so a negative `resolutionBias` is always finer.
resolutionBias `number`
colorEncoding `HicColorEncoding`	The `color` object as it paints, through the shared reader and `count`'s preset: a linear or log ramp whose `reverse`, where unset, follows whether the scheme runs dark at its low end. The `scheme` and `domainQuantile` slots have defaults, so both are always set.
notices `string[]`	What the `color` object says that cannot paint as written, as the corner indicator lists it: the same lines `plotProblems` and `jbrowse validate` report.
colorScaleType `"linear" \| "log"`
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.
colorRamp `Uint8Array<ArrayBufferLike>`	The ramp's 256 entries: the GPU's texture, the Canvas2D fill and the legend read this one table. It reads `colorScheme` and `colorReverse` rather than the encoding, so a domain edit re-uploads no texture.
colorQuantile `number`	`color.domainQuantile`: the quantile of the loaded counts an unset `domainMax` follows, their maximum at 1.
colorFollowsPercentile `boolean`	Whether an unset `color.domainMax` saturates at `colorQuantile` rather than the counts' maximum.
saturationQuantile `number`	The quantile "Emphasize faint contacts" saturates at: `colorQuantile` while it clips, else the one ticking it writes. The worker computes this one whichever is drawn, so the toggle refetches nothing.
showResolutionControls `boolean`
selectedNormalization `string`
hasResolutions `boolean`	Whether the binsize list has arrived; every resolution control gates on it.
activeNormalization `string`	The normalization to request: the selection where the file has it, else the next best it does. A getter, so a file lacking the selection never marks the track edited.
colorDomain `[number, number]`	The domain the counts are colored over, as every ramp spans one: a pinned end holds, and an open one follows the loaded counts from 0, the top at their `colorQuantile` below 1, else their maximum.
awaitingPrerequisite `boolean`	Retry is two-stage: the contact fetch declines until the header it needs lands, and the header's arrival wakes it. `infoFetchFailure.test.ts` pins it.
showResolutionBox `boolean`	Whether the resolution box is up; the chrome starts the key below it.
legendTop `number`
appliedNormalization `string`	The normalization the loaded matrix carries, which falls back per binsize (KR at 5 kb, nothing at 2.5 Mb is typical). The menu ticks this. Fetch-derived, so it stays out of `rpcProps()`.
scaleType `ScaleTypeCode`
autoResolutionIdx `number`	The binsize index auto mode picks: the largest at most 2 bp/px, about half a bin per pixel, else the finest.
colorScales `ColorScale[]`	The count ramp, once there is a domain to span. The ends are where the ramp paints them, and a top below the largest loaded count reads `≥`.
effectiveResolutionIdx `number`	The index in effect after `resolutionBias`, clamped so a bias set at another zoom cannot index out of range.
valueLabel `string`	What the tooltip calls a bin's value.
effectiveResolution `number \| undefined`
canStepResolutionFiner `boolean`
canStepResolutionCoarser `boolean`
renderState `HicRenderState`
viewSignature `string \| undefined`	The static blocks plus the binsize, so a pan inside them redraws and only a block entering or a binsize step refetches. Undefined until the header lands.

73 inherited getters from 9 models

From BaseDisplay: parentTrack, RenderingComponent, DisplayBlurb, adapterConfig, isMinimized, hoveredFeature, featureNoun, featureWidgetType, plotKeys, plot, 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, awaitingDependentData, settingsFetchInputs

From LegendMixin: showLegend, legendRight, legendSpec, hasLegendKey

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

Methods

Member	Description
rpcProps `() => { normalization: string; quantile: number; }`	The settings that refetch. The binsize is zoom-derived, so it travels as its own argument.
hitTest `(mouseX: number, mouseY: number) => HicContactItem \| undefined`	The contact under a display-px point, through the inverse of the transform the matrix was drawn with.
trackMenuItems `() => 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

From TriangleMatrixMixin: cellToScreen, screenToCell

Actions

Member	Description
startRenderingBackend `(backend: HicRenderingBackend) => void`
setLogScale `(log: boolean) => void`	The Log scale toggle: `color.scale` log, or unset for `count`'s linear preset.
setColorFollowsPercentile `(f: boolean) => void`
setShowResolutionControls `(f: boolean) => 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.
setActiveNormalization `(f: string) => void`
setFileInfo `(read: AdapterRead<HicFileInfo>) => void`
resetResolutionBias `() => void`
setResolutionIdx `(idx: number) => void`	Lock to `availableResolutions[idx]`, clamped, stored as an offset from the auto pick so the choice keeps its meaning across zoom.
setResolution `(binSize: number) => void`	Lock to a binsize the file offers; any other is ignored.
stepResolution `(delta: number) => void`