SharedLDModel
Note: this document is automatically generated from @jbrowse/mobx-state-tree objects in our source code. See Core concepts and intro to pluggable elements for more info
Also note: this document represents the state model API for the current released version of jbrowse. If you are not using the current version, please cross reference the markdown files in our repo of the checked out git tag
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Shared state model for LD displays extends
SharedLDModel - Properties
property: configuration
// type signature
any
// code
configuration: ConfigurationReference(configSchema)
property: minorAlleleFrequencyFilterSetting
When undefined, falls back to config value
// type signature
IMaybe<ISimpleType<number>>
// code
minorAlleleFrequencyFilterSetting: types.maybe(types.number)
property: lengthCutoffFilterSetting
When undefined, falls back to config value
// type signature
IMaybe<ISimpleType<number>>
// code
lengthCutoffFilterSetting: types.maybe(types.number)
property: lineZoneHeightSetting
When undefined, falls back to config value Height of the zone for connecting lines at the top
// type signature
IMaybe<ISimpleType<number>>
// code
lineZoneHeightSetting: types.maybe(types.number)
property: ldMetricSetting
When undefined, falls back to config value LD metric to compute: 'r2' (squared correlation) or 'dprime' (normalized D)
// type signature
IMaybe<ISimpleType<string>>
// code
ldMetricSetting: types.maybe(types.string)
property: colorSchemeSetting
When undefined, falls back to config value
// type signature
IMaybe<ISimpleType<string>>
// code
colorSchemeSetting: types.maybe(types.string)
property: showLegendSetting
When undefined, falls back to config value
// type signature
IMaybe<ISimpleType<boolean>>
// code
showLegendSetting: types.maybe(types.boolean)
property: showLDTriangleSetting
When undefined, falls back to config value Whether to show the LD triangle heatmap
// type signature
IMaybe<ISimpleType<boolean>>
// code
showLDTriangleSetting: types.maybe(types.boolean)
property: showRecombinationSetting
When undefined, falls back to config value Whether to show the recombination rate track
// type signature
IMaybe<ISimpleType<boolean>>
// code
showRecombinationSetting: types.maybe(types.boolean)
property: recombinationZoneHeightSetting
When undefined, falls back to config value Height of the recombination track zone at the top
// type signature
IMaybe<ISimpleType<number>>
// code
recombinationZoneHeightSetting: types.maybe(types.number)
property: fitToHeightSetting
When undefined, falls back to config value When true, squash the LD triangle to fit the display height
// type signature
IMaybe<ISimpleType<boolean>>
// code
fitToHeightSetting: types.maybe(types.boolean)
property: hweFilterThresholdSetting
When undefined, falls back to config value HWE filter p-value threshold (variants with HWE p < this are excluded) Set to 0 to disable HWE filtering
// type signature
IMaybe<ISimpleType<number>>
// code
hweFilterThresholdSetting: types.maybe(types.number)
property: showVerticalGuidesSetting
When undefined, falls back to config value Whether to show vertical guides at the connected genome positions on hover
// type signature
IMaybe<ISimpleType<boolean>>
// code
showVerticalGuidesSetting: types.maybe(types.boolean)
property: showLabelsSetting
When undefined, falls back to config value Whether to show variant labels above the tick marks
// type signature
IMaybe<ISimpleType<boolean>>
// code
showLabelsSetting: types.maybe(types.boolean)
property: tickHeightSetting
When undefined, falls back to config value Height of the vertical tick marks at the genomic position
// type signature
IMaybe<ISimpleType<number>>
// code
tickHeightSetting: types.maybe(types.number)
property: useGenomicPositionsSetting
When undefined, falls back to config value When true, draw cells sized according to genomic distance between SNPs rather than uniform squares
// type signature
IMaybe<ISimpleType<boolean>>
// code
useGenomicPositionsSetting: types.maybe(types.boolean)
SharedLDModel - Getters
getter: blockType
// type
string
getter: prefersOffset
// type
boolean
getter: rendererTypeName
// type
string
getter: rendererConfig
// type
any
getter: regionTooLarge
// type
boolean
getter: minorAlleleFrequencyFilter
Returns the effective minor allele frequency filter, falling back to config
// type
any
getter: lengthCutoffFilter
Returns the effective length cutoff filter, falling back to config
// type
any
getter: lineZoneHeight
Returns the effective line zone height, falling back to config
// type
any
getter: ldMetric
Returns the effective LD metric, falling back to config
// type
any
getter: colorScheme
Returns the effective color scheme, falling back to config
// type
any
getter: showLegend
Returns the effective show legend setting, falling back to config
// type
any
getter: showLDTriangle
Returns the effective show LD triangle setting, falling back to config
// type
any
getter: showRecombination
Returns the effective show recombination setting, falling back to config
// type
any
getter: recombinationZoneHeight
Returns the effective recombination zone height, falling back to config
// type
any
getter: fitToHeight
Returns the effective fit to height setting, falling back to config
// type
any
getter: hweFilterThreshold
Returns the effective HWE filter threshold, falling back to config
// type
any
getter: showVerticalGuides
Returns the effective show vertical guides setting, falling back to config
// type
any
getter: showLabels
Returns the effective show labels setting, falling back to config
// type
any
getter: tickHeight
Returns the effective tick height, falling back to config
// type
any
getter: useGenomicPositions
Returns the effective use genomic positions setting, falling back to config
// type
any
getter: ldCanvasHeight
Effective height for the LD canvas (total height minus line zone) Note: Recombination track is overlaid on the line zone, not in a separate zone
// type
number
SharedLDModel - Methods
method: regionCannotBeRendered
// type signature
regionCannotBeRendered: () => any
method: renderProps
// type signature
renderProps: () => any
method: trackMenuItems
// type signature
trackMenuItems: () => any[]
method: renderSvg
// type signature
renderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>
SharedLDModel - Actions
action: setFlatbushData
// type signature
setFlatbushData: (flatbush: ArrayBufferLike, items: LDFlatbushItem[], snps: { id: string; refName: string; start: number; end: number; }[], maxScore: number, yScalar: number, cellWidth: number) => void
action: setLineZoneHeight
// type signature
setLineZoneHeight: (n: number) => void
action: setError
// type signature
setError: (error: unknown) => void
action: reload
// type signature
reload: () => void
action: setMafFilter
// type signature
setMafFilter: (arg: number) => void
action: setLengthCutoffFilter
// type signature
setLengthCutoffFilter: (arg: number) => void
action: setLDMetric
// type signature
setLDMetric: (metric: string) => void
action: setColorScheme
// type signature
setColorScheme: (scheme: string) => void
action: setShowLegend
// type signature
setShowLegend: (show: boolean) => void
action: setShowLDTriangle
// type signature
setShowLDTriangle: (show: boolean) => void
action: setShowRecombination
// type signature
setShowRecombination: (show: boolean) => void
action: setRecombinationZoneHeight
// type signature
setRecombinationZoneHeight: (n: number) => void
action: setFitToHeight
// type signature
setFitToHeight: (value: boolean) => void
action: setHweFilter
// type signature
setHweFilter: (threshold: number) => void
action: setFilterStats
// type signature
setFilterStats: (stats: FilterStats) => void
action: setRecombination
// type signature
setRecombination: (data: { values: number[]; positions: number[]; }) => void
action: setShowVerticalGuides
// type signature
setShowVerticalGuides: (show: boolean) => void
action: setShowLabels
// type signature
setShowLabels: (show: boolean) => void
action: setTickHeight
// type signature
setTickHeight: (height: number) => void
action: setUseGenomicPositions
// type signature
setUseGenomicPositions: (value: boolean) => void