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SharedLDDisplay

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the variants plugin. View source.

Shared config for the two LD displays: LDDisplay (on a VariantTrack, computing pairwise R² from the VCF's own genotypes) and LDTrackDisplay (on an LDTrack, reading pre-computed LD such as PLINK --r2 output). Both register the same slots against different track types, so the slots live here once.

Config slots

SharedLDDisplay is a shared base schema, not a type you name in a config. Set these slots on one of the configs under Extended by above, each of which lists them as inherited and shows the shape in its own example. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
minorAlleleFrequencyFilter
number = 0.1		Filter variants by minor allele frequency (0-1). Variants with MAF below this threshold will be hidden
advanced
lengthCutoffFilter
number = Number.MAX_SAFE_INTEGER		Maximum length of variants to include (in bp)
advanced
lineZoneHeight
number = 100		Height of the zone for connecting lines at the top
advanced
ldMetric
stringEnum (r2, dprime) = 'r2'		LD metric to compute: 'r2' (squared correlation) or 'dprime' (normalized D)
showLegend
maybeBoolean = false promotable		Whether to show the legend. Unset (the default) follows the session-wide default for this display type, falling back to off; an explicit true/false customizes the track.
showLDTriangle
boolean = true		Whether to show the LD triangle heatmap
squashToHeight
boolean = false		When true, squash the LD triangle to fit the display height
advanced
hweFilterThreshold
number = 0		HWE filter p-value threshold (variants with HWE p < this are excluded). Set to 0 to disable HWE filtering
advanced
callRateFilter
number = 0		Call rate filter threshold (0-1). Variants with fewer than this proportion of non-missing genotypes are excluded. Set to 0 to disable.
advanced
maxVariantSeparation
number = 0		Maximum separation, in variants, between the two SNPs of a computed pair. Pairs further apart are not computed and not drawn, which turns the matrix from n²/2 cells into n·k and so makes the cost linear in the variant count rather than quadratic. This is plink's --ld-window, and like it the window is the way to look at a large region at all: the full triangle for 50,000 variants is 1.25e9 cells, which no GPU will allocate. Set to 0 for the full triangle.
advanced
showVerticalGuides
boolean = true		Whether to show vertical guides at the connected genome positions on hover
advanced
showLabels
boolean = false		Whether to show variant labels above the tick marks
advanced
tickHeight
number = 6		Height of the vertical tick marks at the genomic position
advanced
useGenomicPositions
boolean = false		When true, draw cells sized according to genomic distance between SNPs rather than uniform squares
advanced
signedLD
boolean = false		When true, show signed LD values (-1 to 1) instead of absolute values (0 to 1). For R², this shows R (correlation) instead. For D', this preserves the sign.
advanced
ldMethod
stringEnum (auto, phased, composite) = 'auto'		Which LD estimator to compute. 'auto' picks haplotypic LD for a phased callset and the Weir composite estimate for an unphased one, which is the most precise statistic each file can support. 'composite' forces the composite estimate even on phased data — the two are different statistics that coincide only under Hardy-Weinberg, so forcing it is how a phased panel is made comparable to an unphased cohort, or to plink --r2 output. 'phased' is a preference rather than an instruction: unphased data carries no gametes to count, so it declines to composite, and method on the result reports what actually ran.
advanced
height
number = 400		Starting height in pixels for the LD triangle, excluding the lineZoneHeight band; drag-resizable
Inherited from BaseLinearDisplay5 slots
maxFeatureScreenDensity
number = 1		maximum features per pixel before showing a "too many features" message
advanced
mouseover
string = 
'jexl:get(feature,'_mouseOver')||get(feature,'name')||get(feature,'function')||get(feature,'id')'
text to display when the cursor hovers over a feature
callback args: feature
jexlFilters
stringArray = []		config jexlFilters are deferred evaluated so they are prepended with jexl at runtime rather than being stored with jexl in the config
fetchSizeLimit
number = 1_000_000		maximum data to attempt to download for a given track, used if adapter doesn't specify one
advanced
forceLoad
boolean = false		Declarative equivalent of the "Force load" button on the "too much data" banner: when true the display always renders, however large the region or dense the features. Off by default (the gate guards against huge downloads). Set it on a view no one can interact with — an embedded / notebook view, or a screenshot — where the region is known and you want it drawn without a click.
advanced