# LDTrackDisplay Auto-generated config schema for the current JBrowse release — see the [config guide](https://jbrowse.org/jb2-staging/docs/config_guide) for concepts. Provided by the `variants` plugin. [View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/variants/src/LDDisplay/configSchemaLDTrack.ts). ## Example usage The pre-computed heatmap, with the legend on so the R² ramp is labelled: ```js { type: 'LDTrack', trackId: 'ld', name: 'Linkage disequilibrium', assemblyNames: ['hg38'], adapter: { type: 'PlinkLDTabixAdapter', uri: 'https://example.com/plink.ld.gz', }, displays: [ { type: 'LDTrackDisplay', displayId: 'ld-LDTrackDisplay', showLegend: true, }, ], } ``` _See the **Config slots** section below for all available configuration fields._ Linkage disequilibrium heatmap read from an `LDTrack`'s pre-computed file (e.g. PLINK `--r2` output), rather than computed from genotypes. Use [](https://jbrowse.org/jb2-staging/docs/config/lddisplay) instead to compute LD from a `VariantTrack`'s own VCF. The genotype-derived filters the shared base declares (`minorAlleleFrequencyFilter`, `hweFilterThreshold`, `callRateFilter`) have nothing to act on here — the file's rows are already computed — so they are inherited but inert. Every slot comes from the shared base below; this display adds none of its own. ## Related links - **Adapter:** [PlinkLDAdapter](../plinkldadapter) - **Adapter:** [PlinkLDTabixAdapter](../plinkldtabixadapter) - **Base config:** [SharedLDDisplay](../sharedlddisplay) ## Config slots These slots go on a display entry: `"displays": [{ "type": "LDTrackDisplay", ... }]`, or in the track's [`displayDefaults`](https://jbrowse.org/jb2-staging/docs/config_guides/tracks#configuring-displays) when this is its default display. Slot types (`fileLocation`, `frozen`, ...) are explained in the [config slot types reference](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types). Slots a base configuration contributes are listed here too, so this table is the whole surface. | Slot | Description | | --- | --- | | Inherited from [SharedLDDisplay](../sharedlddisplay) | 17 slots | | **minorAlleleFrequencyFilter**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 0.1 | Filter variants by minor allele frequency (0-1). Variants with MAF below this threshold will be hidden
_advanced_ | | **lengthCutoffFilter**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = Number.MAX_SAFE_INTEGER | Maximum length of variants to include (in bp)
_advanced_ | | **lineZoneHeight**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 100 | Height of the zone for connecting lines at the top
_advanced_ | | **ldMetric**
[`stringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#stringenum) (r2, dprime) = 'r2' | LD metric to compute: 'r2' (squared correlation) or 'dprime' (normalized D) | | **showLegend**
[`maybeBoolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = 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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = true | Whether to show the LD triangle heatmap | | **squashToHeight**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = false | When true, squash the LD triangle to fit the display height
_advanced_ | | **hweFilterThreshold**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 0 | HWE filter p-value threshold (variants with HWE p < this are excluded). Set to 0 to disable HWE filtering
_advanced_ | | **callRateFilter**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = true | Whether to show vertical guides at the connected genome positions on hover
_advanced_ | | **showLabels**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = false | Whether to show variant labels above the tick marks
_advanced_ | | **tickHeight**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 6 | Height of the vertical tick marks at the genomic position
_advanced_ | | **useGenomicPositions**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = false | When true, draw cells sized according to genomic distance between SNPs rather than uniform squares
_advanced_ | | **signedLD**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 400 | Starting height in pixels for the LD triangle, excluding the lineZoneHeight band; drag-resizable | | Inherited from [BaseLinearDisplay](../baselineardisplay) | 5 slots | | **maxFeatureScreenDensity**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 1 | maximum features per pixel before showing a "too many features" message
_advanced_ | | **mouseover**
[`string`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 1_000_000 | maximum data to attempt to download for a given track, used if adapter doesn't specify one
_advanced_ | | **forceLoad**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#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_ |