# LinearManhattanDisplay 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 `gwas` plugin. [View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/gwas/src/LinearManhattanDisplay/configSchemaFactory.ts). ## Example usage Minimal `GWASTrack` config. See the [GWAS track guide](https://jbrowse.org/jb2-staging/docs/config_guides/gwas_track) for all options: ```js { type: 'GWASTrack', trackId: 'gwas', name: 'GWAS results', assemblyNames: ['hg38'], adapter: { type: 'GWASAdapter', uri: 'https://example.com/gwas.bed.gz', }, } ``` Taller track, LocusZoom-style coloring: `colorBy: 'ld'` colors each point by its r² to the index SNP read from the adapter's `ldAdapter` sub-adapter. The LD data is a second source on `GWASAdapter` (mirroring MAF's `annotationAdapter`), so it nests under `adapter`, while display-only options like `height`/`colorBy` go in `displayDefaults` — see [configuring displays](https://jbrowse.org/jb2-staging/docs/config_guides/tracks#configuring-displays): ```js { type: 'GWASTrack', trackId: 'gwas', name: 'GWAS results', assemblyNames: ['hg38'], adapter: { type: 'GWASAdapter', uri: 'https://example.com/gwas.bed.gz', ldAdapter: { type: 'PlinkLDTabixAdapter', uri: 'https://example.com/plink.ld.gz', }, }, displayDefaults: { height: 400, colorBy: 'ld', }, } ``` _See the **Config slots** section below for all available configuration fields._ configuration for the Manhattan plot display used by GWAS tracks ## Related links - **Adapter:** [GWASAdapter](../gwasadapter) - **State model:** [runtime API](../../models/linearmanhattandisplay) - **Base config:** [BaseLinearDisplay](../baselineardisplay) ## Config slots These slots go on a display entry: `"displays": [{ "type": "LinearManhattanDisplay", ... }]`, 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 | | --- | --- | | **color**
[`color`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#color) = '#0068d1' | CSS color or jexl callback for Manhattan points
_callback args:_ `feature` | | **colorBy**
[`stringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#stringenum) (normal, ld) = 'normal' | LocusZoom-style coloring. 'normal' uses `color`; 'ld' colors each point by its r² to the index SNP, read from the `GWASAdapter`'s `ldAdapter` sub-adapter. | | **significanceLine**
[`maybeNumber`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) | Draw a horizontal line across the plot at this score, for the threshold a scan is read against: genome-wide significance on a GWAS, or an empirical outlier cutoff on a differentiation scan. Unset (the default) draws none, since there is no threshold that is right for every scan.

On the plot's own scale, so it is a `-log10(p)` where the points are and an Fst where `scoreColumn` names an Fst column. The autoscaled y-axis widens to reach it, so a window where nothing clears the threshold still shows the threshold; an explicit `minScore`/`maxScore` that excludes it still wins, and there the line is not drawn. | | **minimalTicks**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = false | Draw only the min/max Y-axis ticks
_advanced_ | | **scatterPointSize**
[`maybeNumber`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = 4 _promotable_ | Manhattan point diameter in px (adjustable from the track menu). Larger default than wiggle's since Manhattan points are the primary glyph. | | **showLdLegend**
[`maybeBoolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#the-maybe-types) = true _promotable_ | Draw the LD color key, which labels the r² ramp the points are painted against. Only appears while LD coloring is active — the ramp means nothing under the plain single-color scheme. | | **minScore**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = Number.MIN_VALUE | Fixed minimum score bound. The default (Number.MIN_VALUE) is a sentinel meaning "unset, use autoscale"
_advanced_ | | **maxScore**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = Number.MAX_VALUE | Fixed maximum score bound. The default (Number.MAX_VALUE) is a sentinel meaning "unset, use autoscale"
_advanced_ | | **scaleType**
[`stringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#stringenum) (linear, log) = 'linear' | Scale type (linear or log) | | **autoscale**
[`stringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#stringenum) (local, localsd, localpercentile) = 'localpercentile' | Autoscale type: "local" uses the min/max in the visible region, "localsd" uses mean ± numStdDev standard deviations, "localpercentile" uses the numQuantile-th percentile score as the max (robust to skewed/peaky data) | | **numStdDev**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 3 | Number of standard deviations to use for the localsd autoscale type
_advanced_ | | **displayCrossHatches**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = false | Rule the score axis with horizontal cross hatches at the tick positions — the config form of the score menu's "Show cross hatches". Ignored by the density rendering types, which spend color rather than height on the score and so have no axis to rule | | Inherited from [BaseLinearDisplay](../baselineardisplay) | 6 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_ | | **height**
[`number`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#number) = 100 | default height for the track | | **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_ |