LinearManhattanDisplay

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

Example usage#

Minimal GWASTrack config. See the GWAS track guide for all options:

{
  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:

{
  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
• State model: runtime API
• Base config: BaseLinearDisplay
• Guide: A selected haplotype (Dog10K)
• Guide: Custom track and display types
• Guide: Defaults for all tracks
• Guide: GWAS track
• Guide: Tracks

Config slots#

These slots go on a display entry: "displays": [{ "type": "LinearManhattanDisplay", ... }], or in the track's displayDefaults when this is its default display. 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.

'jexl:get(feature,'_mouseOver')||get(feature,'name')||get(feature,'function')||get(feature,'id')'