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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: color: { field: '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/color 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,
    color: { field: 'ld' },
  },
}

A selection scan as a plain FeatureTrack: the plot reads the file's fst column through scoreField and colors each point by its population column, with the color key derived from the values it meets:

{
  type: 'FeatureTrack',
  trackId: 'fst_scan',
  name: 'Fst scan',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'BedTabixAdapter',
    uri: 'https://example.com/fst.bed.gz',
  },
  displays: [
    {
      type: 'LinearManhattanDisplay',
      scoreField: 'fst',
      color: { field: 'population' },
    },
  ],
}

See the Config slots section below for all available configuration fields.

configuration for the Manhattan plot display: the default display of a GWAS track, and one a FeatureTrack can switch to, plotting any numeric feature field as a scored scatter

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.

SlotDescription
color
ManhattanColor		"goldenrod" or a jexl: callback paints every point; { field: "population" } gives each value a palette colour with a key; { field: "ld" } colours by r² to the index SNP.
scales
ValueScale		The y scale: domainMin, domainMax and rules. -log10 p values are pre-transformed, so type admits linear only and the plot's domain is plain min/max over the loaded regions with no autoscale mode to consult — the track menu draws neither radio, because the scale declares neither.

A threshold a scan is read against — genome-wide significance on a GWAS, an empirical outlier cutoff on a differentiation scan — is a scales.y.rules entry, 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. A scan read against two thresholds, suggestive and genome-wide, names both. The axis widens to reach a rule, so a window where nothing clears the threshold still shows it.
displayCrossHatches
boolean = false		Rule the score axis with horizontal cross hatches at the tick positions
minimalTicks
boolean = false		Draw only the min/max Y-axis ticks
advanced
scatterPointSize
number = 4		Manhattan point diameter in px (adjustable from the track menu). Larger default than wiggle's since Manhattan points are the primary glyph.
showLegend
boolean = true		Draw the color key: the r² ramp under LD coloring, the value table under field coloring. Nothing under the plain single-color scheme, which has no key to draw.
height
number = 100		default height for the track
scoreField
string = 'score'		Feature field plotted on the score axis, read natively off each feature. The default score is the field every adapter serves — including the value a BED adapter's scoreColumn rewrote it to — so an explicit name here reaches a raw column the adapter left alone (a BED extra column, a GFF attribute) and takes precedence over that adapter-tier rewrite. The Manhattan plot skips a feature with no finite value in the field; the wiggle renderings plot it at 0