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ManhattanColor

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

Example usage

{ type: 'LinearManhattanDisplay', color: 'goldenrod' }
{
  type: 'LinearManhattanDisplay',
  color: { field: 'population', domain: ['EUR', 'AFR'] },
}
{ type: 'LinearManhattanDisplay', color: { field: 'ld' } }
{
  type: 'LinearManhattanDisplay',
  color: {
    field: 'ld',
    scale: 'threshold',
    domain: [0.5],
    range: ['#357ebd', '#d43f3a'],
  },
}

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

The Manhattan display's color setting: one CSS colour or jexl: callback for every point, a field whose values each take a range colour with a key, a numeric field cut into intervals by a threshold scale, or LocusZoom colouring by r² to the index SNP — which is that threshold scale over field: "ld", whose cuts and colours a config may move. A string is the constant; a field binds the range; field: "ld" reads the GWASAdapter's ldAdapter.

Config slots

These slots go on a display entry: "displays": [{ "type": "ManhattanColor", ... }], 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
value
color = '#0068d1'		A CSS colour, or a jexl callback over feature returning one, for every point under the none scale. Writing color: "red" lands here.
callback args: feature
field
featureField = ''		the feature field whose values each take a range colour, with a key listing the values met: name, refName, a BED extra column, a GFF attribute; ld is each point's r² to the index SNP, read from the GWASAdapter's ldAdapter
scale
maybeStringEnum (none, categorical, threshold)		none paints value and keeps the field for a switch back; categorical a range colour per value of field; threshold a range colour per interval between the cut points domain lists; unset follows field, and is threshold over ld and categorical over anything else
domain
stringArray = []		under a categorical scale, the field's values that take the range first, in order, in the key as on the points, the rest following sorted, each on a colour no listed value paints; under a threshold scale, the cut points in ascending order, range taking one entry more than this, one per interval; r² to the index SNP cuts at 0.2, 0.4, 0.6 and 0.8 into the LocusZoom blue-through-red bins unless these say otherwise
range
colorArray = []		CSS colours a categorical scale hands its domain in order, continuing into the default palette past its end, or a threshold scale hands its intervals, lowest first