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MarkFacet

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

Example usage

{
  type: 'LinearMarkDisplay',
  facet: { field: 'HP', transform: [{ type: 'pileup' }] },
  marks: [{ mark: 'span' }],
}

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

The mark display's facet: the Facet the feature and alignments displays take, one labelled section of the track per value of a field, plus the steps the facet runs over each section's features alone, after the display's transform and before every mark's own. A pileup here packs each section on its own rows, which every mark then stands in. A string is the field; with no field the steps run over the one section there is.

Config slots

These slots go on a display entry: "displays": [{ "type": "MarkFacet", ... }], 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
transform
MarkTransform		Steps over each section's features alone, after the display's transform and before any mark's own: a pileup here packs each section on its own rows, and every mark stands in them.
Inherited from Facet2 slots
field
featureField = ''		The feature field each value of which packs its own labelled section of the track: a field name, a dotted path into a structured field (INFO.SVTYPE, a read's tags.HP), a jexl: expression, or strand. A feature with no value stacks last, under field: none. The multi-sample variant displays read a sample attribute instead, and the multi-row display a row attribute or group, its rowGroups. The alignments displays also take a read dimension here: firstOfPairStrand, pairOrientation, splitRead, mapq or mateAssembly. Writing facet: "strand" lands here.
domain
stringArray = []		The values whose sections stack first, in order; the rest follow sorted. Empty stacks every section sorted, and a strand facet forward, reverse, then unstranded (1, -1, 0).