Skip to main content

Facet

Auto-generated from the config schema in the source — see the config guide for concepts. Built into JBrowse core. View source.

Example usage

{ type: 'LinearBasicDisplay', facet: 'strand' }
{
  type: 'LinearBasicDisplay',
  facet: { field: 'gene_biotype', domain: ['protein_coding', 'lncRNA'] },
}
{
  type: 'LinearAlignmentsDisplay',
  facet: { field: 'tags.HP', domain: ['1', '2'] },
}

The facet setting of the feature, multi-sample variant, multi-row and alignments displays: one labelled section of the track per value of a field. A string is the field; the object adds the order. The mark display's MarkFacet adds the steps each section runs. On the multi-sample variant displays the field is a sample attribute from the samples file, such as population, and it bands the sample rows by its value, with no chip.

Config slots

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
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 group, its rowGroups. The alignments displays also take a read dimension here: firstOfPairStrand, pairOrientation, pairing, split, spliced, mapq, mateRefName 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).