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SyntenyColor

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

Example usage

{ type: 'LinearSyntenyView', colorBy: { field: 'strand' } }
{ type: 'DotplotView', colorBy: { field: 'query' } }
{
  type: 'LinearSyntenyView',
  colorBy: { field: 'gene_group', domain: ['A1a', 'B1'] },
}

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

The linear synteny and dotplot views' colorBy setting, which every track in the view paints with: one colour for every alignment, or a field each alignment carries — its strand, the sequence at either end, the anchor assembly's, the track it came from, a measurement on its preset ramp (identity, mappingQual, dnds), or a column the tracks declare in attributeColumns. A string is the constant.

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
value
maybeColor		The colour of every alignment under the none scale, in place of the view's default scheme: the match block of a synteny ribbon, whose insertions and deletions keep their colours, or a dotplot point. Writing colorBy: "grey" lands here. Unset, the default scheme paints.
field
string = ''		what colours an alignment: strand paints forward and reverse; query and target one colour per sequence on that side, reference one per chromosome of the anchor assembly across a stack, track one per overlaid track (pinned under Track colors); identity, mappingQual and dnds paint the preset ramps; any other name is a column the tracks declare in attributeColumns, a ramp over the values seen for numbers and one colour per label for text (or the colour a color column put beside it)
scale
maybeStringEnum (none)		none paints value and keeps the field for a switch back; unset, a field paints
domain
stringArray = []		a text column's labels that take the palette first, in order, and lead the key, the rest following sorted; a label left out keeps a colour derived from itself that no listed label paints, so every window and session agrees on it