MafColor

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

Example usage#

{ type: 'LinearMafDisplay', color: 'identity' }

{ type: 'LinearMafDisplay', color: 'identity', y: 'identity' }

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

The MAF display's color: what colours each species row's aligned cells. mismatch paints a base only where it differs from the reference, base every base, identity the mean identity to the reference on a red-to-blue ramp, chromosome each block by the rank of its source chromosome within the row, and codon each codon by its amino-acid change, given an annotationAdapter. A string is the field.

Config slots#

These slots go on a display entry: "displays": [{ "type": "MafColor", ... }], 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.