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MultiWaySyntenyDisplay

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

Example usage

Selected on a multi-genome SyntenyTrack (an MCScanBlocksAdapter listing several assemblies) shown in a plain linear genome view. Draws one lane per assembly in that assembly's own local coordinate frame — non-anchored, like the multi-sample variant matrix — with ribbons connecting each gene's placements between adjacent lanes:

{
  type: 'SyntenyTrack',
  trackId: 'grape_peach_cacao',
  name: 'grape/peach/cacao orthologs',
  assemblyNames: ['grape', 'peach', 'cacao'],
  adapter: {
    type: 'MCScanBlocksAdapter',
    uri: 'grape.blocks',
    blockAssemblies: ['grape', 'peach', 'cacao'],
    bedLocations: [
      { uri: 'grape.bed' },
      { uri: 'peach.bed' },
      { uri: 'cacao.bed' },
    ],
    assemblyNames: ['grape', 'peach', 'cacao'],
  },
  displays: [
    {
      type: 'MultiWaySyntenyDisplay',
      displayId: 'grape_peach_cacao-MultiWaySyntenyDisplay',
    },
  ],
}

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

Config slots

These slots go on a display entry: "displays": [{ "type": "MultiWaySyntenyDisplay", ... }], 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
color
color = 'goldenrod'		the fill color of the gene glyphs, matching the canvas gene track default
callback args: feature
utrColor
color = '#357089'		the fill color of the untranslated parts of a gene glyph, matching the canvas gene track default
callback args: feature
ribbonColor
color = 'rgba(130,130,130,0.3)'		the color of the ribbons connecting adjacent lanes
ribbonColorBy
stringEnum (default, strand, identity) = 'default'		what colors a ribbon: default is ribbonColor; strand reads whether the ribbon is crossed — the lower placement runs the other way from the upper one — so an inversion relative to the lane above stands out, in the synteny view's strand colors; identity reads the pair's identity attribute (a PAF's, or an MCScan table's attributeColumns) on the synteny view's viridis ramp, and a pair without one keeps ribbonColor. Every mode keeps ribbonColor's opacity
drawCurves
boolean = false		draw the ribbons as bezier curves rather than straight chords, the same setting the linear synteny view spells drawCurves. Straight is the default there and here: a chord's slant reads directly as the offset between two lanes drawn in different coordinate frames, which is exactly what a curve hides
bridgeSkippedLanes
boolean = true		join a group across a lane that places nothing for it, to the next lane down that does. A ribbon otherwise joins adjacent lanes only, so a sparse lane mid-stack cuts every chain running through it
showLaneTicks
boolean = true		draw each lane's own coordinate ticks, at one interval shared by every lane. Equal spacing between two lanes means equal bp-per-pixel; a lane whose ticks crowd together is zoomed out. Turning this off leaves the header's span and multiple as the only scale statement
height
number = 240		overrides the base schema's 100, which divides into a lane stack at the glyph-height floor with the headers colliding into the glyphs
Inherited from BaseLinearDisplay5 slots
maxFeatureScreenDensity
number = 1		maximum features per pixel before showing a "too many features" message
advanced
mouseover
string = 
'jexl:get(feature,'_mouseOver')||get(feature,'name')||get(feature,'function')||get(feature,'id')'
text to display when the cursor hovers over a feature
callback args: feature
jexlFilters
stringArray = []		config jexlFilters are deferred evaluated so they are prepended with jexl at runtime rather than being stored with jexl in the config
fetchSizeLimit
number = 1_000_000		maximum data to attempt to download for a given track, used if adapter doesn't specify one
advanced
forceLoad
boolean = false		Declarative equivalent of the "Force load" button on the "too much data" banner: when true the display always renders, however large the region or dense the features. Off by default (the gate guards against huge downloads). Set it on a view no one can interact with — an embedded / notebook view, or a screenshot — where the region is known and you want it drawn without a click.
advanced