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MultiWaySyntenyDisplay

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

Draws a multi-genome SyntenyTrack in a linear genome view as one lane per assembly, with ribbons joining each gene's placements in adjacent lanes.

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' },
    ],
  },
  displays: [
    {
      type: 'MultiWaySyntenyDisplay',
      displayId: 'grape_peach_cacao-MultiWaySyntenyDisplay',
    },
  ],
}

The same display with a curated lane order, genes colored by ortholog cluster, and ribbons colored by percent identity:

{
  type: 'SyntenyTrack',
  trackId: 'primate_synteny',
  name: 'Primate synteny',
  assemblyNames: ['hg38', 'panTro6', 'gorGor6', 'ponAbe3'],
  adapter: {
    type: 'MCScanBlocksAdapter',
    uri: 'hg38.blocks',
    blockAssemblies: ['hg38', 'panTro6', 'gorGor6', 'ponAbe3'],
    bedLocations: [
      { uri: 'hg38.bed' },
      { uri: 'panTro6.bed' },
      { uri: 'gorGor6.bed' },
      { uri: 'ponAbe3.bed' },
    ],
  },
  displays: [
    {
      type: 'MultiWaySyntenyDisplay',
      displayId: 'primate_synteny-MultiWaySyntenyDisplay',
      rows: { sort: ['panTro6', 'gorGor6', 'ponAbe3'] },
      encoding: { color: 'cluster' },
      ribbons: { encoding: { color: 'identity' } },
    },
  ],
}

Config slots

Display 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
encoding
MultiWayGeneEncoding		The channels the gene glyphs paint through: encoding.color, their fill.
utrColor
color = '#357089'		the fill color of the untranslated parts of a gene glyph, matching the canvas gene track default
callback args: feature
data
SyntenyData		What the fetch reads, a SyntenyData object: resolution picks a tiered file's stored tier.
rows
LaneRows		The lane order and the lanes drawn, which the Lanes menu, a header drag and the lane picker write.
ribbons
MultiWayRibbons		The bands joining each gene's placements in adjacent lanes: ribbons.encoding.color paints them and ribbons.mark.interpolate curves their sides.
hideUnlabelled
boolean = false		under a text column, draw only the ribbons whose pair has a label
laneGeneTracks
stringArray = []		the trackId of the gene track each lane draws, one per genome, or an entry spelling {assembly}, such as {assembly}-ncbiRefSeq, naming in each lane the track whose id has that lane's genome, or any of its aliases, written there. Plain ids outrank {assembly} entries, and an earlier entry outranks a later one. A lane whose genome no entry names draws the session's best-ranked annotation track for it, which on a config holding several gene sets per genome is whichever is declared first
legend
Legend		The color key: the anchor lane's drawn gene colors, and what ribbons.encoding.color paints — the strand colors, the identity ramp, or a column's labels. Derived from what is on screen, so an encoding.color resolving to one color and a ribbon scale painting nothing key nothing.
showLaneTicks
boolean = true		draw each lane's 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. With this off, the header's span and multiple are the only scale shown
text
featureField = ''		The feature field, or jexl expression over feature, each lane's gene labels print; unset, the gene's name, else its ID.
inlineLaneNames
boolean = false		print each lane's genome name over the left end of its gene row, without its coordinates, instead of on a line above the genes. The stack then fits 12 px less per lane
showGeneLabels
boolean = true		print gene names in a row under each lane's genes, dropping a name where its neighbours leave it no room
laneLayers
MultiWayLaneLayer		Rows of data every lane draws above its genes, each from that genome's own track: a GC or conservation bigWig per genome as bars, say
splitStrands
boolean = true		draw each lane's genes in two rows either side of its line: the ones reading rightwards on screen above, leftwards below, so a flipped lane's genes turn over with it and a collinear block keeps one row down the stack. A lane too short for two rows draws one
height
number = 240		default height for the track
Inherited from BaseLinearDisplay2 slots
fetchSizeLimit
number = 1000000		bytes a region may fetch before the display asks first; an adapter that sets its own limit overrides this
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

Retired keys

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.

KeyOn load
maxFeatureScreenDensityignored
maxDisplayedBpPerPxignored
mouseoverignored
jexlFiltersmoved into a current slot
drawCurvesmoved into a current slot
bridgeSkippedLanesignored