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SharedVariantDisplay

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

Config slots

SharedVariantDisplay is a shared base schema, not a type you name in a config. Set these slots on one of the configs under Extended by above, each of which lists them as inherited and shows the shape in its own example. 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
lineZoneHeight
number = 0		Height of the zone above the rows holding the lines that tie each matrix column to its genomic position. 0 (the default here) means no zone at all — only the matrix display, which lays columns out by feature index rather than at their genomic positions, raises it.
advanced
showTooltips
boolean = true		Show the hover tooltip naming the genotype, the sample and the record under the pointer. On by default; turning it off leaves every other hover affordance — the crosshairs, the highlighted cell, the cross-display session.hovered channel — alone, so the pointer still says where it is while the panel stops covering the rows beside it.

A config slot rather than a display property, so a track config can ship with it off and a figure capture keeps it off across a reload. Both multi-sample displays honor it: they draw the same tooltip off the same hoveredFeature slot.
renderingMode
stringEnum (alleleCount, phased) = 'alleleCount'		'alleleCount' draws one row per sample colored by allele dosage; 'phased' draws one row per haplotype
featureColor
string = ''		Optional per-feature color for the genotype cells: a jexl expression (or plain CSS color) evaluated once per variant in the worker, painting every alt-carrying cell with that color while ref/no-call cells keep their normal coloring so "who carries it" still reads. Empty means the default genotype-based coloring (allele dosage / phasing). The "Color by..." menu offers presets like consequence impact (jexl:impactColor(feature)), but any feature jexl works, same as the standard color slot.
minorAlleleFrequencyFilter
number = 0		Hide variants whose minor allele frequency is below this threshold
advanced
maxMissingnessFilter
number = 1		Hide variants whose fraction of no-call (missing) genotypes is above this threshold; 1 keeps every variant
advanced
showLegend
maybeBoolean = true promotable		Whether to draw the floating legend over the display. It is clipped to the display's own bounds, so while it is on it sets a floor under the lane height: turn it off to size a short lane to its rows rather than to its key, which is what a one-record SV call genotyped across a handful of carriers wants.
colorBy
string = ''		Name of a sample-metadata attribute (a column in the adapter's samplesTsvLocation, e.g. 'population') to color the sidebar rows by; empty means no grouping
groupBy
string = ''		Name of a sample-metadata attribute (a column in the adapter's samplesTsvLocation, e.g. 'population') to order the sample rows by, so each group's rows are contiguous and a group-restricted genotype pattern reads as one band; empty means the rows keep their existing order
referenceDrawingMode
stringEnum (draw, skip) = 'skip'		Whether to paint reference alleles: 'skip' (the default) fills the row background solid grey and paints only ALT alleles, which makes overlapping variants easier to pick out; 'draw' paints reference alleles like any other genotype.
rowHeight
number = 0		per-row height in px, scrolling the rows that do not fit; 0 (the default) fits the rows to the display height instead, dividing it between them
showTree
boolean = true		Show the sample clustering tree in the sidebar
showBranchLength
boolean = true		position tree nodes by branch length (dendrogram) rather than evenly by topology (cladogram)
showRowLabels
boolean = true		Show the per-sample row labels in the sidebar
showRowSeparators
boolean = false		draw a hairline between adjacent rows; off by default, because a painting whose neighbouring rows differ in color already separates itself and the line only earns its pixel where they do not — a run of same-colored rows reads as one block without it, with no way to recover the row count by eye. Drawn only once rows are at least 4px tall: below that the line is as thick as the row it borders, turning a dense painting into a grid of hairlines with a little color between them
Inherited from BaseLinearDisplay5 slots
height
number = 100		default height for the track
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