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LinearBasicDisplay

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

Draws the genes and other features of a FeatureTrack, from a BED, GFF or similar file. The display adds the gene-glyph slots (isoforms, subparts, UTRs, chevrons) to the shared canvas base. The color slots color, connectorColor and utrColor are display-level, set inside a track's displays array, each a CSS color or a jexl: expression for per-feature coloring.

Example usage

A complete FeatureTrack config (e.g. genes from a GFF3) to paste into tracks. displayMode sets the feature height preset (normal, compact, or superCompact), or collapsed for a single-row overview:

{
  type: 'FeatureTrack',
  trackId: 'genes',
  name: 'Genes',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'Gff3TabixAdapter',
    uri: 'https://example.com/genes.gff3.gz',
  },
  displays: [
    {
      type: 'LinearBasicDisplay',
      displayId: 'genes-LinearBasicDisplay',
      height: 200,
      displayMode: 'compact',
    },
  ],
}

Config slots

Display slots go on a display entry: "displays": [{ "type": "LinearBasicDisplay", ... }], 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
fetchSizeLimit
number = 5000000		Feature (GFF/BED) tracks are light text, and the tabix byte estimate is block-granular (a small region still pulls whole BGZF blocks), so a single gene can trip a tighter gate.
advanced
connectorColor
maybeColor		color of the connecting/intron lines between feature segments (defaults to the theme text color)
callback args: feature
utrColor
maybeColor		fill color for UTRs on gene/transcript glyphs. Unset, a feature's own BED itemRgb paints them too (matching UCSC's whole-item coloring), else a contrasting blue
callback args: feature
geneGlyphMode
stringEnum (auto, all, longestCoding) = 'auto'		Gene glyph display mode: "auto" collapses each gene to one transcript when zoomed out and trims the rest to what the track height holds, "all" draws every transcript and scrolls the surplus instead of trimming, "longestCoding" shows one transcript per gene — the one canonicalTranscriptTags names, else the longest coding
subfeatureLabels
stringEnum (auto, none, below, overlay) = 'auto'		subfeature label display mode: auto (the default) names a polyprotein's cleavage products on their rows and nothing else; none, below or overlay apply to every part
chevrons
FeatureChevrons sub-schema		The arrows on a feature's intron lines.
chevrons.show
boolean = true		draw chevrons on intron lines pointing the way the feature reads
transcriptTypes
stringArray = 
['mRNA', 'transcript', 'primary_transcript', 'V_gene_segment', 'C_gene_segment', 'D_gene_segment', 'J_gene_segment']
feature types the geneLike filter field counts beside every gene, transcript and RNA type, plus the fallback for recognizing a CHILDLESS transcript as one of a gene's isoforms.
canonicalTranscriptField
string = 'tag'		feature attribute holding an isoform's curated "this one represents the gene" tag.
canonicalTranscriptTags
stringArray = 
['MANE Select', 'MANE_Select', 'RefSeq Select', 'Ensembl_canonical', 'MANE Plus Clinical', 'MANE_Plus_Clinical']
values of that attribute that mark an isoform as the gene's representative one, which is then ranked ahead of every other isoform: it is the transcript shown by longestCoding, and the first kept when auto caps a gene at the rows the track has.
containerTypes
stringArray = ['proteoform_orf']		top-level feature types that always stack their children on separate rows.
subParts
string = 'CDS,UTR,five_prime_UTR,three_prime_UTR'		subparts for a glyph
proteinFeatures
ProteinFeatures sub-schema		The display draws this track's domains over each transcript's CDS, in a color of their own. A bare string names the track.
proteinFeatures.track
string = ''		The trackId of a BED with a column naming each domain's transcript (join), as jbrowse make-protein-features writes.
proteinFeatures.color
FeatureColor		The domains' color, an encoding.color object over the BED rows, by name while it names no field or value. The track's own encoding.color never reaches the domains, nor this one the exons. A dealt family skips the colors that read as the CDS fill, so it can paint differently here than on its own track.
proteinFeatures.join
ProteinFeaturesJoin sub-schema		Which fields pair a domain with its transcript: the domain row's domain field equals the transcript's gene field. gene: 'name' suits a gene track keyed by transcript name, such as a UCSC bigBed.
proteinFeatures.join.domain
string = 'transcript'		domain row field naming the domain's transcript
proteinFeatures.join.gene
string = 'id'		transcript field the domain field equals
Inherited from LinearCanvasBaseDisplay18 slots
filter
FieldPredicate		The features the display draws, a list of FieldPredicate entries a feature must all pass: a field of the feature's own ({ field: "score", gte: 100 }), a jexl: expression that must hold ("jexl:feature.type == 'gene'"), or geneLike, true for every gene, transcript and RNA type, the transcriptTypes and containerTypes, and a top-level CDS.
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; left at the default, the tooltip adds the description line (labels.description) as a second row
callback args: feature
maxFeatureScreenDensity
number = 1		maximum features per pixel before showing a "too many features" message
advanced
legend
Legend		The display's color key, when it has one: the key an encoding.color field derives, or a variant track's consequence-impact / SV-type presets.
showLabels
stringEnum (auto, nameAndDescription, name, description, none) = 'auto'		Label text drawn beside each feature: "auto" adapts to zoom, dropping descriptions at maxDescriptionFeatureDensity and names at maxLabelFeatureDensity; "nameAndDescription", "name", "description", and "none" pin a choice at every zoom. Defaults to auto. Replaces the former showLabels on/off enum + showDescriptions boolean pair
maxLabelFeatureDensity
number = 0.2		In "auto" showLabels mode, hide labels when visible feature density (features/pixel) exceeds this value
advanced
maxDescriptionFeatureDensity
number = 0.1		In "auto" showLabels mode, hide descriptions when visible feature density (features/pixel) exceeds this value. Lower than maxLabelFeatureDensity so descriptions drop before names
advanced
encoding
FeatureEncoding		The channels the features paint through: encoding.color, each feature's main fill.
showOutline
boolean = false		draw an outline around each feature
outlineColor
maybeColor		the outline's color while showOutline draws one; unset takes the theme's
featureHeight
number = 10		height in pixels of the main body of each feature in the normal display mode; compact draws it at 0.6 of this and superCompact at 0.3
callback args: feature
displayMode
stringEnum (normal, compact, superCompact, collapsed) = 'normal'		Feature height preset, normal by default; compact and superCompact shrink the rows, and collapsed packs every feature onto a single row with all labels hidden
facet
SectionFacet		One labelled section of the track per value of a field: "strand", or { field, sort } with the order its sections stack in.
labels
CanvasFeatureLabels sub-schema		The fields a feature's name label and description line read.
labels.name
featureField = 'jexl:get(feature,'name') || get(feature,'id')'		the field each feature's name label reads, such as gene_name, or a jexl: expression over feature; the default reads the name, else the ID, and an empty value draws no name
labels.description
featureField = 
'jexl:get(feature,'note') || get(feature,'description') || get(feature,'function')'
the field each feature's description line reads, such as note, or a jexl: expression over feature; the default reads note, else description, else function, and an empty value draws no description
heightMode
stringEnum (fixed, grow, fit) = 'fit'		Track-sizing strategy — how the track responds when there are more features than fit (shared vocabulary with the alignments display, exposed in the "Track sizing" menu). fit (the default) keeps the track height and gives up descriptions, then isoforms, then names, then squeezes boxes down to 2px, and scrolls only what still overflows; fixed keeps a scrollable fixed height; grow expands the track to show all features. Orthogonal to the per-feature size set by displayMode, which fit never enlarges.
growMaxHeight
number = 800		Ceiling in pixels for the "autogrow track height" sizing mode; a track with more content than this grows to the ceiling and scrolls the rest. Does not apply to the fixed or fit modes
advanced
Inherited from BaseLinearDisplay2 slots
height
number = 100		default height for the track
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
maxDisplayedBpPerPxignored
jexlFiltersmoved into a current slot
color1moved into a current slot
color2moved into a current slot
color3moved into a current slot
outlinemoved into a current slot
maxHeightignored
hideSourceFeaturesignored
impliedUTRsignored
renderermoved into a current slot
colormoved into a current slot
showChevronsmoved into a current slot
showDescriptionsmoved into a current slot