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LinearCanvasBaseDisplay

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

base config for canvas-based linear feature displays (pileup-style glyphs)

Config slots

LinearCanvasBaseDisplay 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
maxFeatureScreenDensity
number = 1		maximum features per pixel before showing a "too many features" message
advanced
showLegend
boolean = true		show the display's color key when it has one (the legend slot, or a variant track's consequence-impact / SV-type presets).
showLabels
stringEnum (auto, nameAndDescription, name, description, none) = 'auto'		Which label text is 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
color
FeatureColor		The main fill of each feature: a CSS color or a jexl expression ("goldenrod", "jexl:…"), or { field, domain, range } to paint each value of a field its own range color, with a key.
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
outlineColor
color = ''		outline color for features (empty string = no outline)
featureHeight
number = 10		height in pixels of the main body of each feature
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
Facet		One labelled section of the track per value of a field: "strand", or { field, domain } with the order its sections stack in.
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 (none, below, overlay) = 'none'		subfeature label display mode: none (the default), below or overlay
displayDirectionalChevrons
boolean = true		Display directional chevrons on intron lines to indicate strand direction. Defaults to on
transcriptTypes
stringArray = 
[
    'mRNA',
    'transcript',
    'primary_transcript',
    'V_gene_segment',
    'C_gene_segment',
    'D_gene_segment',
    'J_gene_segment',
  ]
feature types the gene-only view (showOnlyGenes) admits 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 carrying 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
impliedUTRs
boolean = true		imply UTRs from exon/CDS differences on transcript glyphs that carry no explicit UTR subfeatures
hideSourceFeatures
boolean = true		hide the GFF3 source record, the whole-molecule type=region feature NCBI RefSeq emits per sequence (gbkey=Src). It spans the entire chromosome and carries only taxon/strain metadata, so it draws as a bar across every window. Set false to draw it. No effect on files that carry no gbkey attribute
labels.name
string = 'jexl:get(feature,'name') || get(feature,'id')'		the primary name of the feature to show
callback args: feature
labels.description
string = 
'jexl:get(feature,'note') || get(feature,'description') || get(feature,'function')'
the text description to show
callback args: feature
heightMode
stringEnum (fixed, grow, fit) = 'fixed'		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). fixed (the default) keeps a scrollable fixed height, grow expands the track to show all features, fit squeezes features to fill the current height. Orthogonal to the per-feature size set by displayMode. Unifies the former autoHeight (grow) + squeezeToDisplayHeight (fit) settings.
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
densityTier
stringEnum (auto, features, density) = 'auto'		when to draw the features-per-bin density band in place of features: "auto" swaps to it where the region is too large to fetch, "features" never does and keeps the banner, "density" always does. Needs a density source on the adapter (its densityAdapter slot)
advanced
densityTierBpPerPx
number = 0		in "auto" mode, also draw the density band from this many bp per pixel outward, before the region is too large to fetch; 0 leaves the swap to the fetch-size gate alone
advanced
jexlFilters
stringArray = []		default set of jexl filters to apply to a track. note: these do not use the jexl prefix because they have a deferred evaluation system
Inherited from BaseLinearDisplay4 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
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