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LinearMarkDisplay

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

Example usage

A BED score column as bars, coloured by strand, with the key on screen, and a per-10 kb count in its place once the view is wider than 100 bp per px:

{
  type: 'FeatureTrack',
  trackId: 'scores',
  name: 'Scores',
  assemblyNames: ['hg38'],
  adapter: { type: 'BedTabixAdapter', uri: 'https://example.com/scores.bed.gz' },
  displays: [
    {
      type: 'LinearMarkDisplay',
      displayId: 'scores-LinearMarkDisplay',
      marks: [
        {
          mark: 'bar',
          encoding: { y: 'score', color: { field: 'strand', scale: 'categorical' } },
          maxBpPerPx: 100,
        },
        {
          mark: 'bar',
          transform: [
            { type: 'bin', step: 10000 },
            { type: 'aggregate', groupby: ['start', 'end'], ops: [{ op: 'count' }] },
          ],
          minBpPerPx: 100,
        },
      ],
    },
  ],
}

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

A grammar of graphics over a feature, alignments or variant track: a list of marks — bars, points, rules, lines, spans, text or links — each with an encoding naming which feature fields feed its channels and a transform list run before it. One fetch per region evaluates every encoding in the worker; the marks draw in order over one score axis.

Config slots

These slots go on a display entry: "displays": [{ "type": "LinearMarkDisplay", ... }], 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
marks.encoding.shape.value
stringEnum = 'circle'		circle, triangle-down or diamond, or a jexl callback over feature returning one, for a point mark whose shape is not a scale.
callback args: feature
marks.encoding.shape.field
featureField = ''		The feature field a categorical scale reads — or a jexl expression over feature, which is slower per feature and so the opt-in.
marks.encoding.shape.scale
maybeStringEnum (none, categorical)		categorical hands a shape from range to each distinct value of field; none draws value. Unset beside a field, it is categorical.
marks.encoding.shape.range
stringEnumArray = []		The shape names a categorical scale hands out, in order. Empty is circle, triangle-down, diamond.
marks.encoding.shape.domain
stringArray = []		The values in legend order, walking range from the first entry; left empty, each value derives its shape from itself, so every region agrees.
marks.encoding.shape.title
maybeString		The heading of the key a categorical scale draws, naming what the shape marks. Unset, the key is titled with field; "" is a key with no title.
marks.encoding.shape.labels
stringArray = []		What the key names each domain value, one each in order; one past the list keeps its own name.
marks.encoding.shape.breaks
stringArray = []		The values the key lists, in this order; empty lists every value the loaded regions met. A value left out still takes its shape.
marks.encoding.shape.missingLabel
maybeString		What the key calls a feature with nothing in field; unset is "(no value)".
marks.encoding.x
featureField = 'start'		The feature field, or jexl expression over feature, giving the mark's left edge in bp.
marks.encoding.x2
MarkLocus		The feature field, or jexl expression, giving the mark's right edge in bp, or for a link its far foot: an object naming the field holding the foot's sequence beside the one holding its position, where a mate may lie on another sequence. Left at end behind a mate step, it is the other end the step found.
marks.encoding.y
featureField = ''		The feature field, or jexl expression over feature, plotted on the score axis. A feature whose value is not a finite number is skipped. Empty reads what the steps before this mark's encode wrote, the way a ggplot2 stat names what its geom plots: a coverage step's depth, or the one summary an aggregate with one op writes. A bar or point with neither draws nothing, and the track's corner notice says so, while a text with neither stands at the apex of a link drawn between its two ends, or in the middle of its band where none is. The scale it is read through is the display's scales.y.
marks.encoding.row
featureField = ''		The feature field, or jexl expression, naming the band the mark stands in, an integer from 0; a feature with nothing there sits on band 0. Empty reads the field the last pileup before this mark's encode wrote, this mark's own, the facet's or the display's, and puts every mark on one band across the whole plot where none packs.
marks.encoding.color
MarkColor		The mark's colour: a field through a categorical or continuous scale, written bare or as an object with the scale's members, or a constant { value }, a CSS colour or a jexl callback returning one. A scale is what the legend describes.
marks.encoding.shape
markShapeSchema		For a point mark: a field through a categorical scale over circle, triangle-down and diamond, written bare or as an object, or a constant { value }, one of those names or a jexl callback returning one. A scale is what the legend describes.
marks.encoding.text
featureField = 'name'		For a text mark: the feature field, or jexl expression over feature, it prints, name unset. A feature with nothing there prints nothing.
marks.encoding.size
MarkSize		The mark's size in px: a number is a point's diameter, a rule's thickness, a line's width or a link's stroke; a field, which a link alone reads, goes through a linear or log scale into a stroke width, range the px at each end of the domain. The track menu's Point size writes every point mark's number.
marks.mark
stringEnum (bar, point, rule, line, span, text, link) = 'bar'		bar stands between origin and y; point is a shape at y over the middle of x to x2; rule is a line across x to x2 at y, encoding.size px thick; line is a stroke through consecutive values, held across each span or run centre to centre as interpolate says, dropping to origin across a gap; span is a band across the whole plot from x to x2; text prints a field over the middle of x to x2, just above y where it names one, at the apex of a link drawn between the same two ends, and in the middle of its band otherwise, and a label that would overlap one already placed to its left is left out; link is a curve from x up and over to x2, which may lie on another sequence, its apex at y where it names one.
marks.interpolate
stringEnum (step, linear) = 'step'		How a line joins its values: step holds each across its span, as the data says; linear runs from one span's centre to the next, smoother where the spans are few. Read by a line alone.
marks.linkShape
stringEnum (dome, arc, line) = 'dome'		How a link mark draws: dome, a half-ellipse whose apex is the pair's half-width clamped to the band, arc, a true semicircle that may leave it, or line, a straight segment between the feet, on the baseline or at the y value. Past three block widths a dome or arc becomes a circle whose legs rise from each foot.
marks.rowProportion
number = 1		The fraction of its row's height a span fills, centred in the row, so below 1 the rows stand apart. Read by a span alone; the track menu's Row height presets write every span's.
marks.encoding
markEncodingSchema		Which feature fields feed the mark's channels. Every channel has a default, so {} draws a bar from start to end with no value.
marks.transform
MarkTransform		Steps over the region's features before this mark encodes them, in order, after the display's own transform, and over each section alone under a facet. A bin then an aggregate grouped by start and end is a density: count per bin, which the mark plots as y unless its encoding names another field.
marks.source
stringEnum (features, density) = 'features'		Where this mark draws from once the byte gate refuses the features. features is off — the mark draws nothing past the budget. density draws the adapter's densityAdapter sidecar in the banner's place, one bar per sidecar bin over this mark's own y axis, and needs no transform: the sidecar has already binned. With no density mark the banner stands.
marks.minBpPerPx
number = 0		The mark draws only when the view is at least this zoomed out, in bp per px. 0 sets no bound. With maxBpPerPx on another mark, one config shows a density zoomed out and the features zoomed in.
marks.maxBpPerPx
number = 0		The mark draws only when the view is zoomed in past this, in bp per px. 0 sets no bound.
marks
markListSchema([])		The marks to draw, in order — a later one paints over an earlier one. Each is a mark and an encoding.
transform
MarkTransform		Steps over the region's features before the facet splits them and before any mark's own, after filter: where a field the facet reads is made, such as a formula lifting a read's tag.
facet
MarkFacet		Labelled sections, one per value of a field, each as tall as its steps pack it: "HP", or { field, domain, transform } with the order the sections stack in and the steps each runs before any mark's, a per-section pileup among them. A chip names each section and hides it. Split after transform and before any mark's own steps.
rows
Rows		One row per value of a field, for bar and point marks: "source" over a multi-BigWig is one xyplot per file. The worker splits the features on the field as it does for facet, and the rows take the tree sidebar, the row labels, clustering and the arrangement dialog, whose order, labels, tree and focus this object holds. Beside a facet, the facet draws; on another field that asks for bands of rows, which are not drawn yet, and a notice says so.
{ rows: 'source' }
{ rows: { field: 'source', domain: ['tumor', 'normal'] } }
rowColor
RowColor		The bar beside each row's label, the marks keeping their own colour: under the default field name, a row's value paired with a colour in domain/range, which the arrangement dialog writes.
scales
ValueScale		The scales the marks are read through, owned by the display rather than by a mark: y alone, and every mark's encoding.y shares it. The same object the wiggle family declares.
origin
number = 0		The value bars grow from. The axis widens to include it whenever a bar mark is drawn.
minWidthPx
number = 1		Narrowest a bar or span is painted, in px, grown off its start edge.
advanced
showLegend
boolean = true		Draw the colour key for every mark whose colour is a scale. Defaults to on.
height
number = 150		default height for the track
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
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
showTree
boolean = true		show the cluster tree beside the rows
showBranchLength
boolean = true		position tree nodes by branch length (dendrogram) rather than evenly by topology (cladogram)
showRowLabels
boolean = true		draw the row value over the left of each row
treeAreaWidth
number = 80		width in px of the tree sidebar, which a drag on its edge also writes
rowHeight
number = 0		per-row height in px under rows, scrolling the rows that do not fit; 0 (the default) fits the rows to the plot instead, dividing it between them
filter
expressionArray = []		jexl: expressions a feature must pass to be drawn