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LinearMarkDisplay

Auto-generated from the config schema in the source. See the config guide for concepts. Provided by the marks plugin. View source.

A grammar-of-graphics display for feature, alignments or variant tracks. It is experimental in v5, and its settings may change. A list of marks — bars, points, rules, lines, rects, 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.

Example usage

A BED score column as bars, colored 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: { type: 'ordinal' } },
          },
          maxBpPerPx: 100,
        },
        {
          mark: 'bar',
          transform: [
            { type: 'bin', step: 10000 },
            { type: 'aggregate', groupby: ['start', 'end'], ops: [{ op: 'count' }] },
          ],
          minBpPerPx: 100,
        },
      ],
    },
  ],
}

Color channels

Setting Page scale.type Preset fields
marks.encoding.color MarkColor ordinal, linear, log, symlog, threshold, identity strand, svType, impact, score
encoding.color MarkColor ordinal, linear, log, symlog, threshold, identity strand, svType, impact, score

Config slots

Display 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.

Slot Description
marks.encoding.shape.value
stringEnum (circle, triangle-down, diamond, square) = 'circle'		 circle, triangle-down, diamond or square, 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 an ordinal scale reads, or a jexl expression over feature, which is slower per feature.
marks.encoding.shape.scale
MarkShapeScale sub-schema		 How the field's values map to shapes, Vega-Lite's scale object.
marks.encoding.shape.scale.type
maybeStringEnum (ordinal)		 ordinal assigns each distinct value of field a shape from range. Unset beside a field, it is ordinal.
marks.encoding.shape.scale.range
stringEnumArray (circle, triangle-down, diamond, square) = []		 The shape names an ordinal scale assigns, in order. When empty, the scale uses circle, triangle-down and diamond. square is used only if listed.
marks.encoding.shape.scale.domain
stringArray = []		 The values in legend order, walking range from the first entry; left empty, each value's shape is computed from the value, so every region agrees.
marks.encoding.shape.scale.names
stringArray = []		 The key's name for each domain value, one each in order; a value past the end of the list shows its name.
marks.encoding.shape.legend
MarkShapeLegend sub-schema		 The key this channel's scale draws.
marks.encoding.shape.legend.title
maybeString		 The heading of the key an ordinal scale draws, naming what the shape marks. Unset, the key is titled with field; "" is a key with no title.
marks.encoding.shape.legend.values
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.legend.missingLabel
maybeString		 The key's name for a feature with nothing in field; unset is "(no value)". Vega-Lite's legend has no such member, so it keeps its JBrowse name.
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. When empty, the field is the one the steps before this mark's encode produce: a coverage step's depth, or the single output of an aggregate with one op. A bar or point with neither draws nothing and the track shows a corner notice, 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 encoding.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 color: a field through an ordinal or continuous scale, written bare or as an object, or a constant { value }, a CSS color or a jexl callback returning one. legend shapes the key the scale draws.
marks.encoding.shape
MarkShape sub-schema		 For a point mark: a field through an ordinal scale over circle, triangle-down and diamond, written bare or as an object, or a constant { value }, one of those names, square, or a jexl callback returning one. legend shapes the key the scale draws.
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		 A point's diameter in px. The track menu's Point size writes every point mark's number. It is a px diameter, not Vega-Lite's area.
marks.encoding.strokeWidth
MarkSize		 A stroked mark's width in px, Vega-Lite's stroke width: a rule's or a line's thickness, or a link's stroke; a field, which a link alone reads, goes through a linear or log scale into a width, scale.range the px at each end of the domain.
marks.mark
MarkDef		 What the mark draws, a MarkDef object or its type alone: bar, point, rule, line, rect, text or link, with the members one type reads, a line's or a link's interpolate, a rect's height and a line's gapBp.
marks.encoding
MarkEncoding sub-schema		 The feature field each of the mark's channels reads. Every channel has a default, so {} draws a bar from start to end with no value.
marks.transform
list of MarkTransform entries		 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.minBpPerPx
number = 0		 The mark draws when the view's bp per px is at least this value. 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
list of Mark entries		 The marks to draw, in order — a later one paints over an earlier one. Each is a mark and an encoding.
transform
list of MarkTransform entries		 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: "tags.HP", or { field, sort, 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. Beside rows, a facet on a row attribute, the group rows.groups writes, stacks the rows in labelled bands instead, each band's rows in their arranged order.
rows
MarkRows		 One row per value of a field: "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, colors, tree and focus this object holds. A row's color, rows.colors pinned on it or rows.color mapped from an attribute, is the bar beside its label, and the color of a mark naming none, or of a mark colored by the rows' own field. A facet on a row attribute, the group rows.groups tags, stacks the rows in bands; a facet on a feature field draws its sections in place of the rows, and the display shows a notice.
{ rows: 'source' }
{ rows: { field: 'source', sort: ['tumor', 'normal'], step: 12 } }
encoding
MarkDisplayEncoding		 The display-level MarkDisplayEncoding, shared by all marks. y is the YChannel that every mark's encoding.y uses, and it names no field because each mark sets its own. color is the default color for any mark whose encoding.color is unset, as a ggplot2 layer inherits the plot's aesthetics. encoding.y.axis is the value axis; the row axis is rows.axis.
{ encoding: { y: { scale: { type: 'log' }, axis: { title: 'depth' } } } }
origin
number = 0		 The value bars grow from. The axis widens to include it whenever a bar mark is drawn.
legend
Legend		 The key for every mark whose color or shape is a scale; show defaults to on.
filter
list of FieldPredicate entries		 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: 5 }) or a jexl: expression that must hold.
height
number = 150		 default height for the track
fetchSizeLimit
number = 1000000		 bytes a region may fetch before the display asks first; an adapter that sets its own limit takes precedence over 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 with no user interaction, such as an embedded or notebook view or a screenshot, where the region is known and should draw 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.

Key On load
maxFeatureScreenDensity ignored
maxDisplayedBpPerPx ignored
mouseover ignored
jexlFilters moved into a current slot
renderer ignored
color ignored