LinearMultiSampleVariantMatrixDisplay

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

Example usage#

Minimal VariantTrack config selecting the matrix display. The displays array form is required here (rather than the object shorthand) because this is a non-default display type — see configuring displays:

{
  type: 'VariantTrack',
  trackId: 'cohort',
  name: 'Cohort variants',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfTabixAdapter',
    uri: 'https://example.com/cohort.vcf.gz',
  },
  displays: [
    {
      type: 'LinearMultiSampleVariantMatrixDisplay',
    },
  ],
}

Preloading sample metadata: point the adapter's samplesTsvLocation at a TSV whose first column is the sample name and whose other columns are per-sample attributes (e.g. population), then colorBy one of those attributes to color the matrix rows on load (same metadata mechanism as the regular LinearMultiSampleVariantDisplay):

{
  type: 'VariantTrack',
  trackId: 'cohort',
  name: 'Cohort variants',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfTabixAdapter',
    uri: 'https://example.com/cohort.vcf.gz',
    samplesTsvLocation: { uri: 'https://example.com/samples.tsv' },
  },
  displays: [
    {
      type: 'LinearMultiSampleVariantMatrixDisplay',
      height: 400,
      colorBy: 'population',
    },
  ],
}

Taller matrix filtering rare variants (MAF < 5 %). Row order, per-row color and group labels come from the adapter's samplesTsvLocation above — the display's own layout holds the arrangement the user then drags into place, so it is session state rather than a config slot:

{
  type: 'VariantTrack',
  trackId: 'cohort',
  name: 'Cohort variants',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfTabixAdapter',
    uri: 'https://example.com/cohort.vcf.gz',
  },
  displays: [
    {
      type: 'LinearMultiSampleVariantMatrixDisplay',
      height: 400,
      minorAlleleFrequencyFilter: 0.05,
    },
  ],
}

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

Related links#

• Adapter: BedpeAdapter
• Adapter: SplitVcfTabixAdapter
• Adapter: StarFusionAdapter
• Adapter: VcfAdapter
• Adapter: VcfTabixAdapter
• State model: runtime API
• Base config: SharedVariantDisplay
• Guide: Custom track and display types
• Guide: Defaults for all tracks
• Guide: LD at a selective sweep (human)
• Guide: Multi-sample variant display
• Guide: Mutation cohort (TCGA)
• Guide: Tracks
• Guide: Variant track

Config slots#

These slots go on a display entry: "displays": [{ "type": "LinearMultiSampleVariantMatrixDisplay", ... }], 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.

'jexl:get(feature,'_mouseOver')||get(feature,'name')||get(feature,'function')||get(feature,'id')'