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LinearVariantMatrixDisplay

Note: this document is automatically generated from configuration objects in our source code. See Config guide for more info

Also note: this document represents the config API for the current released version of jbrowse. If you are not using the current version, please cross reference the markdown files in our repo of the checked out git tag

Source code

GitHub page

Docs​

LinearVariantMatrixDisplay - Slots​

slot: renderer​

MultiLinearVariantMatrixRenderer

renderer: configSchema

slot: height​

height: {
        type: 'number',
        defaultValue: 250,
      }

slot: showReferenceAlleles​

When true, reference alleles are drawn/colored. When false, the background is solid grey and only ALT alleles are colored on top

showReferenceAlleles: {
        type: 'boolean',
        defaultValue: false,
      }

slot: showSidebarLabels​

showSidebarLabels: {
        type: 'boolean',
        defaultValue: true,
      }

slot: showTree​

showTree: {
        type: 'boolean',
        defaultValue: true,
      }

slot: renderingMode​

The rendering mode: 'alleleCount' shows dosage (darker color for homozygous), 'phased' splits samples into haplotype rows

renderingMode: {
        type: 'stringEnum',
        model: types.enumeration('RenderingMode', ['alleleCount', 'phased']),
        defaultValue: 'alleleCount',
      }

slot: minorAlleleFrequencyFilter​

Filter variants by minor allele frequency (0-1). Variants with MAF below this threshold will be hidden

minorAlleleFrequencyFilter: {
        type: 'number',
        defaultValue: 0,
      }

slot: colorBy​

Automatically color samples by this metadata attribute when the track loads. The attribute must be present in the sample metadata TSV file (configured via samplesTsvLocation on the adapter). Leave empty to disable auto-coloring.

colorBy: {
        type: 'string',
        defaultValue: '',
      }

LinearVariantMatrixDisplay - Derives from​

baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager)