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SharedLDDisplay

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​

extends

SharedLDDisplay - Slots​

slot: minorAlleleFrequencyFilter​

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

minorAlleleFrequencyFilter: {
        type: 'number',
        defaultValue: 0.1,
      }

slot: lengthCutoffFilter​

Maximum length of variants to include (in bp)

lengthCutoffFilter: {
        type: 'number',
        defaultValue: Number.MAX_SAFE_INTEGER,
      }

slot: lineZoneHeight​

Height of the zone for connecting lines at the top

lineZoneHeight: {
        type: 'number',
        defaultValue: 100,
      }

slot: ldMetric​

LD metric to compute: 'r2' (squared correlation) or 'dprime' (normalized D)

ldMetric: {
        type: 'stringEnum',
        model: types.enumeration('LDMetric', ['r2', 'dprime']),
        defaultValue: 'r2',
      }

slot: colorScheme​

Color scheme for the LD heatmap

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

slot: showLegend​

Whether to show the legend

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

slot: showLDTriangle​

Whether to show the LD triangle heatmap

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

slot: showRecombination​

Whether to show the recombination rate track

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

slot: recombinationZoneHeight​

Height of the recombination track zone at the top

recombinationZoneHeight: {
        type: 'number',
        defaultValue: 50,
      }

slot: fitToHeight​

When true, squash the LD triangle to fit the display height

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

slot: hweFilterThreshold​

HWE filter p-value threshold (variants with HWE p < this are excluded). Set to 0 to disable HWE filtering

hweFilterThreshold: {
        type: 'number',
        defaultValue: 0.001,
      }

slot: showVerticalGuides​

Whether to show vertical guides at the connected genome positions on hover

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

slot: showLabels​

Whether to show variant labels above the tick marks

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

slot: tickHeight​

Height of the vertical tick marks at the genomic position

tickHeight: {
        type: 'number',
        defaultValue: 6,
      }

slot: useGenomicPositions​

When true, draw cells sized according to genomic distance between SNPs rather than uniform squares

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

SharedLDDisplay - Derives from​

baseConfiguration: baseLinearDisplayConfigSchema