LinearHicDisplay

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

Example usage#

A minimal HicTrack config. See the Hi-C track guide for all options:

{
  type: 'HicTrack',
  trackId: 'hic',
  name: 'Hi-C',
  assemblyNames: ['hg38'],
  adapter: { type: 'HicAdapter', uri: 'https://example.com/contacts.hic' },
}

With log scale and a coarser resolution (resolutionBias nudges the auto-picked binsize; negative = finer, positive = coarser). The displayDefaults object shorthand applies settings to whichever display uses them — equivalent to a full displays: [{ type, displayId, ... }] array. See configuring displays:

{
  type: 'HicTrack',
  trackId: 'hic',
  name: 'Hi-C',
  assemblyNames: ['hg38'],
  adapter: { type: 'HicAdapter', uri: 'https://example.com/contacts.hic' },
  displayDefaults: { useLogScale: true, resolutionBias: 1 },
}

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

Overview#

LinearHicDisplay - Identifier#

Every LinearHicDisplay has a unique displayId, a required top-level field that identifies it (not one of the config slots below).

Related links#

• Adapter: HicAdapter
• State model: runtime API
• Guide: Custom track and display types
• Guide: Defaults for all tracks
• Config guide: Hi-C track
• User guide: Hi-C track
• Guide: Structural variants from Hi-C
• Guide: Tracks

Config slots#

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