LinearHicDisplay

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the hic plugin. View source.

Draws a HicTrack's contact matrix as a triangular heatmap in the linear genome view, at a bin size that follows the zoom.

Example usage#

A log color scale, one binsize coarser than the zoom picks, through the displayDefaults shorthand. See the Hi-C track guide for the rest:

{
  type: 'HicTrack',
  trackId: 'hic',
  name: 'Hi-C',
  assemblyNames: ['hg38'],
  adapter: { type: 'HicAdapter', uri: 'https://example.com/contacts.hic' },
  displayDefaults: {
    encoding: { color: { scale: { type: 'symlog' } } },
    data: { resolution: -1 },
  },
}

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
• User guide: Hi-C track
• Config guide: Hi-C track
• Config guide: Tracks
• Developer guide: Custom track and display types

Config slots#

Display 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.

Retired keys#

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.