# Hi-C track

**TL;DR:** a `HicTrack` with a `HicAdapter` needs only the `.hic` file location.
Loop and interaction calls (BEDPE) are a separate `VariantTrack` drawn with a
`LinearPairedArcDisplay`.

```json addtrack
{
  "type": "HicTrack",
  "trackId": "hic",
  "name": "Hi-C Track",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "HicAdapter",
    "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic"
  }
}
```

`HicAdapter` takes the `.hic` file through the `uri` shorthand; the longhand
slot is `hicLocation` ([](https://jbrowse.org/jb2/docs/config/hicadapter)).

## Display settings

The coloring and its controls are [](https://jbrowse.org/jb2/docs/config/linearhicdisplay) slots, and
[adjusting the color scale](https://jbrowse.org/jb2/docs/user_guides/hic_track#adjusting-the-color-scale)
shows what each does to the picture:

```json addtrack
{
  "type": "HicTrack",
  "trackId": "hic_kr",
  "name": "Hi-C (KR, log scale)",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "HicAdapter",
    "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic"
  },
  "displayDefaults": {
    "selectedNormalization": "KR",
    "useLogScale": true,
    "colorScheme": "viridis",
    "showLegend": true
  }
}
```

- **[`selectedNormalization`](https://jbrowse.org/jb2/docs/config/linearhicdisplay/#slot-selectednormalization)**
  names the matrix-balancing scheme (`KR`, `SCALE`, `VC`, `VC_SQRT`, `NONE`).
  JBrowse resolves it against what the file provides, so a scheme the file lacks
  falls back with no error
  ([normalization](https://jbrowse.org/jb2/docs/user_guides/hic_track#normalization))
- **[`resolutionBias`](https://jbrowse.org/jb2/docs/config/linearhicdisplay/#slot-resolutionbias)** is
  a signed offset from the zoom-derived binsize, so the choice survives zooming:
  negative is finer, positive coarser

## Loops and interactions as arcs

BEDPE loop calls load as a `VariantTrack` with a `LinearPairedArcDisplay`.
`color` is evaluated per feature and `lineWidth` is the arc stroke in pixels.
This draws only the high-scoring calls, in dark red, as thin arcs:

```json addtrack
{
  "type": "VariantTrack",
  "trackId": "hic_loops",
  "name": "Hi-C loops",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedpeAdapter",
    "uri": "https://example.com/loops.bedpe.gz"
  },
  "displays": [
    {
      "type": "LinearPairedArcDisplay",
      "color": "jexl:feature.score>=500?'#8b1a1a':'rgba(0,0,0,0)'",
      "lineWidth": 1
    }
  ]
}
```

## Compartments and subcompartments

The compartment eigenvector is a BigWig, drawn as a
[quantitative track](https://jbrowse.org/jb2/docs/config_guides/quantitative_track) in two colors
around zero. Pin [`minScore`](https://jbrowse.org/jb2/docs/config/linearwiggledisplay/#slot-minscore)
and [`maxScore`](https://jbrowse.org/jb2/docs/config/linearwiggledisplay/#slot-maxscore) when two of
these tracks are read against each other, so neither autoscales to its own
extremes; the
[user guide](https://jbrowse.org/jb2/docs/user_guides/hic_track#compartments-and-subcompartments)
covers the sign check that goes with it:

```json addtrack
{
  "type": "QuantitativeTrack",
  "trackId": "hic_compartments",
  "name": "Compartment eigenvector",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig"
  },
  "displayDefaults": {
    "minScore": -0.03,
    "maxScore": 0.03
  }
}
```

Subcompartments are a BED whose color column carries the class color. ENCODE's
copies are not tabix-indexed, so the plain
[`BedAdapter`](https://jbrowse.org/jb2/docs/config/bedadapter) reads the whole file:

```json addtrack
{
  "type": "FeatureTrack",
  "trackId": "hic_subcompartments",
  "name": "Subcompartments",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2022/08/26/7165fc3e-f186-4fba-be87-f4ea600404b0/ENCFF247IAA.bed.gz",
    "columnNames": [
      "chrom",
      "chromStart",
      "chromEnd",
      "name",
      "score",
      "strand",
      "thickStart",
      "thickEnd",
      "itemRgb",
      "numAltClusterings",
      "altClusterNum",
      "altClusterAssignment"
    ]
  }
}
```

[`columnNames`](https://jbrowse.org/jb2/docs/config/bedadapter/#slot-columnnames) does two jobs here,
and neither failure it prevents raises an error:

- **The file's last three columns are not BED12's block fields**, so the
  positional layout takes the cluster count for a `blockCount` and grows every
  feature a row of nonexistent subfeatures
- **Naming column nine `itemRgb`** is what paints the classes their own colors.
  The file's header spells it `itemRGB`, which JBrowse does not look for, and a
  second comment line follows the column line, so the parser takes that last
  line as the definition and finds no tab-separated fields in it

## See also

- [](https://jbrowse.org/jb2/docs/user_guides/hic_track)
- [LinearPairedArcDisplay config schema](https://jbrowse.org/jb2/docs/config/linearpairedarcdisplay)
- [](https://jbrowse.org/jb2/docs/tutorials/hic_structural_variants)