Skip to main content

Hi-C track

A HicTrack with a HicAdapter needs only the .hic file location. Loop and interaction calls (BEDPE) are a separate VariantTrack drawn as link marks on a LinearMarkDisplay.

Goes in the tracks array of config.json. See Tracks.

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

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "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 (HicAdapter).

Display settings

The coloring and its controls are LinearHicDisplay slots, and adjusting the color scale shows what each does to the picture:

Goes in the tracks array of config.json. See Tracks.

{
  "trackId": "hic_kr",
  "name": "Hi-C (KR, log scale)",
  "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic",
  "assemblyNames": ["hg19"],
  "displayDefaults": {
    "selectedNormalization": "KR",
    "color": { "scale": "log", "scheme": "viridis" },
    "showLegend": true
  }
}
jbrowse add-track https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic \
  --trackId hic_kr \
  --name "Hi-C (KR, log scale)" \
  --assemblyNames hg19 \
  --displayDefaults '{"selectedNormalization":"KR","color":{"scale":"log","scheme":"viridis"},"showLegend":true}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "trackId": "hic_kr",
  "name": "Hi-C (KR, log scale)",
  "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic",
  "assemblyNames": ["hg19"],
  "displayDefaults": {
    "selectedNormalization": "KR",
    "color": { "scale": "log", "scheme": "viridis" },
    "showLegend": true
  }
}
  • 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)
  • resolutionBias is a signed offset from the zoom-derived binsize, so the choice survives zooming: negative is finer, positive coarser
  • color.domainMax pins the count the color scale saturates at. Unset, it follows the loaded counts, so two tracks given the same number share one scale

Loops and interactions as arcs

BEDPE loop calls load as a VariantTrack with a mark display drawing one link per call: a mate step reads each record's other end, x2 names the fields holding it, size is the stroke in pixels and color the stroke colour. A filter step keeps the high-scoring calls, drawn here in dark red as thin arcs:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "VariantTrack",
  "trackId": "hic_loops",
  "name": "Hi-C loops",
  "uri": "https://example.com/loops.bedpe.gz",
  "assemblyNames": ["hg38"],
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "link",
          "encoding": { "color": { "value": "#8b1a1a" }, "size": 1 },
          "transform": [
            { "type": "mate" },
            { "type": "filter", "expr": "jexl:get(feature,'score')>=500" }
          ]
        }
      ]
    }
  ]
}
jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "hic_loops",
  "name": "Hi-C loops",
  "uri": "https://example.com/loops.bedpe.gz",
  "assemblyNames": ["hg38"],
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "link",
          "encoding": { "color": { "value": "#8b1a1a" }, "size": 1 },
          "transform": [
            { "type": "mate" },
            { "type": "filter", "expr": "jexl:get(feature,'\''score'\'')>=500" }
          ]
        }
      ]
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "VariantTrack",
  "trackId": "hic_loops",
  "name": "Hi-C loops",
  "uri": "https://example.com/loops.bedpe.gz",
  "assemblyNames": ["hg38"],
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "link",
          "encoding": { "color": { "value": "#8b1a1a" }, "size": 1 },
          "transform": [
            { "type": "mate" },
            { "type": "filter", "expr": "jexl:get(feature,'score')>=500" }
          ]
        }
      ]
    }
  ]
}

A size bound to a field strokes each loop by its score instead, through a linear or log scale into a range of pixels: Mark display §"Links".

Compartments and subcompartments

The compartment eigenvector is a BigWig, drawn as a quantitative track in two colors around zero. Pin scales.y.domainMin and domainMax when two of these tracks are read against each other, so neither autoscales to its own extremes; the user guide covers the sign check that goes with it:

Goes in the tracks array of config.json. See Tracks.

{
  "trackId": "hic_compartments",
  "name": "Compartment eigenvector",
  "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig",
  "assemblyNames": ["hg38"],
  "displayDefaults": {
    "scales": { "y": { "domainMin": -0.03, "domainMax": 0.03 } }
  }
}
jbrowse add-track https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig \
  --trackId hic_compartments \
  --name "Compartment eigenvector" \
  --assemblyNames hg38 \
  --displayDefaults '{"scales":{"y":{"domainMin":-0.03,"domainMax":0.03}}}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "trackId": "hic_compartments",
  "name": "Compartment eigenvector",
  "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig",
  "assemblyNames": ["hg38"],
  "displayDefaults": {
    "scales": { "y": { "domainMin": -0.03, "domainMax": 0.03 } }
  }
}

Subcompartments are a BED whose color column holds the class color. ENCODE's copies are not tabix-indexed, so the plain BedAdapter reads the whole file:

Goes in the tracks array of config.json. See Tracks.

{
  "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"
    ]
  }
}
jbrowse add-track-json '{
  "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"
    ]
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "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 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 paints the classes in 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