cytobands.json

{
  "name": "ideogram-track",
  "title": {
    "text": "Chromosome Ideogram",
    "style": "track-title"
  },

  "height": 24,
  "data": { "url": "external-data/cytobands.tsv" },
  "transform": [{ "type": "filter", "expr": "!test(/_/, datum.chrom)" }],
  "encoding": {
    "x": {
      "chrom": "chrom",
      "pos": "chromStart",
      "type": "locus",
      "axis": null
    },
    "x2": { "chrom": "chrom", "pos": "chromEnd" }
  },
  "resolve": {
    "scale": {
      "color": "independent"
    }
  },
  "layer": [
    {
      "title": "Cytoband",
      "mark": "rect",
      "encoding": {
        "color": {
          "field": "gieStain",
          "type": "nominal",
          "scale": {
            "domain": [
              "gneg",
              "gpos25",
              "gpos50",
              "gpos75",
              "gpos100",
              "acen",
              "stalk",
              "gvar"
            ],
            "range": [
              "#f0f0f0",
              "#e0e0e0",
              "#d0d0d0",
              "#c0c0c0",
              "#a0a0a0",
              "#cc4444",
              "#338833",
              "#000000"
            ]
          }
        },
        "squeeze": {
          "expr": "datum.gieStain == 'acen' ? (test(/^p/, datum.name) ? 'p' : 'q') : null",
          "type": "nominal",
          "scale": {
            "domain": ["p", "q"],
            "range": ["right", "left"]
          }
        }
      }
    },
    {
      "mark": {
        "type": "text",
        "align": "center",
        "baseline": "middle",
        "paddingX": 4,
        "tooltip": null
      },
      "encoding": {
        "color": {
          "field": "gieStain",
          "type": "nominal",
          "scale": {
            "domain": [
              "gneg",
              "gpos25",
              "gpos50",
              "gpos75",
              "gpos100",
              "acen",
              "stalk",
              "gvar"
            ],
            "range": [
              "black",
              "black",
              "black",
              "black",
              "black",
              "black",
              "white",
              "white"
            ]
          }
        },
        "text": {
          "field": "name",
          "type": "nominal"
        }
      }
    },
    {
      "transform": [
        {
          "type": "filter",
          "expr": "datum.chromStart == 0 && datum.chrom != 'chr1'"
        }
      ],
      "encoding": {
        "x2": null
      },
      "mark": {
        "type": "rule",
        "color": "#a0a0a0",
        "strokeDash": [3, 3],
        "strokeDashOffset": 2
      }
    }
  ]
}