spec.json

{
  "$schema": "https://unpkg.com/@genome-spy/core/dist/schema.json",

  "genome": {
    "name": "hg38"
  },

  "specId": "GenomeSpy paper example",

  "bookmarks": {
    "remote": {
      "url": "tour.json",
      "tour": true
    }
  },

  "description": ["Example Data, Cohort for the GenomeSpy Paper"],

  "spacing": 7,

  "vconcat": [
    {
      "import": { "url": "cytobands.json" }
    },

    {
      "name": "blacklist-tracks",
      "title": "Blacklist tracks",
      "spacing": 3,
      "visible": false,

      "vconcat": [
        { "import": { "url": "hg38-blacklist.v2.json" } },
        { "import": { "url": "decider-cnv-blacklist.json" } }
      ]
    },

    {
      "name": "samples",
      "title": "DECIDER samples",

      "stickySummaries": true,

      "samples": {
        "data": {
          "url": "decider-data/samples.tsv",
          "format": { "type": "tsv" }
        },
        "attributes": {
          "sampleTime": {
            "type": "ordinal",
            "scale": {
              "domain": ["primary", "interval", "relapse"],
              "range": ["#facf5a", "#f95959", "#455d7a"]
            }
          },
          "diagnosis": {
            "type": "nominal"
          },
          "ploidy": {
            "type": "quantitative",
            "scale": {
              "scheme": "yellowgreenblue"
            }
          },
          "purity": {
            "type": "quantitative",
            "scale": {
              "domain": [0, 1],
              "scheme": "yellowgreenblue"
            }
          },
          "sig_HRD": {
            "type": "quantitative",
            "scale": {
              "scheme": "yelloworangered"
            }
          },
          "sig_APOBEC": {
            "type": "quantitative",
            "scale": {
              "scheme": "yelloworangered"
            }
          },
          "mutations": {
            "type": "quantitative",
            "scale": {
              "domain": [0, 60000],
              "scheme": "lightorange"
            }
          },
          "breaks": {
            "type": "quantitative",
            "scale": {
              "scheme": "lightorange"
            },
            "barScale": {},
            "width": 20
          }
        }
      },

      "spec": {
        "title": "Genomic data",

        "resolve": {
          "scale": { "color": "independent", "fill": "independent" }
        },

        "layer": [
          { "import": { "url": "cnv-segments.json" } },
          { "import": { "url": "short-variants.json" } }
        ]
      }
    },

    { "import": { "url": "refSeq-genes.json" } },
    { "import": { "url": "platinum-resistance.json" } }
  ]
}