{
  "$schema": "https://cdn.jsdelivr.net/npm/@genome-spy/app/dist/schema.json",

  "description": "Aggregated copy-number-style segments with logR values across a toy genome indexed from 0 to 100.",

  "data": {
    "values": [
      { "sample": "A", "start": 0, "end": 18, "logR": -0.3 },
      { "sample": "A", "start": 18, "end": 42, "logR": 0.0 },
      { "sample": "A", "start": 42, "end": 58, "logR": 0.45 },
      { "sample": "A", "start": 58, "end": 80, "logR": -0.15 },
      { "sample": "A", "start": 80, "end": 100, "logR": 0.25 },

      { "sample": "B", "start": 0, "end": 25, "logR": 0.1 },
      { "sample": "B", "start": 25, "end": 50, "logR": -0.4 },
      { "sample": "B", "start": 50, "end": 67, "logR": 0.35 },
      { "sample": "B", "start": 67, "end": 100, "logR": 0.05 },

      { "sample": "C", "start": 0, "end": 30, "logR": -0.1 },
      { "sample": "C", "start": 30, "end": 55, "logR": 0.2 },
      { "sample": "C", "start": 55, "end": 72, "logR": 0.6 },
      { "sample": "C", "start": 72, "end": 100, "logR": -0.25 },

      { "sample": "D", "start": 0, "end": 20, "logR": 0.05 },
      { "sample": "D", "start": 20, "end": 45, "logR": 0.4 },
      { "sample": "D", "start": 45, "end": 70, "logR": -0.2 },
      { "sample": "D", "start": 70, "end": 100, "logR": 0.15 },

      { "sample": "E", "start": 0, "end": 15, "logR": -0.5 },
      { "sample": "E", "start": 15, "end": 38, "logR": 0.0 },
      { "sample": "E", "start": 38, "end": 62, "logR": 0.3 },
      { "sample": "E", "start": 62, "end": 88, "logR": -0.1 },
      { "sample": "E", "start": 88, "end": 100, "logR": 0.2 },

      { "sample": "F", "start": 0, "end": 22, "logR": 0.2 },
      { "sample": "F", "start": 22, "end": 48, "logR": -0.15 },
      { "sample": "F", "start": 48, "end": 77, "logR": 0.55 },
      { "sample": "F", "start": 77, "end": 100, "logR": -0.35 }
    ]
  },

  "samples": {},

  "spec": {
    "name": "copy-numbers",

    "view": { "fill": "#f4f4f4" },

    "mark": {
      "type": "rect",
      "minOpacity": 1.0,
      "minWidth": 1.0
    },

    "encoding": {
      "sample": { "field": "sample" },
      "x": {
        "field": "start",
        "type": "index",
        "scale": {
          "domain": [0, 100],
          "zoom": true
        },
        "axis": { "grid": true }
      },
      "x2": { "field": "end" },
      "fill": {
        "field": "logR",
        "type": "quantitative",
        "scale": {
          "domain": [-2.5, 0, 2.5],
          "range": ["#0050f8", "#f6f6f6", "#ff3000"],
          "clamp": true
        }
      }
    },

    "aggregateSamples": [
      {
        "name": "logR-summary",
        "view": { "stroke": "lightgray" },

        "title": {
          "text": "logR summary",
          "style": "overlay-title"
        },

        "height": 50,
        "padding": { "bottom": 4 },

        "transform": [
          {
            "type": "filter",
            "expr": "abs(datum.logR) > 0.1"
          },
          {
            "type": "project",
            "fields": ["sample", "start", "end", "logR"]
          }
        ],

        "encoding": {
          "y": {
            "field": "coverage",
            "type": "quantitative",
            "title": null,
            "axis": { "grid": true },
            "scale": { "nice": true }
          }
        },
        "templates": {
          "coverage": {
            "transform": [
              {
                "type": "filter",
                "expr": "logRSign * datum.logR > 0"
              },
              {
                "type": "coverage",
                "start": "start",
                "end": "end",
                "weight": "logR"
              },
              {
                "type": "formula",
                "expr": "datum.coverage / sampleCount",
                "as": "coverage"
              }
            ],
            "encoding": {
              "fill": { "value": { "expr": "color" } }
            },
            "mark": {
              "type": "rect",
              "tooltip": null
            }
          }
        },
        "layer": [
          {
            "name": "amplification",
            "params": { "logRSign": 1, "color": "#e45756" },
            "import": { "template": "coverage" }
          },
          {
            "name": "deletion",
            "params": { "logRSign": -1, "color": "#4c78a8" },
            "import": { "template": "coverage" }
          }
        ]
      }
    ]
  }
}