short-variants.json

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

  "title": "Short variants",
  "name": "mutations",

  "baseUrl": "decider-data/",

  "configurableVisibility": true,

  "params": [
    {
      "name": "minPointDiameter",
      "value": 0,
      "bind": {
        "input": "range",
        "min": 0.0,
        "max": 10,
        "name": "Minimum point diameter",
        "description": "Specifies how small the variants can become when squeezed in the bird's-eye-view."
      }
    },
    {
      "name": "semanticZoomSlider",
      "value": 0.015,
      "bind": {
        "input": "range",
        "min": 0.0,
        "max": 0.15,
        "step": 0.001,
        "name": "Semantic zoom fraction",
        "description": "The portion of mutations to show at each zoom level. Only those with the highest CADD score are shown."
      }
    }
  ],

  "mark": {
    "type": "point",
    "stroke": "black",
    "fillGradientStrength": 0.3,
    "semanticZoomFraction": { "expr": "semanticZoomSlider" }
  },

  "data": {
    "url": ["patient1.tsv", "patient2.tsv", "patient3.tsv"],
    "format": {
      "type": "tsv",
      "parse": {
        "POS": "number",
        "CADD_phred": "number"
      }
    }
  },
  "transform": [
    {
      "type": "regexFold",
      "columnRegex": "^(.*)\\.AF$",
      "asValue": "VAF",
      "asKey": "sample"
    },
    { "type": "formula", "expr": "+datum.VAF", "as": "VAF" },
    { "type": "filter", "expr": "datum.VAF >= 0.02" }
  ],
  "encoding": {
    "sample": { "field": "sample" },
    "x": {
      "chrom": "CHROM",
      "pos": "POS",
      "type": "locus",
      "offset": 1
    },
    "color": {
      "type": "nominal",
      "field": "Func",
      "scale": {
        "domain": [
          "stopgain",
          "stoploss",
          "frameshift_indel",
          "missense",
          "splicing",
          "inframe_indel",
          "synonymous",
          "genic_other",
          "ncRNA",
          "intergenic"
        ],
        "range": [
          "#e31a1c",
          "#ff7f00",
          "#6a3d9a",
          "#1f78b4",
          "#b2df8a",
          "#cab2d6",
          "#33a02c",
          "#a6cee3",
          "#fdbf6f",
          "#c0c0c0"
        ]
      }
    },
    "size": {
      "field": "VAF",
      "type": "quantitative",
      "scale": {
        "domain": [0, 1],

        "range": [
          { "expr": "0" },
          {
            "expr": "clamp(pow(height * 0.64, 2), pow(minPointDiameter, 2), 350)"
          }
        ]
      }
    },
    "shape": {
      "expr": "datum.FILTER == 'PASS'",
      "type": "nominal",
      "scale": {
        "domain": [true, false],
        "range": ["circle", "cross"]
      }
    },
    "semanticScore": {
      "field": "CADD_phred"
    },
    "strokeOpacity": {
      "value": 0.65
    },
    "strokeWidth": {
      "value": 0.8
    }
  }
}