refSeq-genes.json

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

  "name": "refseq-track",

  "title": {
    "text": "RefSeq Gene annotation",
    "orient": "none"
  },

  "height": { "step": 23 },

  "data": {
    "url": "external-data/refSeq_genes_scored_compressed.hg38.tsv",
    "format": {
      "parse": {
        "symbol": "string",
        "chrom": "string",
        "start": "integer",
        "length": "integer",
        "strand": "string",
        "score": "integer",
        "exons": "string"
      }
    }
  },

  "transform": [
    {
      "type": "linearizeGenomicCoordinate",
      "chrom": "chrom",
      "pos": "start",
      "as": "_start"
    },
    {
      "type": "formula",
      "expr": "datum._start + datum.length",
      "as": "_end"
    },
    {
      "type": "formula",
      "expr": "datum._start + datum.length / 2",
      "as": "_centroid"
    },
    {
      "type": "collect",
      "sort": { "field": ["_start"] }
    },
    {
      "type": "pileup",
      "start": "_start",
      "end": "_end",
      "as": "_lane",
      "preference": "strand",
      "preferredOrder": ["-", "+"]
    },
    {
      "type": "filter",
      "expr": "datum._lane < 3"
    }
  ],

  "encoding": {
    "y": {
      "field": "_lane",
      "type": "ordinal",
      "scale": {
        "type": "index",
        "align": 0,
        "paddingInner": 0.4,
        "paddingOuter": 0.2,
        "domain": [0, 3],
        "reverse": true,
        "zoom": false
      },
      "axis": null
    }
  },

  "layer": [
    {
      "name": "transcripts",

      "opacity": {
        "unitsPerPixel": [100000, 40000],
        "values": [0, 1]
      },

      "encoding": {
        "color": { "value": "#909090" }
      },

      "layer": [
        {
          "name": "exons",

          "transform": [
            { "type": "project", "fields": ["_lane", "_start", "exons"] },
            { "type": "flattenCompressedExons", "start": "_start" }
          ],

          "mark": {
            "type": "rect",
            "minOpacity": 0.2,
            "minWidth": 0.5,
            "tooltip": null
          },

          "encoding": {
            "x": { "field": "exonStart", "type": "locus" },
            "x2": { "field": "exonEnd" }
          }
        },
        {
          "name": "bodies",

          "title": "Gene annotations",

          "mark": {
            "type": "rule",
            "minLength": 0.5,
            "size": 1,
            "tooltip": null
          },
          "encoding": {
            "x": { "field": "_start", "type": "locus", "axis": null },
            "x2": { "field": "_end" },
            "search": { "field": "symbol" }
          }
        }
      ]
    },
    {
      "name": "symbols",

      "transform": [
        {
          "type": "measureText",
          "fontSize": 11,
          "field": "symbol",
          "as": "_textWidth"
        },
        {
          "type": "filterScoredLabels",
          "lane": "_lane",
          "score": "score",
          "width": "_textWidth",
          "pos": "_centroid",
          "padding": 5
        }
      ],

      "layer": [
        {
          "name": "labels",
          "mark": {
            "type": "text",
            "size": 11,
            "yOffset": 7,
            "tooltip": {
              "handler": "refseqgene"
            }
          },
          "encoding": {
            "x": {
              "field": "_centroid",
              "type": "locus"
            },
            "text": { "field": "symbol" }
          }
        },
        {
          "name": "arrows",
          "opacity": {
            "unitsPerPixel": [100000, 40000],
            "values": [0, 1]
          },
          "mark": {
            "type": "point",
            "yOffset": 7,
            "size": 50,
            "tooltip": null
          },
          "encoding": {
            "x": {
              "field": "_centroid",
              "type": "locus"
            },
            "dx": {
              "expr": "(datum._textWidth / 2 + 5) * (datum.strand == '-' ? -1 : 1)",
              "type": "quantitative",
              "scale": null
            },
            "color": { "value": "black" },
            "shape": {
              "field": "strand",
              "type": "nominal",
              "scale": {
                "domain": ["-", "+"],
                "range": ["triangle-left", "triangle-right"]
              }
            }
          }
        }
      ]
    }
  ]
}