
// parametrise graph encoding for MDS plot
function createXYSpec(xyData, xyTable, width, height)
{
  var tooltip = makeVegaTooltip(xyData.cols);

  // if an annotation is given, search for a symbol column (case insensitive)
  if (xyData.annoCols != -1) {
    var symbolIndex = xyData.annoCols.map(x => x.toLowerCase()).indexOf("symbol");
    var symbolField = symbolIndex >= 0 ? xyData.annoCols[symbolIndex] : "symbol";
  }

  return {
    "$schema": "https://vega.github.io/schema/vega/v5.json",
    "description": "Testing ground for GlimmaV2",
    "width": xyData.counts == -1 ? (width*0.9) : (width * 0.5),
    "height": height * 0.35,
    "padding": {"left": 0, "top": 0, "right": 0, "bottom": 10},
    "autosize": {"type": "fit", "resize": true},
    "title": {
      "text": xyData.title
    },
    "signals":
      [
        {
          "name": "click", "value": null,
          "on": [ {"events": "mousedown", "update": "[datum, now()]" } ]
        }
      ],
    "data": 
      [
        {
          "name": "source",
          "values": xyTable,
          "transform": [{
            "type": "formula",
            "expr": "datum.x",
            "as": "tooltip"
          }]
        },
        { "name": "selected_points" }
      ],
    "scales": [
      {
        "name": "x",
        "type": "linear",
        "round": true,
        "nice": true,
        "zero": true,
        "domain": { "data": "source", "field": xyData.x },
        "range": "width"
      },
      {
        "name": "y",
        "type": "linear",
        "round": true,
        "nice": true,
        "zero": true,
        "domain": { "data": "source", "field": xyData.y },
        "range": "height"
      },
      {
        "name": "colour_scale",
        "type": "ordinal",
        // co-ordinate w/ domain of status
        "domain": ["downReg", "nonDE", "upReg"],
        "range": xyData.statusColours
      }
    ],
    "legends": [
      {
        "fill": "colour_scale",
        "title": "Status",
        "symbolStrokeColor": "black",
        "symbolStrokeWidth": 1,
        "symbolOpacity": 0.7,
        "symbolType": "circle"
      }
    ],
    "axes" : [
      {
        "scale": "x",
        "grid": true,
        "domain": false,
        "orient": "bottom",
        "tickCount": 5,
        "title": xyData.x
      },
      {
        "scale": "y",
        "grid": true,
        "domain": false,
        "orient": "left",
        "titlePadding": 5,
        "title": xyData.y
      }
    ],
    "marks": [
      {
        "name": "marks",
        "type": "symbol",
        "from": { "data": "source" },
        "encode": {
          "update": {
            "x": { "scale": "x", "field": xyData.x },
            "y": { "scale": "y", "field": xyData.y },
            "shape": "circle",
            "size" : [ {"test": "datum.status == 0", "value": 5}, {"value": 25} ],
            "opacity": {"value": 0.65},
            "fill": { "scale": "colour_scale", "field": "status" },
            "strokeWidth": {"value": 1},
            "stroke": {"value": "transparent"},
            "tooltip": tooltip
          }
        }
      },
      // overlaying selected points
      {
        "name": "selected_marks",
        "type": "symbol",
        "from": { "data": "selected_points" },
        "encode": {
          "update": {
            "x": { "scale": "x", "field": xyData.x },
            "y": { "scale": "y", "field": xyData.y },
            "shape": "circle",
            "size": {"value": 120},
            "fill": { "scale": "colour_scale", "field": "status" },
            "strokeWidth": { "value": 1 },
            "stroke": { "value": "black" },
            "opacity": { "value": 1 },
            "tooltip": tooltip
          }
        }
      },
      // symbol text
      {
        "name": "selected_text",
        "type": "text",
        "from": { "data": "selected_points" },
        "encode": {
          "update": {
            "x": { "scale": "x", "field": xyData.x },
            "y": { "scale": "y", "field": xyData.y, "offset": -10 },
            "fill": { "value": "black" },
            "fontWeight": {"value": "bold"},
            "opacity": { "value": 1 },
            "text": {"field": xyData.annoCols == -1 ? "symbol" : symbolField },
            "fontSize": {"value": 12}
          }
        }
      }
    ]
  };
}