{
  "$schema": "https://vega.github.io/schema/vega/v5.json",
  "width": 600,
  "height": 200,
  "padding": 0,

  "signals": [
    {
      "name": "legendWidth",
      "value": -155
    },
    {
      "name": "legendPadding",
      "value": 20
    },
    {
      "name": "axesHeight",
      "value": -40
    },
    {
      "name": "chartWidth",
      "update": "max(10, width + legendWidth - legendPadding)"
    },
    {
      "name": "chartHeight",
      "update": "max(10, height + axesHeight)"
    },
    {
      "name": "chartWidthRange",
      "update": "[0, chartWidth]"
    },
    {
      "name": "chartHeightRange",
      "update": "[0, chartHeight]"
    },
    {
      "name": "clear", "value": true,
      "on": [
        {
          "events": "mouseup[!event.item]",
          "update": "true",
          "force": true
        }
      ]
    },
    {
      "name": "shift", "value": false,
      "on": [
        {
          "events": "@legendSymbol:click, @legendLabel:click",
          "update": "event.shiftKey",
          "force":  true
        }
      ]
    },
    {
      "name": "clicked", "value": null,
      "on": [
        {
          "events": "@legendSymbol:click, @legendLabel:click",
          "update": "{value: datum.value}",
          "force":  true
        }
      ]
    }
  ],

  "data": [
    {
      "name": "rawTimeSpeciesConcentrations",
      "sedmlUri": ["BIOMD0000000002_sim.sedml", "report"],
      "values": [
        {
          "label": "Time (dimensionless)",
          "values": [
            0,
            0.1,
            0.2,
            0.30000000000000004,
            0.4,
            0.5
          ]
        },
        {
          "label": "ACh",
          "values": [
            0.000009999999999999999,
            0.000008428551267842631,
            0.000008224949996315645,
            0.00000814432407384582,
            0.00000811222611072247,
            0.000008099303111743507
          ]
        }
      ]
    },
    {
      "name": "timeSpeciesConcentrations",
      "source": "rawTimeSpeciesConcentrations",
      "transform": [
        {
          "type": "filter",
          "expr": "datum.id == 'data_set_time' || indexof(['data_set_B', 'data_set_BL', 'data_set_ALL', 'data_set_ILL', 'data_set_DLL'], datum.id) >= 0"
        },
        {
          "type": "cross",
          "as": ["Time", "SpeciesLabelValues"],
          "filter": "datum.Time.id == 'data_set_time' && datum.SpeciesLabelValues.id != 'data_set_time'"    
        },
        {
          "type": "formula",
          "expr": "datum.Time.values",
          "as": "Time"
        },
        {
          "type": "formula",
          "expr": "datum.SpeciesLabelValues.label",
          "as": "SpeciesLabel"
        },
        {
          "type": "formula",
          "expr": "datum.SpeciesLabelValues.values",
          "as": "SpeciesConcentration"
        },
        {
          "type": "flatten",
          "fields": ["Time", "SpeciesConcentration"]
        },
        {
          "type": "filter",
          "expr": "datum.Time > 0"
        },
        {
          "type": "formula",
          "expr": "datum.SpeciesConcentration * 1e9",
          "as": "SpeciesConcentration"
        }
      ]
    },
    {
      "name": "selected",
      "on": [
        {"trigger": "clear", "remove": true},
        {"trigger": "!shift", "remove": true},
        {"trigger": "!shift && clicked", "insert": "clicked"},
        {"trigger": "shift && clicked", "toggle": "clicked"}
      ]
    }
  ],

  "scales": [
    {
      "name": "TimeScale",
      "type": "log",
      "range": {"signal": "chartWidthRange"},
      "domain": {"data": "timeSpeciesConcentrations", "field": "Time"}
    },
    {
      "name": "SpeciesConcentrationScale",
      "type": "linear",
      "range": {"signal": "chartHeightRange"},
      "nice": true,
      "zero": false,
      "domain": {
        "data": "timeSpeciesConcentrations", 
        "field": "SpeciesConcentration"
      },
      "reverse": true
    },
    {
      "name": "color",
      "type": "ordinal",
      "range": "category",
      "domain": {"data": "timeSpeciesConcentrations", "field": "SpeciesLabel"}
    }
  ],

  "axes": [
    {
      "orient": "bottom", 
      "offset": {"signal": "axesHeight"},
      "scale": "TimeScale", 
      "title": "Time (dimensionless)"
    },
    {
      "orient": "left", 
      "scale": "SpeciesConcentrationScale",
      "title": "Concentration (nM)"
    }
  ],

  "marks": [
    {
      "type": "group",
      "from": {
        "facet": {
          "name": "series",
          "data": "timeSpeciesConcentrations",
          "groupby": "SpeciesLabel"
        }
      },
      "marks": [
        {
          "type": "line",
          "from": {"data": "series"},
          "encode": {
            "enter": {
              "x": {"scale": "TimeScale", "field": "Time"},
              "y": {"scale": "SpeciesConcentrationScale", "field": "SpeciesConcentration"},
              "stroke": {"scale": "color", "field": "SpeciesLabel"},
              "strokeWidth": {"value": 2},
              "tooltip": {"field": "SpeciesLabel"}
            },
            "update": {
              "strokeOpacity": [                
                {"test": "(!length(data('selected')) || indata('selected', 'value', datum.SpeciesLabel))", "value": 1 },
                {"value": 0.15}
              ]
            },
            "hover": {
              "strokeOpacity": {"value": 0.5}
            }
          }
        }
      ]
    }
  ],

  "legends": [
    {
      "stroke": "color",
      "title": "Species",
      "orient": "right",
      "offset": {"signal": "legendWidth"},
      "encode": {
        "symbols": {
          "name": "legendSymbol",
          "interactive": true,
          "update": {
            "fill": {"value": "transparent"},
            "strokeWidth": {"value": 2},
            "opacity": [
              {"test": "!length(data('selected')) || indata('selected', 'value', datum.value)", "value": 0.7},
              {"value": 0.15}
            ],
            "size": {"value": 64}
          }
        },
        "labels": {
          "name": "legendLabel",
          "interactive": true,
          "update": {
            "opacity": [
              {"test": "!length(data('selected')) || indata('selected', 'value', datum.value)", "value": 1},
              {"value": 0.25}
            ]
          }
        }
      }
    }
  ]
}