biosharing-f1-network-vega.json

{
  "$schema": "https://vega.github.io/schema/vega/v3.0.json",
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  "height": 500,
  "padding": 0,
  "autosize": "none",
  "signals": [
    {
      "name": "cx",
      "update": "width / 2"
    },
    {
      "name": "cy",
      "update": "height / 2"
    },
    {
      "name": "nodeRadius",
      "value": 8,
      "bind": {
        "input": "range",
        "min": 1,
        "max": 50,
        "step": 1
      }
    },
    {
      "name": "nodeCharge",
      "value": -30,
      "bind": {
        "input": "range",
        "min": -100,
        "max": 10,
        "step": 1
      }
    },
    {
      "name": "linkDistance",
      "value": 30,
      "bind": {
        "input": "range",
        "min": 5,
        "max": 100,
        "step": 1
      }
    },
    {
      "name": "static",
      "value": true,
      "bind": {
        "input": "checkbox"
      }
    },
    {
      "description": "State variable for active node fix status.",
      "name": "fix",
      "value": 0,
      "on": [
        {
          "events": "symbol:mouseout[!event.buttons], window:mouseup",
          "update": "0"
        },
        {
          "events": "symbol:mouseover",
          "update": "fix || 1"
        },
        {
          "events": "[symbol:mousedown, window:mouseup] > window:mousemove!",
          "update": "2",
          "force": true
        }
      ]
    },
    {
      "description": "Graph node most recently interacted with.",
      "name": "node",
      "value": null,
      "on": [
        {
          "events": "symbol:mouseover",
          "update": "fix === 1 ? item() : node"
        }
      ]
    },
    {
      "description": "Flag to restart Force simulation upon data changes.",
      "name": "restart",
      "value": false,
      "on": [
        {
          "events": {
            "signal": "fix"
          },
          "update": "fix > 1"
        }
      ]
    }
  ],
  "data": [
    {
      "name": "node-data",
      "values": [
        {
          "name": "Reporting guidelines",
          "type": "Reporting guidelines",
          "size": 116,
          "index": 0
        },
        {
          "name": "Models/formats",
          "type": "Models/formats",
          "size": 223,
          "index": 1
        },
        {
          "name": "Terminology artifacts",
          "type": "Terminology artifacts",
          "size": 343,
          "index": 2
        },
        {
          "name": "MIRIAM",
          "type": "Reporting guidelines",
          "size": 5,
          "index": 3
        },
        {
          "name": "MIAME/Env",
          "type": "Reporting guidelines",
          "size": 4,
          "index": 4
        },

        {
          "name": "MIAME",
          "type": "Reporting guidelines",
          "size": 5,
          "index": 5
        },

        {
          "name": "FASTA Sequence Format",
          "type": "Models/formats",
          "size": 252,
          "index": 6
        },
        {
          "name": "PDB Format",
          "type": "Models/formats",
          "size": 58,
          "index": 7
        },
        {
          "name": "GFF3",
          "type": "Models/formats",
          "size": 46,
          "index": 8
        },

         {
          "name": "GO",
          "type": "Terminology artifacts",
          "size": 140,
          "index": 9
        },

        {
          "name": "ChEBI",
          "type": "Terminology artifacts",
          "size": 28,
          "index": 10
        },

         {
          "name": "NCBI Taxonomy",
          "type": "Terminology artifacts",
          "size": 21,
          "index": 11
        }
        
      ],
      "format": {
        "type": "json"
      }
    },
    {
      "name": "link-data",
      "values": [
        {"source": 0, "target": 4},
        {"source": 0, "target": 3},
        {"source": 0, "target": 5},
        {"source": 1, "target": 6},
        {"source": 1, "target": 7},
        {"source": 1, "target": 8},
        {"source": 2, "target": 9},
        {"source": 2, "target": 10},
        {"source": 2, "target": 11}
      ],
      "format": {
        "type": "json"
      }
    }
  ],
  "scales": [
    {
      "name": "color",
      "type": "ordinal",
      "range": {
        "scheme": "category10"
      }
    }
  ],
  "marks": [
    {
      "name": "nodes",
      "type": "symbol",
      "zindex": 1,
      "from": {
        "data": "node-data"
      },
      "on": [
        {
          "trigger": "fix",
          "modify": "node",
          "values": "fix === 1 ? {fx:node.x, fy:node.y} : {fx:x(), fy:y()}"
        },
        {
          "trigger": "!fix",
          "modify": "node",
          "values": "{fx: null, fy: null}"
        }
      ],
      "encode": {
        "enter": {
          "fill": {
            "scale": "color",
            "field": "type"
          },
          "stroke": {
            "value": "white"
          }
        },
        "update": {
          "size": {
            "field":"size"
          },
          "cursor": {
            "value": "pointer"
          }
        }
      },
      "transform": [
        {
          "type": "force",
          "iterations": 300,
          "restart": {
            "signal": "restart"
          },
          "static": {
            "signal": "static"
          },
          "forces": [
            {
              "force": "center",
              "x": {
                "signal": "cx"
              },
              "y": {
                "signal": "cy"
              }
            },
            {
              "force": "collide",
              "radius": {
                "signal": "nodeRadius"
              }
            },
            {
              "force": "nbody",
              "strength": {
                "signal": "nodeCharge"
              }
            },
            {
              "force": "link",
              "links": "link-data",
              "distance": {
                "signal": "linkDistance"
              }
            }
          ]
        }
      ]
    },
    {
      "type": "path",
      "from": {
        "data": "link-data"
      },
      "interactive": false,
      "encode": {
        "update": {
          "stroke": {
            "value": "#ccc"
          },
          "strokeWidth": {
            "value": 0.5
          }
        }
      },
      "transform": [
        {
          "type": "linkpath",
          "shape": "line",
          "sourceX": "datum.source.x",
          "sourceY": "datum.source.y",
          "targetX": "datum.target.x",
          "targetY": "datum.target.y"
        }
      ]
    }
  ]
}