BioGraphia/test.html at main · LeiLiLab/BioGraphia · GitHub

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<html>
    <head>
        <meta charset="utf-8">

            <script src="lib/bindings/utils.js"></script>
            <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/vis-network/9.1.2/dist/dist/vis-network.min.css" integrity="sha512-WgxfT5LWjfszlPHXRmBWHkV2eceiWTOBvrKCNbdgDYTHrT2AeLCGbF4sZlZw3UMN3WtL0tGUoIAKsu8mllg/XA==" crossorigin="anonymous" referrerpolicy="no-referrer" />
            <script src="https://cdnjs.cloudflare.com/ajax/libs/vis-network/9.1.2/dist/vis-network.min.js" integrity="sha512-LnvoEWDFrqGHlHmDD2101OrLcbsfkrzoSpvtSQtxK3RMnRV0eOkhhBN2dXHKRrUU8p2DGRTk35n4O8nWSVe1mQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>


<center>
<h1></h1>
</center>

<!-- <link rel="stylesheet" href="../node_modules/vis/dist/vis.min.css" type="text/css" />
<script type="text/javascript" src="../node_modules/vis/dist/vis.js"> </script>-->
        <link
          href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/css/bootstrap.min.css"
          rel="stylesheet"
          integrity="sha384-eOJMYsd53ii+scO/bJGFsiCZc+5NDVN2yr8+0RDqr0Ql0h+rP48ckxlpbzKgwra6"
          crossorigin="anonymous"
        />
        <script
          src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/js/bootstrap.bundle.min.js"
          integrity="sha384-JEW9xMcG8R+pH31jmWH6WWP0WintQrMb4s7ZOdauHnUtxwoG2vI5DkLtS3qm9Ekf"
          crossorigin="anonymous"
        ></script>


        <center>
          <h1></h1>
        </center>
        <style type="text/css">

             #mynetwork {
                 width: 1400px;
                 height: 800px;
                 background-color: #ffffff;
                 border: 1px solid lightgray;
                 position: relative;
                 float: left;
             }


        </style>
    </head>


    <body>
        <div class="card" style="width: 100%">


            <div id="mynetwork" class="card-body"></div>
        </div>


        <script type="text/javascript">

              // initialize global variables.
              var edges;
              var nodes;
              var allNodes;
              var allEdges;
              var nodeColors;
              var originalNodes;
              var network;
              var container;
              var options, data;
              var filter = {
                  item : '',
                  property : '',
                  value : []
              };


              // This method is responsible for drawing the graph, returns the drawn network
              function drawGraph() {
                  var container = document.getElementById('mynetwork');


                  // parsing and collecting nodes and edges from the python
                  nodes = new vis.DataSet([{"color": "#1f78b4", "font": {"size": 16}, "id": "YTHDF2", "label": "YTHDF2", "shape": "dot", "size": 40}, {"color": "#1f78b4", "font": {"size": 16}, "id": "m6A", "label": "m6A", "shape": "dot", "size": 40}, {"color": "#1f78b4", "font": {"size": 16}, "id": "CCNA", "label": "CCNA", "shape": "dot", "size": 40}, {"color": "#1f78b4", "font": {"size": 16}, "id": "CDK2", "label": "CDK2", "shape": "dot", "size": 40}, {"color": "#1f78b4", "font": {"size": 16}, "id": "FTO", "label": "FTO", "shape": "dot", "size": 40}, {"color": "#1f78b4", "font": {"size": 16}, "id": "MCE", "label": "MCE", "shape": "dot", "size": 40}, {"color": "#1f78b4", "font": {"size": 16}, "id": "adipogenesis", "label": "adipogenesis", "shape": "dot", "size": 40}, {"color": "#1f78b4", "font": {"size": 16}, "id": "EGCG", "label": "EGCG", "shape": "dot", "size": 40}, {"color": "#1f78b4", "fixed": {"x": true, "y": true}, "font": {"color": "#1f78b4", "size": 14}, "id": "recognize_YTHDF2_m6A", "label": "recognize", "physics": false, "shape": "text", "size": 1}]);
                  edges = new vis.DataSet([{"arrows": "to", "color": "#1f78b4", "from": "YTHDF2", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "Interestingly, EGCG increased the expression of YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), which recognized and decayed methylated mRNAs, resulting in decreased protein levels of CCNA2 and CDK2.", "to": "m6A", "width": 2}, {"arrows": "to", "color": "#1f78b4", "from": "YTHDF2", "hidden": true, "length": 100, "physics": true, "smooth": false, "to": "recognize_YTHDF2_m6A", "width": 0.1}, {"arrows": "to", "color": "#1f78b4", "from": "recognize_YTHDF2_m6A", "hidden": true, "length": 100, "physics": true, "smooth": false, "to": "m6A", "width": 0.1}, {"arrows": "to", "color": "#ff4444", "dashes": true, "font": {"size": 14}, "from": "recognize_YTHDF2_m6A", "label": "downregulate", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "downregulate", "to": "CCNA", "width": 2}, {"arrows": "to", "color": "#ff4444", "dashes": true, "font": {"size": 14}, "from": "recognize_YTHDF2_m6A", "label": "downregulate", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "downregulate", "to": "CDK2", "width": 2}, {"arrows": "to", "color": "#1f78b4", "font": {"size": 14}, "from": "EGCG", "label": "upregulate", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "Interestingly, EGCG increased the expression of YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), which recognized and decayed methylated mRNAs, resulting in decreased protein levels of CCNA2 and CDK2.", "to": "YTHDF2", "width": 2}, {"arrows": "to", "color": "#1f78b4", "font": {"size": 14}, "from": "EGCG", "label": "downregulate", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "Exposing 3T3-L1 cells to EGCG reduced the expression of fat mass and obesity-associated (FTO) protein, an m6A demethylase, which led to increased overall levels of RNA m6A methylation.", "to": "FTO", "width": 2}, {"arrows": "to", "color": "#1f78b4", "font": {"size": 14}, "from": "FTO", "label": "decrease", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "Exposing 3T3-L1 cells to EGCG reduced the expression of fat mass and obesity-associated (FTO) protein, an m6A demethylase, which led to increased overall levels of RNA m6A methylation.", "to": "m6A", "width": 2}, {"arrows": "to", "color": "#1f78b4", "font": {"size": 14}, "from": "CCNA", "label": "associated with", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "Cyclin A2 (CCNA2) and cyclin dependent kinase 2 (CDK2) play vital roles in MCE.", "to": "MCE", "width": 2}, {"arrows": "to", "color": "#1f78b4", "font": {"size": 14}, "from": "CDK2", "label": "associated with", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "Cyclin A2 (CCNA2) and cyclin dependent kinase 2 (CDK2) play vital roles in MCE.", "to": "MCE", "width": 2}, {"arrows": "to", "color": "#1f78b4", "font": {"size": 14}, "from": "MCE", "label": "associated with", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "Here we showed that EGCG inhibited adipogenesis by blocking the mitotic clonal expansion (MCE) at the early stage of adipocyte differentiation.", "to": "adipogenesis", "width": 2}, {"arrows": "to", "color": "#1f78b4", "font": {"size": 14}, "from": "EGCG", "label": "inhibit", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "Here we showed that EGCG inhibited adipogenesis by blocking the mitotic clonal expansion (MCE) at the early stage of adipocyte differentiation.", "to": "MCE", "width": 2}, {"arrows": "to", "color": "#1f78b4", "font": {"size": 14}, "from": "EGCG", "label": "inhibit", "smooth": {"roundness": 0.2, "type": "continuous"}, "title": "Here we showed that EGCG inhibited adipogenesis by blocking the mitotic clonal expansion (MCE) at the early stage of adipocyte differentiation.", "to": "adipogenesis", "width": 2}]);

                  nodeColors = {};
                  allNodes = nodes.get({ returnType: "Object" });
                  for (nodeId in allNodes) {
                    nodeColors[nodeId] = allNodes[nodeId].color;
                  }
                  allEdges = edges.get({ returnType: "Object" });
                  // adding nodes and edges to the graph
                  data = {nodes: nodes, edges: edges};

                  var options = {"physics": {"enabled": true, "barnesHut": {"gravitationalConstant": -20000, "centralGravity": 0.1, "springLength": 150, "springConstant": 0.08, "damping": 0.09, "avoidOverlap": 0.5}, "minVelocity": 0.75, "maxVelocity": 50}, "nodes": {"font": {"size": 16, "face": "arial"}, "borderWidth": 2, "shape": "box", "fixed": false}, "edges": {"font": {"size": 14, "align": "middle"}, "smooth": {"enabled": true, "type": "continuous", "roundness": 0.2}, "arrows": {"to": {"enabled": true, "scaleFactor": 1}}}, "layout": {"randomSeed": 42, "improvedLayout": true, "hierarchical": {"enabled": false}}, "interaction": {"navigationButtons": true, "hover": true, "multiselect": true}};


                  network = new vis.Network(container, data, options);


                  return network;

              }
              drawGraph();
        </script>
    </body>
</html>