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         <style>
         <style>
             /* The Cytoscape Web container must have its dimensions set. */
             /* The Cytoscape Web container must have its dimensions set. */
             #cytoscapeweb { width: 100%; height: 100%; }
             #cytoscapeweb { width: 100%; height: 100%; }
         </style>
         </style>


         <h1 id="firstHeading" class="firstHeading">FF:10563-108A5</h1>
         <h1 id="firstHeading" class="firstHeading">FF:10717-109I6, TF to Motif to TF network</h1>
 
<p>Mouseover nodes and edges to see attributes.  Motifs are shown in orange, TFs are shown in blue.  Promoter and z-score are attributes of the Motif to TF edges (blue arrow).  TF to Motif edges are shown in orange.</p>
<p>Motifs shown are the top (maximum 30) motifs in the sample.  TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample.  Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).
</p>
 
         <div id="cytoscapeweb" style="width:800px;height:600px">
         <div id="cytoscapeweb" style="width:800px;height:600px">
             Cytoscape Web will replace the contents of this div with your graph.
             Cytoscape Web will replace the contents of this div with your graph.
Line 21: Line 25:
         <script type="text/javascript" src="/resource_browser/rb_js/cytoscapeweb/js/min/cytoscapeweb.min.js"></script>
         <script type="text/javascript" src="/resource_browser/rb_js/cytoscapeweb/js/min/cytoscapeweb.min.js"></script>


     
         <!-- Load data -->
         <!-- Load data -->
<script type="text/javascript">
<script type="text/javascript">
var request = new XMLHttpRequest();
var request = new XMLHttpRequest();
request.open("GET", "https://fantom5-collaboration.gsc.riken.jp/resource_browser/nwfiles/10563-108A5.gml", false);
request.open("GET", "https://fantom5-collaboration.gsc.riken.jp/resource_browser/nwfiles/10717-109I6_2.graphml", false);
request.send(null);
request.send(null);
xml = request.responseText;
xml = request.responseText;
</script>
</script>


<p>TF to TF network. Motif is an attribute of the source TF node.  Promoter is an attribute of the TF to TF edge.</p>
       
         <script type="text/javascript">
         <script type="text/javascript">
            window.onload=function() {
$(function(){
                // id of Cytoscape Web container div
                var div_id = "cytoscapeweb";
var z_min = 0;
               
var z_max = 1;
                // you could also use other formats (e.g. GraphML) or grab the network data via AJAX
var t;
var selected = false;
function graphClick(event) {
var target = event.target;
var lurl = "https://fantom5-collaboration.gsc.riken.jp/resource_browser/RB_SearchResults?sq="+target.data["label"];
window.location = lurl;
//alert(lurl);
}
function graphSelect() {
var edges = vis.selected("edges");
var nodes = vis.selected("nodes");


                //var sif = 'node1 typeA node2 node3 node4 node5\nnode2 typeB node6';
selected = ((edges.length > 0) || (nodes.length > 0));
               
vis.visualStyle(visual_style);
                // initialization options
}
// id of Cytoscape Web container div
var div_id = "cytoscapeweb";
var colorMapper = {
attrName: "type",
entries: [ { attrValue: "motif", value: "#ff9900" },
  { attrValue: "tf", value: "#0099ff" } ]
};
var shapeMapper = {
attrName: "type",
entries: [ { attrValue: "motif", value: "rectangle" },
  { attrValue: "tf", value: "ELLIPSE" } ]
};
var edgeColorMapper = {
attrName: "type",
entries: [ { attrValue: "has_motif", value: "#ff9900" }, { attrValue: "promotes", value: "#0099ff" } ]
};
var edgeArrowMapper = {
attrName: "type",
entries: [ { attrValue: "has_motif", value: "arrow" }, { attrValue: "promotes", value: "delta" } ]
};
var edgeTooltipMapper = {
attrName: "type",
entries: [ { attrValue: "has_motif", value: "" }, { attrValue: "promotes", value: "<b>Promoter: ${promoter}</b><br />Z-Score: ${zscore}" } ]
};
// visual style we will use
var visual_style = {
global: {
backgroundColor: "#ffffff",
opacity: 0.1,
tooltipDelay: 10
},
nodes: {
//label: { passthroughMapper: { attrName: "id" } },
tooltipText: "<b>${type}: ${label}</b>",
shape: { defaultValue: "ellipse", discreteMapper: shapeMapper },
borderWidth: 1,
borderColor: "#000000",
size: 30,
//color: "#ff9900",
color: { defaultValue: "#ff9900", discreteMapper: colorMapper },
//opacity: 0.8,
opacity: { customMapper: { functionName: "customOpacity" } },
selectionOpacity: 0.8,
hoverOpacity: 0.8,
labelHorizontalAnchor: "center"
},
edges: {
width: { defaultValue: 5, passthroughMapper: { attrName: "zscore" } },
label: { passthroughMapper: { attrName: "promoter" } },
//tooltipText: "<b>Promoter: ${promoter}</b><br />Z-Score: ${zscore}",
tooltipText: { defaultValue: "", discreteMapper: edgeTooltipMapper },
//color: "#011e59",
color: { defaultValue: "#011e59", discreteMapper: edgeColorMapper },
targetArrowShape: { defaultValue: "delta", discreteMapper: edgeArrowMapper },
sourceArrowShape: "",
labelGlowOpacity: 0.8,
//opacity: 0.8,
opacity: { customMapper: { functionName: "customOpacity" } },
selectionOpacity: 0.8,
hoverOpacity: 0.8,
labelGlowColor: "#000000"
}
};
// initialization options
                 var options = {
                 var options = {
                     // where you have the Cytoscape Web SWF
                     // where you have the Cytoscape Web SWF
Line 47: Line 136:
                     flashInstallerPath: "/resource_browser/rb_js/cytoscapeweb/swf/playerProductInstall"
                     flashInstallerPath: "/resource_browser/rb_js/cytoscapeweb/swf/playerProductInstall"
                 };
                 };
               
            var vis = new org.cytoscapeweb.Visualization(div_id, options);
vis["customOpacity"] = function (data) {
return (selected) ? 0.3 : 0.6;
};
               
            // callback when Cytoscape Web has finished drawing
vis.ready(function() {
// add a listener for when nodes and edges are clicked
vis.addListener("dblclick", "nodes", graphClick)
.addListener("dblclick", "edges", graphClick)
.addListener("select", "", graphSelect)
.addListener("deselect", "", graphSelect);
});


                // visual options
// draw options
                var visual_style = {
var draw_options = {
                    global: {
// your data goes here
                        backgroundColor: "#ffffff",
network: xml,
opacity: 0.1,
visualStyle: visual_style,
tooltipDelay: 10
nodeTooltipsEnabled: true,
                    },
edgeTooltipsEnabled: true,
                    nodes: {
// hide pan zoom
label: { passthroughMapper: { attrName: "id" } },
panZoomControlVisible: true
tf: { passthroughMapper: { attrName: "id" } },
};
tooltipText: "<b>${id}</b><br />${motif}",
                        shape: "ellipse",
                        borderWidth: 1,
                        borderColor: "#000000",
                        size: 40,
                        color: "#0099ff",
opacity: 0.4,
                        labelHorizontalAnchor: "center"
                    },
                    edges: {
                        width: { passthroughMapper: { attrName: "zscore" } },
label: { passthroughMapper: { attrName: "id" } },
tooltipText: { passthroughMapper: { attrName: "id" } },
tooltipText: "<b>${id}</b><br />${zscore}",
                        color: "#011e59",
targetArrowShape: "delta",
sourceArrowShape: "",
labelGlowOpacity: 0.8,
labelGlowColor: "#000000"
                    }
                };
 
                // draw options
                var draw_options = {
                    // your data goes here
                    network: xml,
    visualStyle: visual_style,
    nodeTooltipsEnabled: true,
    edgeTooltipsEnabled: true,
                    panZoomControlVisible: true
                };
 
                // init and draw
                var vis = new org.cytoscapeweb.Visualization(div_id, options);
 
                // callback when Cytoscape Web has finished drawing
                vis.ready(function() {
                  
                  
                    // add a listener for when nodes and edges are clicked
            vis.draw(draw_options);
                    vis.addListener("dblclick", "nodes", function(event) {
        });
                        handle_click(event);
                    })
                    .addListener("dblclick", "edges", function(event) {
                        handle_click(event);
                    });
                   
                    function handle_click(event) {
                        var target = event.target;
var lurl = "https://fantom5-collaboration.gsc.riken.jp/resource_browser/RB_SearchResults?sq="+target.data["id"];
window.location = lurl;
                    }
                   
                });


                vis.draw(draw_options);
            };
         </script>
         </script>
          
          


</html>
</html>

Latest revision as of 12:57, 8 May 2012

FF:10717-109I6, TF to Motif to TF network

Mouseover nodes and edges to see attributes. Motifs are shown in orange, TFs are shown in blue. Promoter and z-score are attributes of the Motif to TF edges (blue arrow). TF to Motif edges are shown in orange.

Motifs shown are the top (maximum 30) motifs in the sample. TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample. Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).

Cytoscape Web will replace the contents of this div with your graph.

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