Personal tools

Cytoscape test2: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(19 intermediate revisions by the same user not shown)
Line 6: Line 6:
         </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 20: 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>


<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>
     
       
         <!-- 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;
Line 41: Line 45:
var target = event.target;
var target = event.target;
 
 
var lurl = "https://fantom5-collaboration.gsc.riken.jp/resource_browser/RB_SearchResults?sq="+target.data["id"];
var lurl = "https://fantom5-collaboration.gsc.riken.jp/resource_browser/RB_SearchResults?sq="+target.data["label"];
//window.location = lurl;
window.location = lurl;
alert(lurl);
//alert(lurl);
}
}
Line 59: Line 63:
var colorMapper = {
var colorMapper = {
attrName: "motif",
attrName: "type",
entries: [ { attrValue: "", value: "#ff9900" } ]
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}" } ]
};
};
Line 71: Line 97:
},
},
nodes: {
nodes: {
tooltipText: "<b>TF: ${id}</b>Motif: ${motif}",
//label: { passthroughMapper: { attrName: "id" } },
shape: "ellipse",
tooltipText: "<b>${type}: ${label}</b>",
shape: { defaultValue: "ellipse", discreteMapper: shapeMapper },
borderWidth: 1,
borderWidth: 1,
borderColor: "#000000",
borderColor: "#000000",
size: 30,
size: 30,
color: "#ff9900",
//color: "#ff9900",
//color: { defaultValue: "#ff9900", discreteMapper: colorMapper },
color: { defaultValue: "#ff9900", discreteMapper: colorMapper },
//opacity: 0.8,
//opacity: 0.8,
opacity: { customMapper: { functionName: "customOpacity" } },
opacity: { customMapper: { functionName: "customOpacity" } },
Line 85: Line 112:
},
},
edges: {
edges: {
width: { passthroughMapper: { attrName: "zscore" } },
width: { defaultValue: 5, passthroughMapper: { attrName: "zscore" } },
label: { passthroughMapper: { attrName: "promoter" } },
label: { passthroughMapper: { attrName: "promoter" } },
tooltipText: "<b>Promoter: ${promoter}</b><br />Z-Score: ${zscore}",
//tooltipText: "<b>Promoter: ${promoter}</b><br />Z-Score: ${zscore}",
color: "#011e59",
tooltipText: { defaultValue: "", discreteMapper: edgeTooltipMapper },
//color: { defaultValue: "#011e59", discreteMapper: edgeColorMapper },
//color: "#011e59",
//targetArrowShape: { defaultValue: "delta", discreteMapper: edgeArrowMapper },
color: { defaultValue: "#011e59", discreteMapper: edgeColorMapper },
targetArrowShape: { defaultValue: "delta", discreteMapper: edgeArrowMapper },
sourceArrowShape: "",
sourceArrowShape: "",
labelGlowOpacity: 0.8,
labelGlowOpacity: 0.8,

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.