Cytoscape test4: Difference between revisions
From FANTOM5_SSTAR
(Created page with "4th cytoscape test page") |
No edit summary |
||
| Line 1: | Line 1: | ||
<html> | |||
<style> | |||
/* The Cytoscape Web container must have its dimensions set. */ | |||
#cytoscapeweb { width: 50%; height: 100%; float: left; } | |||
</style> | |||
<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;"> | |||
Cytoscape Web will replace the contents of this div with your graph. | |||
</div> | |||
<div id="style_panel"> | |||
<h3>Style</h3> | |||
Layout: <select id="cyto_layout"> | |||
<option value="Preset">Preset</option> | |||
<option value="ForceDirected">Force Directed</option> | |||
<option value="Circle">Circle</option> | |||
<option value="Radial">Radial</option> | |||
<option value="Tree">Tree</option> | |||
</select><a href="#" id="cyto_recalc">(recalculate)</a> | |||
</div> | |||
<div id="filter_panel"> | |||
<h3>Filter</h3> | |||
<table> | |||
<tr><th>Z-Score filter:</th><tr> | |||
<tr><td><span id="cyto_zscore_min">0.00</span> </td><td> <div id="slider1" class="sliderbar"></div> </td><td> <span id="cyto_zscore_max">0.00</span></td></tr> | |||
<tr><td></td><td><input type="text" id="cyto_zscore_filter_min" value="0" style="float: left;"/> <input type="text" id="cyto_zscore_filter_max" value="100" style="float: right;"/></td><td></td></tr> | |||
</table> | |||
Show edges: <input type="checkbox" id="cyto_edges_binds_to" checked>TF->MOTIF</input> <input type="checkbox" id="cyto_edges_promotes" checked>TF->MOTIF</input> | |||
<br />Show nodes: <input type="checkbox" id="cyto_nodes_tf_src" checked>Source TF</input> <input type="checkbox" id="cyto_nodes_tf" checked>Target TF</input> <input type="checkbox" id="cyto_nodes_motif" checked>MOTIF</input> | |||
</div> | |||
<p /><div id="properties_panel" style="font-size: x-small; overflow-y:scroll; height: 300px;"> | |||
<div> | |||
<table id="nodes_list" border="1" width="100%" class="wikitable"> | |||
<tr><th>Node</th><th>Type</th></tr> | |||
</table> | |||
</div> | |||
<div> | |||
<table id="edges_list" border="1" width="100%" class="wikitable"> | |||
<tr><th>Source TF</th><th>Target TF</th><th>Promoter</th><th>Z-Score</th></tr> | |||
</table> | |||
</div> | |||
</div> | |||
<script src="/resource_browser/nwfiles/jquery.nouislider.min.js"></script> | |||
<link href="/resource_browser/nwfiles/nouislider.css" rel="stylesheet"> | |||
<!-- JSON support for IE (needed to use JS API) --> | |||
<script type="text/javascript" src="/resource_browser/rb_js/cytoscapeweb/js/min/json2.min.js"></script> | |||
<!-- Flash embedding utility (needed to embed Cytoscape Web) --> | |||
<script type="text/javascript" src="/resource_browser/rb_js/cytoscapeweb/js/min/AC_OETags.min.js"></script> | |||
<!-- Cytoscape Web JS API (needed to reference org.cytoscapeweb.Visualization) --> | |||
<script type="text/javascript" src="/resource_browser/rb_js/cytoscapeweb/js/min/cytoscapeweb.min.js"></script> | |||
<!-- Load data --> | |||
<script type="text/javascript"> | |||
var durl = "/resource_browser/nwfiles/10717-109I6_2.xgmml"; | |||
//$.get(durl, function(data) { | |||
// xml = data; | |||
// //alert('Load was performed.'); | |||
//}) | |||
var request = new XMLHttpRequest(); | |||
request.open("GET", durl , false); | |||
request.send(null); | |||
var xml = request.responseText; | |||
</script> | |||
<script type="text/javascript" src="/resource_browser/nwfiles/f5_cytoview.js"></script> | |||
</html> | |||
Revision as of 18:01, 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.
Style
Layout: (recalculate)Filter
| Z-Score filter: | ||
|---|---|---|
| 0.00 | 0.00 | |
Show nodes: Source TF Target TF MOTIF
| Node | Type |
|---|
| Source TF | Target TF | Promoter | Z-Score |
|---|
