Cytoscape test3: Difference between revisions
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</html> | </html> | ||
{{ | <html> | ||
<!-- F5 Cytoscape App HTML --> | |||
<div id="f5_cytoscapeweb"> | |||
<div id="tabs_box"> | |||
<div id="tabs"> | |||
<ul> | |||
<li><a href="#style_panel">Layout</a></li> | |||
<li><a href="#filter_panel">Filter</a></li> | |||
<li><a href="#export_panel">Export</a></li> | |||
<li><a href="#properties_panel_nodes">Nodes</a></li> | |||
<li><a href="#properties_panel_edges">Edges</a></li> | |||
</ul> | |||
<div id="style_panel"> | |||
<label class="style">Layout:</label> | |||
<select id="cyto_layout" class="ui-button ui-widget ui-state-default ui-corner-all ui-button-text-only"> | |||
<option value="Preset">Preset</option> | |||
<option value="ForceDirected" selected>Force Directed</option> | |||
<option value="Circle">Circle</option> | |||
<option value="Radial">Radial</option> | |||
<option value="Tree">Tree</option> | |||
</select> | |||
<button id="cyto_recalc">Recalculate</button> | |||
<label class="style">Labels:</label> | |||
<input type="checkbox" id="cyto_node_labels" checked> Nodes</td></tr> | |||
<br /><input type="checkbox" id="cyto_edge_labels"> Edges</td></tr> | |||
</div> | |||
<div id="filter_panel"> | |||
<div> | |||
<label class="filter">Show edges:</label> | |||
<div id="edge_type_filter"> | |||
<input type="checkbox" id="cyto_edges_binds_to" value="binds_to" checked>TF->MOTIF</input> | |||
<br /><input type="checkbox" id="cyto_edges_promotes" value="promotes" checked>Promoters</input> | |||
</div> | |||
<div id="z_filter" class="slider">Promoter Z-Score:</div> | |||
<p /> | |||
<div id="degree_filter" class="slider">Motif degree:</div> | |||
<div id="tf_indegree_filter" class="slider">TF indegree:</div> | |||
<div id="nodes_type_filter"> | |||
<label class="filter">TF outdegree:</label> | |||
<input type="checkbox" id="cyto_nodes_tf_src" value="tf" checked>Source (Outdegree > 0)</input> | |||
<br /><input type="checkbox" id="cyto_nodes_tf" value="tf" checked>Target (Outdegree = 0)</input> | |||
</div> | |||
</div> | |||
</div> | |||
<div id="properties_panel_nodes" class="properties_panel scrollable"> | |||
<div> | |||
<button id="btn_show_all_nodes" class="rt_btn">Show all nodes</button> | |||
<button id="btn_show_select_nodes" class="rt_btn">Show only selected nodes</button> | |||
<p /><table id="nodes_list" class="wikitable"> | |||
</table> | |||
</div> | |||
</div> | |||
<div id="properties_panel_edges" class="properties_panel scrollable"> | |||
<div> | |||
<button id="btn_show_all_edges" class="rt_btn">Show all edges</button> | |||
<button id="btn_show_select_edges" class="rt_btn">Show only selected edges</button> | |||
<p /><table id="edges_list" class="wikitable"> | |||
</table> | |||
</div> | |||
</div> | |||
<div id="export_panel"> | |||
<label class="export">Export Network:</label> | |||
<button id="btn_exportGraphml">graphml</button> | |||
<button id="btn_exportXgmml">xgmml</button> | |||
<button id="btn_exportSIF">sif</button> | |||
<button id="btn_exportJSON">JSON</button> | |||
<label class="export">Export Image:</label> | |||
<button id="btn_exportPDF">PDF</button> | |||
<button id="btn_exportPNG">PNG</button> | |||
<button id="btn_exportSVG">SVG</button> | |||
</div> | |||
</div> | |||
</div> | |||
<div id="cytoscapeweb"></div> | |||
<div id="legend"><b>LEGEND:</b> <span class="tf">TF <img src="/resource_browser/nwfiles/tf.png" /></span>, <span class="motif">MOTIF <img src="/resource_browser/nwfiles/motif.png" /></span>, | |||
<br /><span class="tf">MOTIF->TF <img src="/resource_browser/nwfiles/motif-tf.png" /></span>, <span class="motif">TF->MOTIF <img src="/resource_browser/nwfiles/tf-motif.png" /></span></div> | |||
</div> | |||
<!-- Header Section --> | |||
<!-- JQuery UI --> | |||
<script type="text/javascript" src="/resource_browser/nwfiles/jquery-ui.min.js"></script> | |||
<link href="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.10/themes/base/jquery-ui.css" rel="stylesheet" /> | |||
<link href="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.10/themes/redmond/jquery-ui.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> | |||
<!-- F5 Cytoscape app --> | |||
<link href="/resource_browser/nwfiles/f5_cytoview_2.css" rel="stylesheet"/> | |||
<script type="text/javascript" src="/resource_browser/nwfiles/f5_cytoview_5.js"></script> | |||
<!-- Data Loading Section --> | |||
<script type="text/javascript"> | |||
// Load Data | |||
//var durl = "/resource_browser/nwfiles/</html>{{{CNhs}}}.{{{FFid}}}.xgmml<html>"; | |||
var durl = "/resource_browser/nwfiles/CNhs10630.10024-101D6.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; | |||
// initialization cytoscape options | |||
var options = { | |||
swfPath: "/resource_browser/rb_js/cytoscapeweb/swf/CytoscapeWeb", | |||
flashInstallerPath: "/resource_browser/rb_js/cytoscapeweb/swf/playerProductInstall" | |||
}; | |||
</script> | |||
</html> | |||
Latest revision as of 11:28, 20 July 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).
