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cytoscape.php
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<!DOCTYPE html>
<html>
<head>
<meta name="description" content="[Visual style example]" />
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js"></script>
<meta charset=utf-8 />
<title>Visual style example</title>
<!--<script src="http://cytoscape.github.io/cytoscape.js/api/cytoscape.js-latest/cytoscape.min.js"></script>-->
<script src="cytoscape/cytoscape.min.js"></script>
<script type="text/javascript" src="cytoscape/arbor.js"></script>
<!--<script type="text/javascript" src="http://cytoscape.github.io/cytoscape.js/api/cytoscape.js-latest/arbor.js"></script>-->
<script src="http://code.jquery.com/ui/1.10.3/jquery-ui.js"></script>
<link rel="stylesheet" href="http://code.jquery.com/ui/1.10.3/themes/smoothness/jquery-ui.css"/>
<link rel="stylesheet" href="css-ui/jquery-ui.css"/>
<!--<link rel="stylesheet" href="/resources/demos/style.css"/>-->
<?php
require_once('display_fns.php');
if(preg_match("/[A-Za-z0-9\_]+/", $_GET['fileName']) == TRUE){
$fileName = test_input($_GET['fileName']);
$conceptName = $_GET['conceptName'];
}else{
exit();
}
//$fileName="usrID/id_1378400413_14_gene_iterm.txt";
echo '<script src="data.php?fileName='.$fileName.'"></script>';
?>
<script>
$(function(){
$( "#menu" ).menu({
select: function( event, ui ) {
//console.log(ui.item.text());
if(ui.item.text()=='Diagram'){
$( "#dialog" ).dialog({ position: 'left top',width:250});
}
else if(ui.item.text()=='Layout'){
$( "#dialog-layout" ).dialog({ position: 'left top',width:250});
}
//else if(ui.item.text()=='Tool'){
else if(ui.item.text()=='Tool'){
//uncheck all the check box
$('#showNode2').prop('checked', false);
$( "#dialog-tool" ).dialog({ position: 'left top',width:250});
//console.log('Liang');
}
//alert(ui.item.text());
}
});
var cy = $("#cy").cytoscape("get");
//global variable
//var selectAll;
var selectedNode=cy.collection();
var intersectedNode=cy.collection();
var flag=0;
var target;
//cy.layout({ name: 'arbor' });
// trigger layout method
$( ".target" ).change(function () {
$var=$( "select option:selected" ).val();
if ($var=='tree'){
cy.layout({ name: 'breadthfirst', fit:false, directed: true,padding: 0 });
}
else if ($var=='random'){
cy.layout({ name: 'random' });
}
else if ($var=='circle'){
cy.layout({ name: 'circle', fit: true});
}
else{
cy.layout({ name: 'arbor',liveUpdate: true});
}
//console.log($var);
});
//cy.elements().unselectify();
// ********left click node**************
cy.on('tap', 'node', function(e){
var node = e.cyTarget;
//selectAll = cy.collection();
var neighborhood = node.neighborhood().add(node);
//console.log('neighborhood:'+neighborhood.data());
if(flag==0 || flag==1){
intersectedNode=neighborhood.intersect(selectedNode);
}
else{
intersectedNode=neighborhood.intersect(intersectedNode);
}
//console.log(intersectedNode.length);
if (intersectedNode.length){
intersectedNode.removeClass('intersect');
}
selectedNode=selectedNode.add(neighborhood);
cy.elements().addClass('faded');
//neighborhood.removeClass('faded');
selectedNode.removeClass('faded');
intersectedNode.addClass('intersect');
//cy.$('.faded').css('text-opacity',0.2);
//console.log(cy.$('.faded').css()['text-opacity'] );
flag++;
});
//2.tap and dialog
cy.on('cxttap','node',function(e) {
//var target = e.cyTarget;
target = e.cyTarget;
target.addClass('rightClick');
//go to check this gene or iterm in NCBI
$("#ncbi").attr("href","http://www.ncbi.nlm.nih.gov/pubmed/?term="+target.id());
//$('a').attr("href", "/search/?what=parks&city=" + newCity);
$("#dialog-rightClick").dialog({
width:250,
title:target.id(),
//to do:very close to clicked node
position:{my: 'left',at: 'right',of:e}
//position:{e.pageX+3, e.pageY+3}
//to do: provide different link based on different clicked node, something like html.write to change div text.
});
//uncheck all the check box
$('#hdNode').prop('checked', false);
$('#showNode').prop('checked', false);
$('#hdNode').change(function(){
if(this.checked){
// for (var i=0;i<target.length;i++)
//{
// console.log(target[i].data());
// }
target.hide();
//e.cyTarget.hide();
}
else{
target.show();
}
});
$('#showNode').change(function(){
if(this.checked){
//console.log(target);
cy.$().show();
}
else {
target.hide();
}
});
$('#rmNode').click(function(){
cy.remove(target);
//cy.$(':selected').remove();
//remove all the edge and node from all selected node
selectedNode.each(function(i,ele){
if(ele.group()=='edges'){
if(ele.data()['source']==target.id() || ele.data()['target']==target.id() ){
selectedNode = selectedNode.not(ele);
}
}
});
selectedNode = selectedNode.not(target);
//intersectedNode = intersectedNode.not(target);
//selectAll.each(function(i,ele){
// if(ele.group()=='edges'){
// if(ele.data()['source']==target.id() || ele.data()['target']==target.id() ){
// selectAll = selectAll.not(ele);
// }
// }
//});
//selectAll = selectAll.not(target);
});
});
$('#showNode2').change(function(){
if(this.checked){
//console.log(target);
cy.$().show();
}
else {
target.hide();
}
});
// right click edge to get the gene-iterm pair in NCBI
var target_edge;
cy.on('click','edge',function(e) {
//console.log('I am here');
target_edge = e.cyTarget;
//console.log(target_edge.data()['source']);
$("#ncbi-edge").attr("href","http://www.ncbi.nlm.nih.gov/gquery/?term="+target_edge.data()['source']+'+'+target_edge.data()['target']);
$("#egift-edge").attr("href","http://biotm.cis.udel.edu/udelafc/getSentencePage.php?user=liang&pass=SentencesForLiang&redirect=yes&gene="+target_edge.data()['source']+"&term="+target_edge.data()['target'].toLowerCase());
$("#dialog-edgeClick").dialog({
width:250,
title:target_edge.data()['source']+'-'+target_edge.data()['target'],
//to do:very close to clicked node
position:{my: 'left',at: 'right',of:e}
//position:{e.pageX+3, e.pageY+3}
//to do: provide different link based on different clicked node, something like html.write to change div text.
});
});
//click the background of the graph.
cy.on('tap', function(e){
if( e.cyTarget === cy ){
//cy.nodes().unselect();
selectedNode= cy.collection();
//selectAll = cy.collection();
intersectedNode=null;
flag=0;
cy.elements().removeClass('faded');
cy.elements().removeClass('intersect');
cy.elements().removeClass('rightClick');
}
});
//save image as PNG
$("#save-right").click(function () {
$.post("save.php", {data: cy.png(),type:"image"}, function (file) {
window.location.href = "download.php?path="+ file
});
//zero selected node;
//selectedNode=cy.collection();
//cy.layout('arbor');
//location.reload();
//cy.load([{data: { id: 'foo' }, group: 'nodes'}, {data: { id: 'bar' },group: 'nodes'}, { data: { id: "e1", source: "n1", target: "n2" }, group: "edges" }]);
});
//save subset of the graph data
$('#subset').click(function(){
//var subset_array=new array();
var subset_string='';
//console.log(selecAll);
//console.log('I am here\n'+selectedNode);
//if (selectAll.length){
// selectAll.each(function(i,ele){
// //console.log(ele.data()['source']+'\n');
// if(ele.group()=='edges'){
// subset_string = subset_string+ele.data()['source']+'\t'+ele.data()['target']+'\n';
// }
// });
//}
//else{
if (selectedNode.length){
selectedNode.each(function(i,ele){
//console.log(ele.group());
//console.log(ele.data()['source']+'\n');
if(ele.group()=='edges'){
subset_string = subset_string+ele.data()['source']+'\t'+ele.data()['target']+'\n';
}
});
$.post("save.php",{data:subset_string,type:"subset"},function(file){
window.location.href = "download.php?path="+ file
});
}else{
alert("You don't select any nodes or edges!");
}
// }
});
//subset the selected nodes and edges
$('#subset_graph').click(function(){
//cy.load([{data: { id: 'foo' }, group: 'nodes'}, {data: { id: 'bar' },group: 'nodes'}]); { data: { id: "e1", source: "n1", target: "n2" }, group: "edges" }
var subset_json='[';
//console.log(selectedNode);
if (selectedNode.length){
//console.log("I am here1!");
selectedNode.each(function(i,ele){
//console.log(ele+'--'+ele.group());
if(ele.group()=='nodes'){
if(ele.data()['borderColor']){
subset_json = subset_json + '{ data: {id:"'+ele.data()['id']+'",faveColor:"'+ele.data()['faveColor']+'",borderColor:"'+ele.data()['borderColor'];
subset_json = subset_json + '",width:"'+ele.data()['width']+'",height:"'+ele.data()['height']+'"},group:"nodes"},';
}else{
subset_json = subset_json + '{ data: {id:"'+ele.data()['id']+'",faveColor:"'+ele.data()['faveColor']+'"},group:"nodes"},';
}
}
if(ele.group()=='edges'){
subset_json = subset_json + '{ data: {id:"'+ele.data()['id']+'", source:"'+ele.data()['source']+'",target:"'+ele.data()['target']+'"},group:"edges"},';
}
//console.log(subset_json+ele.json()['data']);
});
subset_json=subset_json+']';
//var json=new array();
//var json='[{ data: {id:"oxid"},group:"nodes"},{ data: {id:"e40", source:"HK1",target:"oxid"},group:"edges"},{ data: {id:"skeletal muscles"},group:"nodes"},{ data: {id:"e41", source:"HK1",target:"skeletal muscles"},group:"edges"},{ data: {id:"atp"},group:"nodes"},{ data: {id:"e42", source:"HK1",target:"atp"},group:"edges"},{ data: {id:"mitochondria"},group:"nodes"},{ data: {id:"e43", source:"HK1",target:"mitochondria"},group:"edges"},{ data: {id:"mitochondrial"},group:"nodes"},{ data: {id:"e44", source:"HK1",target:"mitochondrial"},group:"edges"},{ data: {id:"metabolism"},group:"nodes"},{ data: {id:"e45", source:"HK1",target:"metabolism"},group:"edges"},{ data: {id:"rat"},group:"nodes"},{ data: {id:"e46", source:"HK1",target:"rat"},group:"edges"},{ data: {id:"binding"},group:"nodes"},{ data: {id:"e47", source:"HK1",target:"binding"},group:"edges"},{ data: {id:"HK1"},group:"nodes"},]';
//var json='[{ data: {"id":"oxid"},group:"nodes"}]';
//subset_json=jQuery.parseJSON('[{ data: {id:"extracellular"},group:"nodes"}]');
var obj=eval("("+subset_json+")");
//var json_string=JSON.stringify(json);
//var obj=jQuery.parseJSON(json_string);
//var json=cy.$(':selected').json()
//console.log(json);
cy.load(obj);
//try to zero selected node collection after load subset.
selectedNode=cy.collection();
flag=0;
}
else{
//console.log("I am here!");
alert("You don't select any nodes or edges!");
// selectAll=cy.$().select();
// //console.log("I am here!");
// selectAll.each(function(i,ele){
// console.log(ele+'--'+ele.group());
// if(ele.group()=='nodes'){
// if(ele.data()['borderColor']){
// subset_json = subset_json + '{ data: {id:"'+ele.data()['id']+'",faveColor:"'+ele.data()['faveColor']+'",borderColor:"'+ele.data()['borderColor'];
// subset_json = subset_json + '",width:"'+ele.data()['width']+'",height:"'+ele.data()['height']+'"},group:"nodes"},';
// }else{
// subset_json = subset_json + '{ data: {id:"'+ele.data()['id']+'",faveColor:"'+ele.data()['faveColor']+'"},group:"nodes"},';
// }
//
// }
// if(ele.group()=='edges'){
// subset_json = subset_json + '{ data: {id:"'+ele.data()['id']+'", source:"'+ele.data()['source']+'",target:"'+ele.data()['target']+'"},group:"edges"},';
// }
//
// //console.log(subset_json+ele.json()['data']);
//});
}
});
// select all nodes from graphics
$('#selectAll').click(function(){
//selectAll=cy.$().select();
selectedNode=cy.$().select();
//console.log(selectAll);
//selectAll.each(function(i,ele){
// console.log(ele.data()['id']+'\n');
//});
});
//slider-opacity
$("#slider-blue").slider({
orientation: "horizontal",
range: "min",
max: 100,
value: 25,
// slide: refreshSwatch,
slide: function (event, ui){
//var val=ui.value/100;
cy.$('.faded').css('opacity',ui.value/100);
}
});
//slider text opacity
$("#slider-green").slider({
orientation: "horizontal",
range: "min",
max: 100,
value: 10,
// slide: refreshSwatch,
slide: function (event, ui){
//console.log(ui.value);
//var val=ui.value/100;
cy.$('.faded').css('text-opacity',ui.value/100);
}
});
});
</script>
<!--<link rel="stylesheet" type="text/css" href="style.css">-->
</head>
<body>
<ul id="menu">
<li><a id='legend'>Diagram</a></li>
<li><a href="#">Layout</a></li>
<li><a href="#">Tool</a></li>
<li><a href="contact.php" target="_blank">Contact</a></li>
</ul>
<?php
if (trim($conceptName)!=''){ echo "<div><p><b> Analysis Name:</b> ".$conceptName."</p></div>"; }
?>
<div id="dialog" title="Graph Legend">
<canvas id='myLegend' width="400" height="200">Your browser doesn't support canvas</canvas>
<script>
var canvas = document.getElementById('myLegend');
var context = canvas.getContext('2d');
//draw symbol circle
context.beginPath();
x=15;y=15; radius=10;
context.arc(x, y, radius, 0, 2 * Math.PI, false);
context.strokeStyle = 'black';
context.fillStyle = '#FFFF00'
context.stroke();
context.fill();
context.closePath();
//draw another iterm circle
context.beginPath();
context.arc(x, y+25, radius, 0, 2 * Math.PI, false);
context.strokeStyle = 'red';
context.stroke();
context.closePath();
//draw selected circle
context.beginPath();
context.arc(x, y+50, radius, 0, 2 * Math.PI, false);
context.fillStyle = '#98FF98';
context.fill();
context.closePath();
//draw shared circle
context.beginPath();
context.arc(x, y+75, radius, 0, 2 * Math.PI, false);
context.fillStyle = '#56CAFF';
context.fill();
context.closePath();
//draw text
context.font = '10pt';
context.fillStyle = 'black';
context.fillText('Gene Symbol', x+25, y+3);
context.fillText('eGIFT iTerm', x+25, y+28);
context.fillText('Selected Node', x+25, y+53);
context.fillText('Shared Node', x+25, y+78);
</script>
<!--<img src="images/node-yellow.png" border="0"style="margin-left: 0px"><span style="font-size: 16px"> Gene</span></br>-->
<!--<img src="images/node-red.png" border="0"style="margin-left: 0px"><span style="font-size: 16px"> Iterm</span></br>-->
<!--<img src="images/node-mintgreen.png" border="0"style="margin-left: 0px"><span style="font-size: 16px"> Node Selected</span></br>-->
<!--<img src="images/node-lightblue.png" border="0"style="margin-left: 0px"><span style="font-size: 16px"> Node Intersection</span></br>-->
</div>
<div id="dialog-layout" title="Layout Method">
<form><span>Layout:</span>
<select class="target">
<option value="force" selected="selected">Force Directed</option>
<option value="tree">Tree</option>
<option value="random">Random</option>
<!-- <option value="circle">Circle</option> -->
</select>
</form>
</div>
<div id="dialog-tool" title="Tool">
<form>
<input type='checkbox' id='showNode2' name='showNode'>Show All Nodes</br></br>
<label>Opacity:</label><div id="slider-blue"></div>
<label>Opacity-Text:</label><div id="slider-green"></div></br>
<label>Image:</label><input type="button" id="save-right" value="Save"/></br>
<label>Select All Nodes:</label><input type="button" id='selectAll' value="GO"/></br>
<label>Selected Graph Data:</label><input type='button' id='subset' value="Save"/></br>
<label>Selected Graph:</label><input type='button' id='subset_graph' value="Subset"/></br>
</form>
</div>
<div id="dialog-rightClick">
<form>
<input type='checkbox' id='hdNode' name='hdNode'>Hide Node</br>
<input type='checkbox' id='showNode' name='showNode'>Show All Nodes</br>
</form>
<span>Node: <input type="button" id='rmNode' value="Remove"/></span></br>
<span><b>NCBI: </b><a id='ncbi' href='http://www.ncbi.nlm.nih.gov/' target='_blank'><input type="button" value="GO"/></a></span>
</div>
<div id="dialog-edgeClick">
<span><b>NCBI: </b><a id='ncbi-edge' href='http://www.ncbi.nlm.nih.gov/' target='_blank'><input type="button" value="GO" /></a></span></br>
<span><b>eGIFT Sentence: </b><a id='egift-edge' href='#' target='_blank'><input type="button" value="GO"/></a></span>
</div>
<!-- graph below-->
<div id="cy"> </div>
</body>
</html>