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3745 lines (3049 loc) · 122 KB
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<!DOCTYPE html>
<meta charset="utf-8">
<script src="../authentication/js/environment.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" href="https://www.w3schools.com/w3css/4/w3.css">
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Poppins">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<script type="text/javascript" src="script/jquery-3.3.1.js"></script>
<!-- <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script> -->
<!-- <script src='/script/jquery-ui.js'></script>
<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js" integrity="sha256-VazP97ZCwtekAsvgPBSUwPFKdrwD3unUfSGVYrahUqU=" crossorigin="anonymous"></script>-->
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/FileSaver.js/1.3.8/FileSaver.js"></script>
<script src="http://d3js.org/d3.v3.min.js"></script>
<script type="text/javascript" src="script/d3-legend.min.js"></script>
<script type="text/javascript" src="script/math.js"></script>
<link rel="stylesheet" type="text/css" href="css/network.css">
<!-- <script src="./.url.js"></script> -->
<script>
//An ajax call to read universal node file which contain data for different filters.
// $.getJSON( "data/json/GRCH38-p12-uniNode_V4.json", function( json ) {
// console.log( "JSON Data received, name is " + json.name);
// });
$.ajax({
//url: 'data/json/GRCH38-p12-uniNode_V4.json', // taking long time to load
url: 'data/json/PD_universal_GRCH38p13_V4.json', // taking long time to load
dataType: 'json',
// crossDomain: 'http://*',
success: function (data) {
// relevence in radial analysis
// for(let key=0; key<uniNodeRelevence.length; key++){
// $('<option/>').val(uniNodeGLogFC[key]).text(jsUcFirst(uniNodeGLogFC[key])).appendTo('#nodeDegreeID4Size')
// }
//console.log("uniNode: ", uniNode)
},
statusCode: {
404: function () {
alert('There was a problem with the server. Try again soon!');
}
}
});
//End of ajax call.
</script>
<body>
<div id="loader" class="spinner-box">
<div class="circle-border">
<div class="circle-core"></div>
</div>
</div>
<!-- table for selected nodes -->
<div style="display: none;" id="node-modal-background">
<div id="nodeModal">
<div class="modal-header">
<span class="header-text">
Node Details
</span>
<button class="modal-close-btn" onclick="closeModal()">x</button>
</div>
<div class="modal-body">
<table class="fixed_header">
<thead>
<tr>
<th style="width: 50px;">No.</th>
<th>Gene</th>
<th>Ensemble</th>
<th>Description</th>
</tr>
</thead>
<tbody id="table_data-ip">
<tr>
<td>row 1-0</td>
<td>row 1-1</td>
<td>row 1-2</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<!-- table for selected hub genes -->
<div style="display:none" id="node-modal-background-2">
<div id="nodeModal-2">
<div class="modal-header">
<span class="header-text">
Node Details(hub genes)
</span>
<button class="modal-close-btn" onclick="closeModalHUB()">x</button>
</div>
<div class="modal-body">
<table class="fixed_header">
<thead>
<tr>
<th style="width: 50px;">No.</th>
<th>Gene</th>
<th>Ensemble</th>
<th>Description</th>
</tr>
</thead>
<tbody id="table_data-ip-2">
<tr>
<td style="width: 50px;">2000.</td>
<td>row 1-1</td>
<td>row 1-2</td>
<td style="width: 360px;">row 1-2</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<!-- Following DIV will display FORCE DIRECTED GRAPH-->
<div class="network" style="float:left; width:100%; position:relative; outline: 0;">
<div id="openDraw"
style="font-size:20px;cursor:pointer;display:inline-block; background: rgb(255, 255, 255, 0.3); position:absolute; top: 0px;"
onclick="openNav()">☰ open</div> <!-- Open Menu Button-->
</div>
<!-- Following DIV will create a LEFT MENU for network filters/modifications features-->
<div id="mySidenav" class="sidenav">
<!-- Close Menu Button-->
<div class="heading" style="word-wrap: normal;">
<a style="top: 0; font-size: 25px; right: 0px !important" href="javascript:void(0)" class="closebtn"
onclick="closeNav()" style="padding: 0px;">×</a>
</div>
<div class="legends" style="background: rgb(255, 255, 255, 0.6);">
<button class="accordion active">Node Color</button>
<!-- To change the color of nodes based on different parameters-->
<div class="panel" style="max-height:600px;">
<p>
<input type="radio" name="nodeColor" id="none" value="0" checked> None <br>
<input type="radio" name="nodeColor" id="Direction" value="1"> Direction <br>
<input type="radio" name="nodeColor" id="logFC" value="2"> logFC <br>
<input type="radio" name="nodeColor" id="Pathways" value="3"> Pathways <br>
<!-- <input type="radio" name="nodeColor" id="Proteomic1" value="5"> OTHER PROTEOMIC <br> -->
<input type="radio" name="nodeColor" id="Traits" value="4"> Traits<br>
<input type="radio" name="nodeColor" id="gwas" value="5"> GWAS <br>
<input type="radio" name="nodeColor" id="DBs" value="6"> Databases <br>
<input type="radio" name="nodeColor" id="markers" value="7"> Celltype Markers <br>
<!-- Dropdown for pathways name to highlight nodes-->
<div id="pathwayInput" style="padding-bottom:5px;display:none;">
Select Pathway:
<select id="pathwayID4Color" name="pathwayID4Color" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<!-- Dropdown for GWAS DATA TO highlight nodes-->
<div id="GWASInput" style="padding-bottom:5px;display:none;">
Select GWAS data:
<select id="GWAS4Color" name="GWAS4Color" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<!-- logFC Dropdown to highlight node with color spectrum-->
<div id="logFCInput" style="padding-bottom:5px;display:none;">
Select logFC:
<select id="logFCID4Color" name="logFCID4Color" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<!-- Direction Dropdown to highlight nodes-->
<div id="directionInput" style="padding-bottom:5px;display:none;">
Select Direction:
<select id="directionID4Color" name="directionID4Color" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<!-- Trait dropdown to highlight nodes -->
<div id="traitInput" style="padding-bottom:5px;display:none;">
Select Trait:
<select id="traitID4Color" name="traitID4Color" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<!-- Database and assocition dropdown to highlight nodes -->
<div id="DBsInput" style="padding-bottom:5px;display:none;">
Select significance from databases:
<select id="DBs4Color" name="DBsID4Color" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<!-- celltype markers dropdown to highlight nodes -->
<div id="celltypemarkerInput" style="padding-bottom:5px;display:none;">
Select celltype markers:
<select id="markers4Color" name="markers4Color" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
</p>
</div>
<!-- Node size change button -->
<button class="accordion active">Node Size</button>
<div class="panel" style="max-height: 300px;">
<p>
<input type="radio" name="nodeSize" id="none" value="0" checked> None <br>
<input type="radio" name="nodeSize" id="GlogFC" value="1"> LogFC <br>
<!-- <input type="radio" name="nodeSize" id="PlogFC" value="2"> Proteomic logFC <br> -->
<input type="radio" name="nodeSize" id="Traits4Size" value="2"> Traits <br>
<!-- <input type="radio" name="nodeSize" id="GWAS4Size" value="3"> GWAS <br>
<input type="radio" name="nodeSize" id="direction4Size" value="4"> Direction <br> -->
<!-- Genomic logFC Dropdown to change the node size-->
<div id="GlogFCInput4Size" style="padding-bottom:5px;display:none;">
Select logFC:
<select id="GlogFCID4Size" name="GlogFCID4Size" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<!-- Trait P-values Dropdown to change the node size-->
<div id="traitInput4Size" style="padding-bottom:5px;display:none;">
Select Trait:
<select id="traitID4Size" name="traitID4Size" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<!-- GWAS Dropdown to change the node size-->
<div id="gwasInput4Size" style="padding-bottom:5px;display:none;">
Select GWAS:
<select id="gwasID4Size" name="gwasID4Size" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<!-- Direction Dropdown to change the node size-->
<div id="directionInput4Size" style="padding-bottom:5px;display:none;">
Select Direction:
<select id="directionID4Size" name="directionID4Size" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
</p>
</div>
<!-- Node Shape -->
<!-- <div class="legends" style="background: rgb(255, 255, 255, 0.6);">
<button class="accordion active">Node Shape</button>
<div class="panel" style="max-height: 300px;">
<p>
<input type="radio" name="nodeShape" id="none" value="0" checked> None <br>
<input type="radio" name="nodeShape" id="PathwaysShape" value="2"> Pathways <br>
<input type="radio" name="nodeShape" id="gwasShape" value="4"> GWAS <br>
<input type="radio" name="nodeShape" id="DBsShape" value="5"> Databases <br>
<input type="radio" name="nodeShape" id="markersShape" value="6"> Celltype Markers <br>
<div id="pathwayShapeInput" style="padding-bottom:5px;display:none;">
Select Pathway:
<select id="pathwayID4Shape" name="pathwayID4Shape" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<div id="GWASShapeInput" style="padding-bottom:5px;display:none;">
Select GWAS data:
<select id="GWAS4Shape" name="GWAS4Shape" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<div id="directionShapeInput" style="padding-bottom:5px;display:none;">
Select Direction:
<select id="directionID4Shape" name="directionID4Shape" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<div id="traitShapeInput" style="padding-bottom:5px;display:none;">
Select Trait:
<select id="traitID4Shape" name="traitID4Shape" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<div id="DBsShapeInput" style="padding-bottom:5px;display:none;">
Select significance from databases:
<select id="DBs4Shape" name="DBsID4Shape" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
<div id="celltypemarkerShapeInput" style="padding-bottom:5px;display:none;">
Select celltype markers:
<select id="markers4Shape" name="markers4Shape" style="max-width:90%;">
<option value="none" selected="selected">None</option>
</select>
</div>
</p>
</div> -->
<!-- Radial Analysis -->
<button class="accordion active">Radial Analysis</button>
<div class="panel" style="max-height: 250px;">
<p>
<input type="radio" name="radialAnylisis" id="none" value="0" checked> None <br>
<input type="radio" name="radialAnylisis" id="EdgeWeightCutOff" value="1"> Edge weight cut-off
<br>
<input type="radio" name="radialAnylisis" id="NodeDegree" value="2"> Node cutoff <br>
<input type="radio" name="radialAnylisis" id="HubGenes" value="3"> Hub genes <br>
<!-- <input type="radio" name="radialAnylisis" id="stringDBchanal" value="4"> Interaction Type <br> -->
<!-- Threshold for weight -->
<div class="slidecontainer" id="EdgeWeightCutOffRange" style="padding-bottom:5px;display:none;">
<input type="range" min="0" max="1" step=".1" value="0" class="slider" id="myRange">
<br>
<p>Edge Weight: <span id="thresh"></span></p>
</div>
<!-- node weight dropdown options -->
<div id="db4weight" class="slidecontainer" style="padding-bottom:5px;display:none;">
Select Interaction Type:
<select id="stringDBchanal4weight" name="stringDBchanal4weight" style="width:100%;">
<option value="none" selected="selected">Combined score </option>
<option value="tm">Textmining</option>
<option value="expr">Experiments</option>
<option value="db">Databases</option>
<option value="coex">Co-expression</option>
<option value="nbrhd">Neighborhood</option>
<option value="genefu">Gene Fusion</option>
<option value="occur">Co-occurrence</option>
</select>
</div>
<!-- node degree dropdown options -->
<div id="nodeDegreeInput4Size" class="slidecontainer" style="padding-bottom:5px;display:none;">
Select Node cutoff:
<select id="nodeDegreeID4Size" name="nodeDegreeID4Size" style="max-width:90%;">
<option value="none" selected="selected">None</option>
<option value="node_degree">Gene Degree</option>
</select>
</div>
<!-- Threshold for Degree -->
<div class="slidecontainer" id="NodeDegreeRange" style="padding-bottom:5px;display:none;">
<input type="range" min="0" max="20" step="1" value="0" class="slider" id="myDegree">
<p>node Degree: <span id="thresh1"></span></p>
</div>
<!-- Gene connections -->
<div class="slidecontainer" id="HubGenesRange" style="padding-bottom:5px;display:none;">
<input type="range" min="0" max="50" step="1" value="0" class="slider" id="myConnection">
<br>
<p>Hub Node Size: <span id="thresh2"></span></p>
</div>
<div id="hub_genes_button_div"></div>
</p>
</div>
<!-- Find node panel-->
<button class="accordion">Custom search</button>
<div class="panel">
<div id="geneinput">
<form name="geneinput">
<br>
<p>Find Node<span id="thresh1"></span></p>
<textarea rows="2" style="width:90%" id="gene_list" name="gene_list" form="form3"
placeholder="Enter Genes list (comma seperated)"></textarea>
<!-- <input id="genesymbol" type="text" value="" name="genesymbol" placeholder="Gene symbol"/> -->
<input type="submit" id="submit" value="Submit" />
<button type="reset" value="Reset" onclick="resetText()">Reset </button>
<a id="currentgenesymbol"></a>
</form>
</div>
</div>
<!-- Node colors legend-->
<button class="accordion">Legends</button>
<div class="panel" id="legendPanel">
<p></p>
</div>
<button id="button_snap" style="outline: 0;" type="button" class="btn btn-default">Take a
Screenshot!
</button>
<script>
var width = 1440,
height = 700;
// function takesnapshot() {
d3.select('#button_snap').on('click', function () {
jQuery('#button_snap').html('loading ...');
$('#button_snap').css('background', 'transparent');
$('#button_snap').css('pointer-events', 'none');
$('#button_snap').css('border', 'none');
var svgString = getSVGString(svg.node());
svgString2Image(svgString, 10 * width, 10 * height, 'png',
save); // passes Blob and filesize String to the callback
function save(dataBlob, filesize) {
// console.log('BLOB', dataBlob, jsonFile)
jQuery('#button_snap').html('Take a Screenshot!');
jQuery('#button_snap').css('background', 'white');
$('#button_snap').css('pointer-events', 'all');
// $('#button_snap').append("Take a Screenshot!")
saveAs(dataBlob, `${'savethis'}.png`); // FileSaver.js function
}
});
function getSVGString(svgNode) {
svgNode.setAttribute('xlink', 'http://www.w3.org/1999/xlink');
var cssStyleText = getCSSStyles(svgNode);
appendCSS(cssStyleText, svgNode);
var serializer = new XMLSerializer();
var svgString = serializer.serializeToString(svgNode);
svgString = svgString.replace(/(\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace
svgString = svgString.replace(/NS\d+:href/g, 'xlink:href'); // Safari NS namespace fix
return svgString;
function getCSSStyles(parentElement) {
var selectorTextArr = [];
// Add Parent element Id and Classes to the list
selectorTextArr.push('#' + parentElement.id);
for (var c = 0; c < parentElement.classList.length; c++)
if (!contains('.' + parentElement.classList[c], selectorTextArr))
selectorTextArr.push('.' + parentElement.classList[c]);
// Add Children element Ids and Classes to the list
var nodes = parentElement.getElementsByTagName("*");
for (var i = 0; i < nodes.length; i++) {
var id = nodes[i].id;
if (!contains('#' + id, selectorTextArr))
selectorTextArr.push('#' + id);
var classes = nodes[i].classList;
for (var c = 0; c < classes.length; c++)
if (!contains('.' + classes[c], selectorTextArr))
selectorTextArr.push('.' + classes[c]);
}
// Extract CSS Rules
var extractedCSSText = "";
for (var i = 0; i < document.styleSheets.length; i++) {
var s = document.styleSheets[i];
try {
if (!s.cssRules) continue;
} catch (e) {
if (e.name !== 'SecurityError') throw e; // for Firefox
continue;
}
var cssRules = s.cssRules;
for (var r = 0; r < cssRules.length; r++) {
if (contains(cssRules[r].selectorText, selectorTextArr))
extractedCSSText += cssRules[r].cssText;
}
}
return extractedCSSText;
function contains(str, arr) {
return arr.indexOf(str) === -1 ? false : true;
}
}
function appendCSS(cssText, element) {
var styleElement = document.createElement("style");
styleElement.setAttribute("type", "text/css");
styleElement.innerHTML = cssText;
var refNode = element.hasChildNodes() ? element.children[0] : null;
element.insertBefore(styleElement, refNode);
}
}
function svgString2Image(svgString, width, height, format, callback) {
var format = format ? format : 'png';
var imgsrc = 'data:image/svg+xml;base64,' + btoa(unescape(encodeURIComponent(
svgString))); // Convert SVG string to data URL
var canvas = document.createElement("canvas");
var context = canvas.getContext("2d");
canvas.width = width;
canvas.height = height;
var image = new Image();
image.onload = function () {
context.clearRect(0, 0, width, height);
context.drawImage(image, 0, 0, width, height);
canvas.toBlob(function (blob) {
var filesize = Math.round(blob.length / 1024) + ' KB';
if (callback) callback(blob, filesize);
});
};
// console.log(imgsrc);
image.src = imgsrc;
}
// }
</script>
<!-- <button class="reset-all-btn">Reset All</button> -->
<!-- network setting page -->
<!-- Select node panel-->
<!-- <button class="accordion">Selected Node</button>
<div class="panel" id="sgeneinput">
<p>
<div id="sgeneinput1">
<textarea rows="2" style="width:90%" id="sgene_list" name="sgene_list" placeholder="Nothing selected"></textarea>
</div></p>
</div>
<div class="resetBtn">
<button type="reset" value="Reset" onclick="resetText()" style="margin:auto;display:block; box-shadow: 0 8px 16px 0 rgba(0,0,0,0.2), 0 6px 20px 0 rgba(0,0,0,0.19);" >Reset the network </button>
</div> -->
<!--button type="reset" value="Reset" onclick="resetText()" >Reset </button-->
<!-- <div class="resetBtn">
<button type="reset" value="Reset" onclick="resetText()"
style="margin:auto;display:block; box-shadow: 0 8px 16px 0 rgba(0,0,0,0.2), 0 6px 20px 0 rgba(0,0,0,0.19);">Reset
the network </button>
</div> -->
</div>
</div>
<div class="setting_wrapper" id="mysetting" style="display: none">
<div class="setting_close">
close
<a href="javascript:void(0)" class="closebtn" onclick="closeSetting()" style="padding: 0px;">×</a>
</div>
<!-- // gravity .1
// distance infinity
// chargeDistance infinity
// linkStrength 1
// theta .8 -->
<button class="accordion active">Network layout</button>
<div class="panel" style="max-height: 202px;">
<p>
<input type="radio" name="force_setting" id="none" value="0" checked> None <br>
<input type="radio" name="force_setting" id="link_distance" value="1"> Link Distance<br>
<input type="radio" name="force_setting" id="charge" value="2"> Link Charge <br>
<input type="radio" name="force_setting" id="link_Strength" value="3"> Distance<br>
<p>
<button onclick="stopAnimation()" style="color: black">Stop Animation</button>
</p>
<!-- <input type="radio" name="force_setting" id="gravity" value="3"> Link Distance<br>
<input type="radio" name="force_setting" id="theta" value="1"> Link Distance<br> -->
<!-- Threshold for weight -->
<div class="forcecontainer" id="linkdistanceRange" style="padding-bottom:5px;display:none;">
<input type="range" min="1" max="100" step="1" value="0" class="slider" id="linkdistance">
<br>
<p>link distance: <span id="linkdistanceinput"></span></p>
</div>
<!-- Threshold for Degree -->
<div class="forcecontainer" id="linkchargeRange" style="padding-bottom:5px;display:none;">
<input type="range" min="-300" max="50" step="1" value="-200" class="slider" id="linkcharge">
<br>
<p>node charge: <span id="linkchargeinput"></span></p>
</div>
<div class="forcecontainer" id="linkStrengthRange" style="padding-bottom:5px;display:none;">
<input type="range" min="1" max="1000" step="10" value="1" class="slider" id="linkStrength">
<br>
<p>distance: <span id="linkStrengthinput"></span></p>
</div>
<!-- <button type="reset" value="Reset" class="networklayoutreset" onclick="resetLayout()">Reset
</button> -->
<!-- Gene connections -->
</p>
</div>
<button class="accordion active">Network parameters</button>
<div class="panel" style="max-height:400px;">
<p>
<input type="radio" name="network_parameters" id="none" value="0" checked> None <br>
<input type="radio" name="network_parameters" id="nodecolor" value="1"> Node Color Change<br>
<input type="radio" name="network_parameters" id="linkcolor" value="2"> Link Color Opacity<br>
<input type="radio" name="network_parameters" id="linkcolor" value="3"> Node Size<br>
<input type="radio" name="network_parameters" id="linkcolor" value="4"> Text Size<br>
<!-- <input type="radio" name="network_parameters" id="linkcolor" value="5"> Network Zoom<br> -->
<!-- <input type="radio" name="force_setting" id="gravity" value="3"> Link Distance<br>
<input type="radio" name="force_setting" id="theta" value="1"> Link Distance<br> -->
<!-- Threshold for weight -->
<div class="networkcontainer" id="color_range" style="padding-bottom:5px;display:none;">
<div class="colorParam" id="color_ouput" style="background: rgb(23,190,207)"></div>
<p>color R: <span id="rRange">23</span></p>
<input type="range" min="0" max="255" step="1" value="23" class="slider" id="redRange"
onchange="colorFinc()">
<br>
<p>color G: <span id="gRange">190</span></p>
<input type="range" min="0" max="255" step="1" value="190" class="slider" id="greenRange"
onchange="colorFinc()">
<br>
<p>color B: <span id="bRange">207</span></p>
<input type="range" min="0" max="255" step="1" value="207" class="slider" id="blueRange"
onchange="colorFinc()">
</div>
<div class="networkcontainer" id="opacity_range" style="padding-bottom:5px;display:none;">
<p>opacity: <span id="oRange">1</span></p>
<input type="range" min="0" max="1" step=".1" value="1" class="slider" id="opacityRange"
onchange="opacityFunc()">
</div>
<div class="networkcontainer" id="node_size" style="padding-bottom:5px;display:none;">
<p>node size: <span id="nRange">8</span></p>
<input type="range" min="8" max="15" step="1" value="8" class="slider" id="nodeRange"
onchange="nodeSizeFunc()">
</div>
<div class="networkcontainer" id="text_size" style="padding-bottom:5px;display:none;">
<p>text size: <span id="tRange">8</span></p>
<input type="range" min="2" max="15" step="1" value="8" class="slider" id="textRange"
onchange="textSizeFunc()">
<!--CHANGE IS NEEDED-->
</div>
<div class="networkcontainer" id="zoom_network" style="padding-bottom:5px;display:none;">
<button class="zoom_btn" id="zoom_in">+</button>
<button class="zoom_btn" id="zoom_out">-</button>
</div>
<!-- Threshold for Degree -->
<!-- <div class="forcecontainer" id="linkchargeRange" style="padding-bottom:5px;display:none;">
<input type="range" min="-300" max="50" step="1" value="-200" class="slider" id="linkcharge">
<br>
<p>node charge: <span id="linkchargeinput"></span></p>
</div>
<div class="forcecontainer" id="linkStrengthRange" style="padding-bottom:5px;display:none;">
<input type="range" min="1" max="1000" step="10" value="1" class="slider" id="linkStrength">
<br>
<p>distance: <span id="linkStrengthinput"></span></p>
</div> -->
<!-- <button type="reset" value="Reset" class="networklayoutreset" onclick="reset_param()">Reset
</button> -->
<!-- Gene connections -->
</p>
</div>
<button class="accordion active">Annotations</button>
<div class="panel" style="max-height:200px;">
<div id="gene_info"></div>
</div>
<div style="margin: 10px">
<b>NETWORK INFO:</b>
<div id="network_details">
</div>
</div>
<!-- Node colors legend 2-->
<!-- <button class="accordion">Legends</button>
<div class="panel" id="legendPanel">
<p></p>
</div> -->
</div>
</div>
<div class="networksetting">
<h4 style="cursor: pointer;" onclick="settingFunc()">Setting ⚙ </h4>
</div>
<script>
function closeModal() {
$("#node-modal-background").css("display", "none");
}
function closeModalHUB() {
$("#node-modal-background-2").css("display", "none");
}
//Open left menu function
function openNav() {
document.getElementById("mySidenav").style.width = "250px";
document.getElementById("openDraw").style.display = "none";
}
//Close left menu function
function closeNav() {
document.getElementById("mySidenav").style.width = "0";
document.getElementById("openDraw").style.display = "block";
}
// Close setting drawer
function closeSetting() {
document.getElementById("mysetting").style.display = "none";
$('.networksetting').css('top', '0px')
// document.getElementsByClassName("networksetting").style.display = "block";
}
//Capitalize first letter
window.jsUcFirst = function (string) {
return string.charAt(0).toUpperCase() + string.slice(1);
}
//Handling left menu hight
var acc = document.getElementsByClassName("accordion");
var i;
for (i = 0; i < acc.length; i++) {
acc[i].addEventListener("click", function () {
this.classList.toggle("active");
var panel = this.nextElementSibling;
if (panel.style.maxHeight) {
panel.style.maxHeight = null;
} else {
panel.style.maxHeight = 600 + "px";
}
});
}
//Reset "find Node" box as well network to its previous stage
function resetText() {
$("#gene_list").val('');
$("#logFCID4Color").val('none')
$("#directionID4Color").val('none')
$("#pathwayID4Color").val('none')
$("#traitID4Color").val('none')
// console.log($("#logFCID4Color").val());
$("input[name='nodeColor']")[0].checked = true; // rectified nodecolor
if ($("input[name='nodeColor']:checked").val() == 3) {
//$("input[name='nodeColor']:checked").trigger('change');
$("#pathwayID4Color option:selected").trigger('change');
} else {
$("input[name='nodeColor']:checked").trigger('change');
// console.log('-->', $("input[name='nodeColor']:checked").val());
//$("#pathwayID4Color option:selected").trigger('change');
}
//$(".country option:selected")
}
</script>
<script>
var jsonFile;
var nodeSize;
var hubGenesArray = []
//Get JSON file name received through get method
function processUser() {
var parameters = location.search.substring(1).split("&");
var temp = parameters[0].split("=");
jsonFile = unescape(temp[1]);
// console.log('HERE-->', jsonFile, '<--ends') // Rectify
var heading = jsonFile.split("/");
if (jsonFile == 'undefined') {
heading = ["", 'Temporary File']
}
d3.select("body").selectAll(".heading").selectAll("p").remove("*");
d3.select("body").selectAll(".heading").append("p").style("word-wrap", "break-word").text(heading[1]);
d3.select("body").selectAll(".heading p").style("margin-top", "18px");
d3.select("body").selectAll(".heading p").style("margin-left", "10px");
d3.select("body").selectAll(".heading p").style("font-size", "12px");
}
processUser();
//Get Quartile of array of values
function quartileBounds(_sample) {
// find the median as you did
var _median = math.median(_sample)
// split the data by the median
var _firstHalf = _sample.filter(function (f) {
return f < _median
})
var _secondHalf = _sample.filter(function (f) {
return f >= _median
})
// find the medians for each split
var _25percent = math.median(_firstHalf);
var _75percent = math.median(_secondHalf);
var iqr = _75percent - _25percent;
var lowerBound = _25percent - (1.5 * iqr)
var upperBound = _75percent + (1.5 * iqr)
// this will be the upper bounds for each quartile
return [lowerBound, upperBound, _25percent, _75percent];
}
// returns [26,33,78.5,288]
//get window width and height
var w = window.innerWidth;
var h = window.innerHeight;
var keyc = true,
keys = true,
keyt = true,
keyr = true,
keyx = true,
keyd = true,
keyl = true,
keym = true,
keyh = true,
key1 = true,
key2 = true,
key3 = true,
key0 = true
var focus_node = null,
highlight_node = null;
var text_center = false;
var outline = false;
var min_score = 0;
var max_score = 1;
//linear scale for coloring nodes
/*var color = d3.scale.linear()
.domain([min_score, (min_score+max_score)/2, max_score])
.range(["lime", "yellow", "red"]); */
var highlight_color = "blue";
var highlight_trans = 0.1;
var xScale = d3.scale.linear()
.domain([0, w]).range([0, w]);
var yScale = d3.scale.linear()
.domain([0, h]).range([0, h]);
//Node size scale
var size = d3.scale.pow().exponent(1)
.domain([50, 200])
.range([10, 30]);
//Define force layout
// console.log(d3.layout.force().distance())
var force = d3.layout.force()
.linkDistance(15)
.charge(-200)
.size([w, h]);
// gravity .1
// distance infinity
// chargeDistance infinity
// linkStrength 1
// theta .8
//deferent variables used in plot generation
var nodeSize_sel = "";
var default_node_color = "rgb(23, 190, 207)"; //#17becf
//var default_node_color = "rgb(3,190,100)";
//var default_link_color = "#888";
var default_link_color = "#c5c5c5";
var nominal_base_node_size = 8;
var nominal_text_size = 8;
var nominal_text_size_hovar = 15;
var max_text_size = 10;
var max_text_size_hovar = 15;
var nominal_stroke = 1;
var max_stroke = 4.5;
var max_base_node_size = 25;
var max_base_node_size1 = 200;
var min_base_node_size = 50;
var min_zoom = 0.1;
var max_zoom = 7;
var svg = d3.select("body").selectAll(".network").attr("tabindex", 1).on("keydown.brush", keydown)
//var svg = d3.select("body").selectAll(".network").attr("tabindex", 1)
.on("keyup.brush", keyup).each(function () {
this.focus();
}).append("svg");
var zoom = d3.behavior.zoom().scaleExtent([min_zoom, max_zoom])
var zoomer = d3.behavior.zoom().
scaleExtent([min_zoom, max_zoom]).
x(xScale).
y(yScale).
on("zoomstart", zoomstart).
on("zoom", redraw);
function zoomstart() {
node.selectAll("path").each(function (d) {
d.selected = false;
d.previouslySelected = false;
});
node.selectAll("path").classed("selected", false);
}
function redraw() {
vis.attr("transform",
"translate(" + d3.event.translate + ")" + " scale(" + d3.event.scale + ")");
//console.log("zoom")
var text_size = nominal_text_size;
//var text_size_hovar = nominal_text_size_hovar;
// console.log('TEXT CHECK ->>', nominal_text_size, zoomer.scale(), max_text_size, '<<----'); // rectify
// console.log('nominal_text_size',nominal_text_size);
// console.log('zoomer.scale()', zoomer.scale());
// console.log('max_text_size', max_text_size);
// console.log('text_size', text_size, '\n\n');
if (nominal_text_size * zoomer.scale() > max_text_size) text_size = max_text_size / zoomer.scale();
//if (nominal_text_size_hovar*zoom.scale()>max_text_size_hovar) text_size_hovar = max_text_size_hovar/zoom.scale();
// text.style("font-size", text_size + "px"); // rectified , just commented out this line
// console.log('text_size', text_size, '\n\n');
nominal_text_size_hovar * zoom.scale() > max_text_size_hovar ? text_size = max_text_size_hovar :
nominal_text_size_hovar * zoom.scale() < nominal_text_size_hovar ? text_size = nominal_text_size_hovar :
text_size = nominal_text_size_hovar * zoom.scale();
//text.style("font-size",text_size + "px");
//text.style("font-size","5px");
gbTootip.style("font-size", text_size + "px"); // rectify
vis.attr("transform", "translate(" + d3.event.translate + ")scale(" + d3.event.scale + ")");
}
//var g = svg.append("g");
svg.style("cursor", "move");
var graph = {};
var expressionColor, nodeSizeScale, nodeSizeScaleFC, nodeSizeScalePval, shiftKey, ctrlKey;;
var uniNode = {};
var link;
var node;
// Node tool-tip
var gbTootip = d3.select("body") // rectify
.append("div")
.attr("class", "gtip")