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1578 lines (1353 loc) · 93.3 KB
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<head>
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-7ETP8E6M3Y"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-7ETP8E6M3Y');
</script>
<link rel="shortcut icon" type="image/x-icon" href="img/favicon.ico">
<script src="libraries/3d-force-graph.js"></script>
<script src="libraries/three.js"></script>
<script src="libraries/three-spritetext.min.js"></script>
<script src="libraries/rainbowvis.js"></script>
<script src="js/hgnc_dict.js"></script>
<script src="js/recordScript.js"></script>
<script src="js/animation.js"></script>
<script src="https://cdn.jsdelivr.net/npm/whatwg-fetch@3.6.2/dist/fetch.umd.min.js"></script>
<script src="backendApi/unitProtGeneMapping.js"></script>
<script src="backendApi/enrich.js"></script>
<script src="https://cdn.jsdelivr.net/npm/underscore@1.13.3/underscore-umd-min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/tweakpane@3.0.2/dist/tweakpane.min.js"></script>
<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.2.1/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-iYQeCzEYFbKjA/T2uDLTpkwGzCiq6soy8tYaI1GyVh/UjpbCx/TYkiZhlZB6+fzT" crossorigin="anonymous">
<script src="https://cdn.jsdelivr.net/npm/@tweakpane/plugin-essentials@0.1.5/dist/tweakpane-plugin-essentials.min.js"></script>
<script src="js/fstdropdown.js"></script>
<script src="https://code.jquery.com/jquery-3.5.1.slim.min.js"></script>
<script src="//unpkg.com/element-resize-detector/dist/element-resize-detector.min.js"></script>
<link rel="stylesheet" href="css/fstdropdown.css">
<link rel="stylesheet" href="css/visualization.css">
<meta name="viewport" content="width=device-width, initial-scale=1" charset="utf-8">
<title>3D Visualization</title>
<style type="text/css">
@font-face {
font-family: "MyriadPro-Regular";
src: url("fonts/MYRIADPROREGULAR.woff") format("woff");
}
@font-face {
font-family: "Century Gothic";
src: url("fonts/CenturyGothic.woff") format("woff");
}
@font-face {
font-family: "CenturyGothicPro";
src: url("fonts/CenturyGothic.woff") format("woff");
}
@font-face {
font-family: "CenturyGothicPro-Bold";
src: url("fonts/CenturyGothic-Bold.woff") format("woff");
}
@font-face {
font-family: "helveticaBold";
src: url("fonts/helvetica-bold-webfont.woff") format("woff");
}
.overlay {
position: fixed;
top: 0;
left: 0;
width: 100%;
height: 100%;
background-color: rgba(0, 0, 0, 0.5); /* Semi-transparent black background */
display: flex;
justify-content: center;
align-items: center;
z-index: 999; /* Ensure the overlay is above other content */
display: none;
}
.loader {
display: block;
animation: rotate 1.5s infinite;
height: 50px;
width: 50px;
justify-content: center;
}
.loader:before,
.loader:after {
border-radius: 50%;
content: '';
display: block;
height: 20px;
width: 20px;
}
.loader:before {
animation: ball1 1s infinite;
background-color: #cb2025;
box-shadow: 30px 0 0 #f8b334;
margin-bottom: 10px;
}
.loader:after {
animation: ball2 1s infinite;
background-color: #00a096;
box-shadow: 30px 0 0 #97bf0d;
}
@keyframes rotate {
0% {
-webkit-transform: rotate(0deg) scale(0.8);
-moz-transform: rotate(0deg) scale(0.8);
}
50% {
-webkit-transform: rotate(360deg) scale(1.2);
-moz-transform: rotate(360deg) scale(1.2);
}
100% {
-webkit-transform: rotate(720deg) scale(0.8);
-moz-transform: rotate(720deg) scale(0.8);
}
}
@keyframes ball1 {
0% {
box-shadow: 30px 0 0 #f8b334;
}
50% {
box-shadow: 0 0 0 #f8b334;
margin-bottom: 0;
-webkit-transform: translate(15px,15px);
-moz-transform: translate(15px, 15px);
}
100% {
box-shadow: 30px 0 0 #f8b334;
margin-bottom: 10px;
}
}
@keyframes ball2 {
0% {
box-shadow: 30px 0 0 #97bf0d;
}
50% {
box-shadow: 0 0 0 #97bf0d;
margin-top: -20px;
-webkit-transform: translate(15px,15px);
-moz-transform: translate(15px, 15px);
}
100% {
box-shadow: 30px 0 0 #97bf0d;
margin-top: 0;
}
}
</style>
</head>
<body id = "screen">
<div>
<svg version="1.1" id="Layer_1" onclick="window.location.href = 'index.html'" xmlns="http://www.w3.org/2000/svg" width = "150px" style="top:2%;left:1%;position:absolute;cursor: pointer;z-index:10;" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" viewBox="0 0 710.3 222.4" xml:space="preserve"> <style type="text/css"> .st0b{fill:#424A60;} .st1b{fill:#DC298D;} .st2b{fill:#7383BF;} .st3b{fill:#969696;} .st4b{fill:#EBBA16;} .st5b{fill:#06ABEB;} .st6b{font-family:'helveticaBold';} .st7b{font-size:84.3397px;} .st8b{letter-spacing:-1;} </style> <g id="Layer_1_00000056390415183483724190000009750584087129516189_"> <g id="path5"> <rect x="92.8" y="154.2" transform="matrix(0.3589 -0.9334 0.9334 0.3589 -62.6169 220.6174)" class="st0b" width="72.9" height="3.3"/> </g> <rect id="path4" x="156.9" y="60.1" transform="matrix(0.8102 -0.5861 0.5861 0.8102 0.7614 131.2305)" class="st0b" width="92.3" height="8.7"/> <g id="path3"> <rect x="19" y="127.2" transform="matrix(0.9138 -0.4063 0.4063 0.9138 -46.9835 44.8278)" class="st0b" width="126.2" height="11.8"/> </g> <g id="path2"> <rect x="122.6" y="16.9" transform="matrix(0.9138 -0.4063 0.4063 0.9138 -9.3065 55.4032)" class="st0b" width="6.4" height="65.4"/> </g> <rect id="path1" x="169" y="110.3" transform="matrix(0.9138 -0.4063 0.4063 0.9138 -48.6296 83.9257)" class="st0b" width="8.7" height="92.3"/> <circle id="circle6" class="st1b" cx="249.7" cy="34.5" r="21.8"/> <circle id="circle5" class="st2b" cx="112.1" cy="200.6" r="21.8"/> <circle id="circle4" class="st1b" cx="21.8" cy="156.5" r="21.8"/> <circle id="circle3" class="st3b" cx="109.6" cy="13.1" r="13.1"/> <circle id="circle2" class="st4b" cx="189.6" cy="193.1" r="13.1"/> <circle id="circle1" class="st5b" cx="149.5" cy="102.8" r="37.3"/> </g> <g id="Layer_2_00000013871697503241264390000008040421359665832584_"> <text transform="matrix(1 -3.490651e-03 3.490651e-03 1 243.0089 140.7256)" class="st6b st7b">PhosNet</text> <text transform="matrix(1 -3.490651e-03 3.490651e-03 1 585.1035 139.5315)" class="st6b st7b st8b">V</text> <text transform="matrix(1 -3.490651e-03 3.490651e-03 1 639.8698 139.3403)" class="st6b st7b">is</text> </g> </svg>
</div>
<div class="openbutton" id = "openbutton" value = 0 onclick="hideShowMenu(this.value)" style="cursor: pointer;">
<button class="dropbtn" id="openbutton-button">
<svg xmlns="http://www.w3.org/2000/svg" width="18px" viewBox="0 0 13 16"> <g id="Rectangle_1581" data-name="Rectangle 1581" transform="translate(0 1)" fill="#fff" stroke="#2e3137" stroke-width="1"> <rect width="13" height="13" stroke="none"/> <rect x="0.5" y="0.5" width="12" height="12" fill="none"/> </g> <text id="x" transform="translate(6.5 11)" fill="#9f9f9f" stroke="#2e3137" stroke-width="1" font-size="14" font-family="CenturyGothicPro-Bold, Century Gothic Pro" font-weight="700"><tspan x="-3.92" y="0">x</tspan></text> </svg>
</button>
<div class="openbutton-content" id = "openbutton-content">
</div>
</div>
<div id="nodequeryMain">
<select class='fstdropdown-select' id="nodequery" onchange="updateSearch()">
<option value="">Node Query</option>
</select>
</div>
<div id="infoBox" style="display: none;">
<div id="infoTop">
<p id="nodeName" style="font-family: CenturyGothicPro-Bold; margin:6px;">Node: <a id = "nodehref" href="https://www.w3schools.com" target="_blank" style="color: #00709d;">placeholder1</a> <img style = "width: 20px; margin-bottom: 5px;" src="https://www.phosphosite.org/images/header/logo_psp_white_cp.png"/></p>
<p id = "nodeType" style="font-family: CenturyGothicPro-Bold; margin:6px;">Type: <a id="typetext">placeholder2</a> <a id="activityText">| Activity: </a> <a id="activityNum">10 </a></p>
<p style="font-family: CenturyGothicPro-Bold; margin:6px;"> <u>Phosphorylation Info</u> <h style="font-family: CenturyGothicPro-Bold; font-size: 12px;">*(scrollable)</h></p>
</div>
<table id = "phosTable" class="table table-striped table-bordered">
<thead>
<tr>
<th style="background-color:rgba(240, 240, 240, .8);">Site</th>
<th style="background-color:rgba(240, 240, 240, .8)">log2FC</th>
<th style="background-color:rgba(240, 240, 240, .8)">pValue</th>
</tr>
</thead>
<tbody id = "tbody">
</tbody>
</table>
</div>
<div class="overlay" id="loader-class">
<div class="loader"></div>
</div>
<div id="guiplace"> </div>
<!-- LEGEND SHAPES -->
<div class="dropdown" id = "dropdown" value = "0" onclick="hideShowLegend(this.value)" style="cursor: pointer;">
<button class="dropbtn" id = "dropbtn">
<svg xmlns="http://www.w3.org/2000/svg" width="20px" viewBox="0 0 13 13"> <g id="Rectangle_1580" data-name="Rectangle 1580" fill="#fff" stroke="#000000" stroke-width="1"> <rect width="13" height="13" stroke="none"/> <rect x="0.5" y="0.5" width="12" height="12" fill="none"/> </g> <g id="Polygon_11" data-name="Polygon 11" transform="translate(11 2) rotate(90)" fill="#9f9f9f"> <path d="M 8.145074844360352 7.5 L 0.8549256324768066 7.5 L 4.5 1.019867777824402 L 8.145074844360352 7.5 Z" stroke="none"/> <path d="M 4.5 2.039735317230225 L 1.709851264953613 7 L 7.290148735046387 7 L 4.5 2.039735317230225 M 4.5 0 L 9 8 L 0 8 L 4.5 0 Z" stroke="none" fill="#000000"/> </g> </svg>
</button>
<div class="dropdown-content" id = "dropdown-content">
<svg xmlns="http://www.w3.org/2000/svg" width="70" viewBox="0 0 75 11">
<text id="hide_legend" data-name="hide legend" transform="translate(30 8)" fill="#5e6365" font-size="12" font-family="CenturyGothicPro, Century Gothic Pro"><tspan x="-29.45" y="0">hide legend</tspan></text>
</svg>
</div>
</div>
<div id="legendPlace">
<svg id = "legend" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="124.5px" viewBox="0 0 108 275">
<defs>
<pattern id="pattern" preserveAspectRatio="xMidYMid slice" width="100%" height="100%" viewBox="0 0 716 152">
<image width="716" height="152" 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<line id="Line_192" data-name="Line 192" x2="17" transform="translate(39 105)" fill="none" stroke="#363535" stroke-width="1"/>
<g id="Polygon_6" data-name="Polygon 6" transform="matrix(-0.358, 0.934, -0.934, -0.358, 58.388, 110.3)" fill="#fff">
<path d="M 3.065736532211304 2.5 L 0.9342632293701172 2.5 L 1.99999988079071 0.9013950228691101 L 3.065736532211304 2.5 Z" stroke="none"/>
<path d="M 1.99999988079071 0 L 4 3 L -2.384185791015625e-07 3 L 1.99999988079071 0 Z" stroke="none" fill="#363535"/>
</g>
<line id="Line_193" data-name="Line 193" x2="17" transform="matrix(0.934, 0.358, -0.358, 0.934, 39, 105)" fill="none" stroke="#363535" stroke-width="1"/>
<g id="Polygon_7" data-name="Polygon 7" transform="translate(56.953 95.791) rotate(69)" fill="#fff">
<path d="M 3.065761566162109 2.499997138977051 L 0.9342533349990845 2.499997138977051 L 2.000007390975952 0.9013741612434387 L 3.065761566162109 2.499997138977051 Z" stroke="none"/>
<path d="M 2.000007390975952 -2.622604370117188e-06 L 4.000017166137695 2.999997138977051 L -2.384185791015625e-06 2.999997138977051 L 2.000007390975952 -2.622604370117188e-06 Z" stroke="none" fill="#363535"/>
</g>
<line id="Line_194" data-name="Line 194" x2="17" transform="translate(39 104.825) rotate(-21)" fill="none" stroke="#363535" stroke-width="1"/>
</svg>
</div>
<!-- LEGEND NUMBERS -->
<div id = "legendNumbers">
<p id="p1" style = "font-family:'CenturyGothicPro-Bold'; position:absolute; right:26px; z-index:150; font-size: 20; bottom:220px">–</p>
<p id="p2" style = "font-family:'CenturyGothicPro-Bold'; position:absolute; right:98px; z-index:150; font-size: 20; bottom:220px">–</p>
<p id="s1" style = "font-family:'CenturyGothicPro-Bold'; position:absolute; right:26px; z-index:150;font-size: 20; bottom:140px">–</p>
<p id="s2" style = "font-family:'CenturyGothicPro-Bold'; position:absolute; right:98px; z-index:150;font-size: 20; bottom:140px">–</p>
<p id="c1" style = "font-family:'CenturyGothicPro-Bold'; position:absolute; right:26px; z-index:150;font-size: 20; bottom:70px">–</p>
<p id="c2" style = "font-family:'CenturyGothicPro-Bold'; position:absolute; right:98px; z-index:150;font-size: 20; bottom:70px">–</p>
<p id="w1" style = "font-family:'CenturyGothicPro-Bold'; position:absolute; right:26px; z-index:150;font-size: 20; bottom:-12px">–</p>
<p id="w2" style = "font-family:'CenturyGothicPro-Bold'; position:absolute; right:98px; z-index:150;font-size: 20; bottom:-12px">–</p>
</div>
<!-- LEGEND REMOVERS -->
<div id="legendRemovers">
<div id="nodeColorRemover">
<svg xmlns="http://www.w3.org/2000/svg" width="119px" style="z-index: 151; position: absolute;right: 5px; bottom: 240px;" viewBox="0 0 95 61">
<rect id="Rectangle_1579" data-name="Rectangle 1579" width="95" height="61" rx="15" fill="rgba(255,255,255,0.85)"/>
</svg>
</div>
<div id="nodeSizeRemover">
<svg xmlns="http://www.w3.org/2000/svg" width="119px" style="z-index: 151; position: absolute;right: 5px; bottom: 160px;" viewBox="0 0 95 61">
<rect id="Rectangle_1579" data-name="Rectangle 1579" width="95" height="61" rx="15" fill="rgba(255,255,255,0.85)"/>
</svg>
</div>
<div id="edgeColorRemover">
<svg xmlns="http://www.w3.org/2000/svg" width="119px" style="z-index: 151; position: absolute;right: 5px; bottom: 80px;" viewBox="0 0 95 61">
<rect id="Rectangle_1579" data-name="Rectangle 1579" width="95" height="61" rx="15" fill="rgba(255,255,255,0.85)"/>
</svg>
</div>
<div id="edgeWeightRemover">
<svg xmlns="http://www.w3.org/2000/svg" width="119px" style="z-index: 151; position: absolute;right: 5px; bottom: 10px;" viewBox="0 0 95 61">
<rect id="Rectangle_1579" data-name="Rectangle 1579" width="95" height="61" rx="15" fill="rgba(255,255,255,0.85)"/>
</svg>
</div>
</div>
<div id="3d-graph" class="full-height"> </div>
<div id = "footer" style="font-family: CenturyGothicPro; z-index: 1000;">
<span style="font-size:0.8vw;color:#6f6f6f;"> Left-click: rotate, Mouse-wheel: zoom, Right-click: pan, Double-click on node: node info, Double-click on background: reset view </span>
</div>
<a href="#" id="downloadbtn" style="display: none; width: 0px; height: 0px;"><button> Download Video </button></a>
<script>
/////////////////////////////////////////////////
///// ENTER AND EXIT FULLSCREEN FUNCTIONS //////
///////////////////////////////////////////////
function fullscreen() {
let isInFullScreen = (document.fullscreenElement && document.fullscreenElement !== null) ||
(document.webkitFullscreenElement && document.webkitFullscreenElement !== null) ||
(document.mozFullScreenElement && document.mozFullScreenElement !== null) ||
(document.msFullscreenElement && document.msFullscreenElement !== null);
let docElm = document.documentElement;
if (!isInFullScreen) {
if (docElm.requestFullscreen) {
docElm.requestFullscreen();
} else if (docElm.mozRequestFullScreen) {
docElm.mozRequestFullScreen();
} else if (docElm.webkitRequestFullScreen) {
docElm.webkitRequestFullScreen();
} else if (docElm.msRequestFullscreen) {
docElm.msRequestFullscreen();
}
} else {
if (document.exitFullscreen) {
document.exitFullscreen();
} else if (document.webkitExitFullscreen) {
document.webkitExitFullscreen();
} else if (document.mozCancelFullScreen) {
document.mozCancelFullScreen();
} else if (document.msExitFullscreen) {
document.msExitFullscreen();
}
}
}
////////////////////////////////////////////////
// DOUBLE CLICK IMPLEMENTATION FOR NODE CLICK //
////////////////////////////////////////////////
var doubleclick = false
window.addEventListener("dblclick", event => {doubleclick = true})
setInterval(myTimer, 100);
function myTimer() {doubleclick = false}
////////////////////////////////////////////////
// HIDE SHOW LEGEND AND MENU IMPLEMENTATIONS ///
////////////////////////////////////////////////
function hideShowLegend(val){
if(val === 0 || val === undefined){
document.getElementById("legendPlace").style.display = "none";
document.getElementById("legendNumbers").style.display = "none";
document.getElementById("legendRemovers").style.display = "none";
document.getElementById("dropdown").value = 1;
document.getElementById("dropbtn").style.transform = "rotate(180deg)";
document.getElementById("dropdown").style.right = "0px";
document.getElementById("dropdown-content").style.left = "-71px";
document.getElementById("dropdown-content").innerHTML = '<svg xmlns="http://www.w3.org/2000/svg" width="70" viewBox="0 0 75 11"> <text id="show_legend" data-name="show legend" transform="translate(32 8)" fill="#5e6365" font-size="12" font-family="CenturyGothicPro, Century Gothic Pro"><tspan x="-31.145" y="0">show legend</tspan></text> </svg>'
}
else{
document.getElementById("legendPlace").style.display = "block";
document.getElementById("legendNumbers").style.display = "block";
document.getElementById("legendRemovers").style.display = "block";
document.getElementById("dropdown").value = 0;
document.getElementById("dropbtn").style.transform = "rotate(0deg)";
document.getElementById("dropdown").style.right = "85px";
document.getElementById("dropdown-content").style.left = "25px";
document.getElementById("dropdown-content").innerHTML = '<svg xmlns="http://www.w3.org/2000/svg" width="70" viewBox="0 0 75 11"> <text id="hide_legend" data-name="hide legend" transform="translate(30 8)" fill="#5e6365" font-size="12" font-family="CenturyGothicPro, Century Gothic Pro"><tspan x="-29.45" y="0">hide legend</tspan></text> </svg>'
}
}
function hideShowMenu(val) {
if(val===0 || val === undefined){
// document.getElementById("nqText").style.display = "none";
document.getElementById("nodequeryMain").style.display = "none";
document.getElementById("openbutton-content").innerHTML = '<svg xmlns="http://www.w3.org/2000/svg" width="80px" viewBox="0 0 81 11"> <text id="close_controls" data-name="close controls" transform="translate(30 8)" fill="#5e6365" font-size="12" font-family="CenturyGothicPro, Century Gothic Pro"><tspan x="-29.45" y="0">open controls</tspan></text> </svg>';
document.getElementById("openbutton-button").innerHTML = '<svg xmlns="http://www.w3.org/2000/svg" width="20px" viewBox="0 0 13 13"> <g id="Rectangle_1582" data-name="Rectangle 1582" fill="#fff" stroke="#2e3137" stroke-width="1"> <rect width="13" height="13" stroke="none"/> <rect x="0.5" y="0.5" width="12" height="12" fill="none"/> </g> <line id="Line_201" data-name="Line 201" x2="6.5" transform="translate(3.25 4.5)" fill="none" stroke="#2e3137" stroke-width="1.2"/> <line id="Line_202" data-name="Line 202" x2="6.5" transform="translate(3.25 6.5)" fill="none" stroke="#2e3137" stroke-width="1.2"/> <line id="Line_203" data-name="Line 203" x2="6.5" transform="translate(3.25 8.5)" fill="none" stroke="#2e3137" stroke-width="1.2"/> </svg> '
document.getElementById("openbutton").value = 1;
document.getElementById("guiplace").style.display = "none";
}
else{
// document.getElementById("nqText").style.display = "block";
document.getElementById("nodequeryMain").style.display = "block";
document.getElementById("openbutton-content").innerHTML = ''
document.getElementById("openbutton-button").innerHTML = '<svg xmlns="http://www.w3.org/2000/svg" width="20px" viewBox="0 0 13 16"> <g id="Rectangle_1581" data-name="Rectangle 1581" transform="translate(0 1)" fill="#fff" stroke="#2e3137" stroke-width="1"> <rect width="13" height="13" stroke="none"/> <rect x="0.5" y="0.5" width="12" height="12" fill="none"/> </g> <text id="x" transform="translate(6.5 11)" fill="#9f9f9f" stroke="#2e3137" stroke-width="1" font-size="14" font-family="CenturyGothicPro-Bold, Century Gothic Pro" font-weight="700"><tspan x="-3.92" y="0">x</tspan></text> </svg>'
document.getElementById("openbutton").value = 0;
document.getElementById("guiplace").style.display = "block";
}
}
////////////////////////////////////////////////
//////////////// DATA CREATION ////////////////
///////////////////////////////////////////////
function linkExist(sourceTargetTuples,kinaseID,targetID){
for (let idx = 0; idx < sourceTargetTuples.length; idx++) {
currTuple = sourceTargetTuples[idx]
if (currTuple[0] === kinaseID && currTuple[1] === targetID){
return true
}
}
return false
}
function parseCSV(file_name) {
let dict = {"nodes": [], "links": []}
var userData = JSON.parse(window.localStorage.getItem(file_name));
for (let i = 0; i < userData.length; i++) {
dataLine = userData[i]
kinaseID = dataLine['KinaseID']
kinaseSize = dataLine['KinaseSize']
kinaseActivity = dataLine['KinaseActivity']
edgeWeight = dataLine['EdgeWeight']
edgeColor = dataLine['EdgeHue']
targetID = dataLine['TargetID']
targetSize = dataLine['TargetSize']
diffPhos = dataLine['log2FC']
PhosphoSiteID = dataLine['PhosphoSiteID']
pValue = dataLine['pValue']
currentNodeList = dict["nodes"].map(el => el.id)
//kinase is type 1, target is type 2
if (!(currentNodeList.includes(kinaseID))){ // if kinase id does not occur in nodes
dict["nodes"].push({'id': kinaseID, "type": 1, "kinaseActivity":kinaseActivity, "nodeSize": kinaseSize, "nodeColors": [], "partitionIDs":[], "pValues":[]})
currentNodeList.push(kinaseID)
}
else { // kinase id occurs, need to check if it is labeled as target and change its type into kinase (1)
nodeIndex = currentNodeList.indexOf(kinaseID)
dict['nodes'][nodeIndex]['type'] = 1
}
if (!(currentNodeList.includes(targetID))){
let currentNodeColors = []
if(diffPhos!=undefined){currentNodeColors.push(diffPhos)}
let currentNodePartitions = []
if(PhosphoSiteID!=undefined){currentNodePartitions.push(PhosphoSiteID)}
let currentpValues = []
if(pValue!=undefined){currentpValues.push(pValue)}
dict["nodes"].push({'id': targetID, "type": 2, "kinaseActivity":0, "nodeSize": targetSize, "nodeColors": currentNodeColors, "partitionIDs": currentNodePartitions, "pValues": currentpValues})
}
else{ // target id occurs again (may have partitions!!!), if so we need to append diffPhos to nodecolors and PhosphoSiteID to partitionIDs
// no need to update its type as target !!!!!!!!
nonDirtyNodeList = dict["nodes"].map(el => el.id)
nodeIndex = nonDirtyNodeList.indexOf(targetID)
if(PhosphoSiteID != undefined && !(dict['nodes'][nodeIndex]['partitionIDs'].includes(PhosphoSiteID))){
dict['nodes'][nodeIndex]['partitionIDs'].push(PhosphoSiteID)
if(diffPhos!=undefined){dict['nodes'][nodeIndex]['nodeColors'].push(diffPhos)}
if(pValue!=undefined){ dict['nodes'][nodeIndex]['pValues'].push(pValue)}
}
else if (dict['nodes'][nodeIndex]['nodeColors'].length == 0) // if target id reoccurs again because it is a phosphorylated kinase
{
if(diffPhos!=undefined){dict['nodes'][nodeIndex]['nodeColors'].push(diffPhos)}
if(pValue!=undefined){ dict['nodes'][nodeIndex]['pValues'].push(pValue)}
}
}
sourceTargetTuples = dict["links"].map(el => [el.source,el.target])
if(!(linkExist(sourceTargetTuples,kinaseID,targetID))){
if(kinaseID===targetID){
dict['links'].push({'source': kinaseID, 'target': targetID, 'edgeWeight': edgeWeight, 'edgeColor': edgeColor, 'curvature':.4})
}
else{
dict['links'].push({'source': kinaseID, 'target': targetID, 'edgeWeight': edgeWeight, 'edgeColor': edgeColor, 'curvature':0})
}
}
}
for(let nodeIndex = 0 ; nodeIndex<dict['nodes'].length; nodeIndex++){
let tempColors = dict['nodes'][nodeIndex]['nodeColors']
indices = Array.from(tempColors.keys()).sort( (a,b) => tempColors[b]-tempColors[a]) // sorting partitions by colors
dict['nodes'][nodeIndex]['partitionIDs'] = indices.map(i => dict['nodes'][nodeIndex]['partitionIDs'][i])
dict['nodes'][nodeIndex]['nodeColors'] = indices.map(i => dict['nodes'][nodeIndex]['nodeColors'][i])
dict['nodes'][nodeIndex]['pValues'] = indices.map(i => dict['nodes'][nodeIndex]['pValues'][i])
if(dict['nodes'][nodeIndex]['nodeColors'].length>10){ // only getting top 10
dict['nodes'][nodeIndex]['partitionIDs'] = [...dict['nodes'][nodeIndex]['partitionIDs'].slice(0,10)]
dict['nodes'][nodeIndex]['nodeColors'] = [...dict['nodes'][nodeIndex]['nodeColors'].slice(0,10)]
dict['nodes'][nodeIndex]['pValues'] = [...dict['nodes'][nodeIndex]['pValues'].slice(0,10)]
}
let tempPartitions = dict['nodes'][nodeIndex]['partitionIDs']
if(tempPartitions.length > 0){ // sorting partitions by number
try{
phindices = Array.from(tempPartitions.keys()).sort((a,b) => parseFloat(tempPartitions[a].replace(/^\D+/g, ''))-parseFloat(tempPartitions[b].replace(/^\D+/g, '')))
dict['nodes'][nodeIndex]['partitionIDs'] = phindices.map(i => dict['nodes'][nodeIndex]['partitionIDs'][i])
dict['nodes'][nodeIndex]['nodeColors'] = phindices.map(i => dict['nodes'][nodeIndex]['nodeColors'][i])
dict['nodes'][nodeIndex]['pValues'] = phindices.map(i => dict['nodes'][nodeIndex]['pValues'][i])
}
catch(err) {
console.log("no numerical attributes in phosphosites to order!")
}
}
}
dict['ids'] = dict["nodes"].map(el => el.id)
return dict;
}
const CAMERA_DISTANCE2NODES_FACTOR = 170;
var file_names = JSON.parse(localStorage.getItem("file_names"))
var index = localStorage.getItem("idx")
var finalDataObj = parseCSV(localStorage.getItem(file_names[index]))
// var dataStr = "data:text/json;charset=utf-8," + encodeURIComponent(JSON.stringify(finalDataObj));
// var downloadAnchorNode = document.createElement('a');
// downloadAnchorNode.setAttribute("href", dataStr);
// downloadAnchorNode.setAttribute("download", file_names[index] + ".json");
// document.body.appendChild(downloadAnchorNode); // required for firefox
// downloadAnchorNode.click();
// downloadAnchorNode.remove();
function thresholdDecider(DataObj){
let nodeSizes = (DataObj["nodes"].map(el => el.nodeSize)).filter(x => x != undefined)
let nodeColors = ((DataObj["nodes"].map(el => el.nodeColors)).flat()).filter(x => x != undefined)
let nodeSizeRange = [Math.min.apply(Math, nodeSizes), Math.max.apply(Math, nodeSizes)]
let nodeColorRange = [Math.min.apply(Math, nodeColors), Math.max.apply(Math, nodeColors)]
let nodeColorThreshold = null
if (nodeColorRange[0] != undefined && nodeColorRange[1] != undefined){
let minPositive = 0
let maxPositive = 0
nodeColorRange[0]<0 ? minPositive = - nodeColorRange[0] : minPositive = nodeColorRange[0]
nodeColorRange[1]<0 ? maxPositive = - nodeColorRange[1] : maxPositive = nodeColorRange[1]
minPositive>maxPositive ? nodeColorThreshold = minPositive : nodeColorThreshold = maxPositive
}
let edgeWeights = (DataObj["links"].map(el => el.edgeWeight)).filter(x => x != undefined)
let edgeColors = (DataObj["links"].map(el => el.edgeColor)).filter(x => x != undefined)
let edgeWeightRange = [Math.min.apply(Math, edgeWeights), Math.max.apply(Math, edgeWeights)]
let edgeColorRange = [Math.min.apply(Math, edgeColors), Math.max.apply(Math, edgeColors)]
return {"nodeSizes":nodeSizes, "nodeColors":nodeColors, "nodeSizeRange":nodeSizeRange, "nodeColorRange":nodeColorRange, "nodeColorThreshold":nodeColorThreshold, "edgeWeights":edgeWeights, "edgeColors":edgeColors, "edgeWeightRange":edgeWeightRange, "edgeColorRange":edgeColorRange}
}
var thresholds = thresholdDecider(finalDataObj)
var [nodeSizes, nodeColors, nodeSizeRange, nodeColorRange, nodeColorThreshold, edgeWeights, edgeColors, edgeWeightRange, edgeColorRange] = [thresholds["nodeSizes"], thresholds["nodeColors"], thresholds["nodeSizeRange"], thresholds["nodeColorRange"], thresholds["nodeColorThreshold"], thresholds["edgeWeights"],thresholds["edgeColors"],thresholds["edgeWeightRange"],thresholds["edgeColorRange"]]
var nodesList = finalDataObj["ids"]
const searchNodes = new Set();
const searchLinks = new Set();
/////////////////////////////////////////////////
///////// LEGEND IMPLEMENTATION /////////////////
/////////////////////////////////////////////////
function nodeColorLegend(phosOption){
if(nodeColorThreshold != null && nodeColorThreshold != Infinity && nodeColorThreshold != NaN && phosOption === "Show"){
let nodeColorThresholdL = nodeColorThreshold > 3 ? 3 : nodeColorThreshold
document.getElementById("p1").innerHTML = Number(-nodeColorThresholdL).toFixed(2)
document.getElementById("p2").innerHTML = Number(nodeColorThresholdL).toFixed(2)
document.getElementById("p1").style.bottom ="225px"
document.getElementById("p2").style.bottom = "225px"
document.getElementById("p1").style.right = "85px"
document.getElementById("p2").style.right = "15px"
document.getElementById("p1").style.fontFamily = "CenturyGothicPro"
document.getElementById("p2").style.fontFamily = "CenturyGothicPro"
document.getElementById("p1").style.fontSize = 15
document.getElementById("p2").style.fontSize = 15
document.getElementById("nodeColorRemover").style.display = "none"
}
else{
if(searchNodes.size === 0 || animationActive) {
document.getElementById("p1").innerHTML = "–"
document.getElementById("p2").innerHTML = "–"
document.getElementById("p1").style.bottom ="220px"
document.getElementById("p2").style.bottom = "220px"
document.getElementById("p1").style.right = "98px"
document.getElementById("p2").style.right = "26px"
document.getElementById("p1").style.fontFamily = "CenturyGothicPro-Bold"
document.getElementById("p2").style.fontFamily = "CenturyGothicPro-Bold"
document.getElementById("p1").style.fontSize = 20
document.getElementById("p2").style.fontSize = 20
document.getElementById("nodeColorRemover").style.display = "block"
}
}
}
nodeColorLegend("Show");
function restOfLegends(){
if(nodeSizes.length>0 && nodeSizes.length>0){
document.getElementById("s1").innerHTML = Number(nodeSizeRange[0]).toFixed(2)
document.getElementById("s2").innerHTML = Number(nodeSizeRange[1]).toFixed(2)
document.getElementById("s1").style.bottom = "145px"
document.getElementById("s2").style.bottom = "145px"
document.getElementById("s1").style.right = nodeSizeRange[0]<0 ? "80px":"85px"
document.getElementById("s2").style.right = nodeSizeRange[1]<0 ? "10px":"15px"
document.getElementById("s1").style.fontFamily = "CenturyGothicPro"
document.getElementById("s2").style.fontFamily = "CenturyGothicPro"
document.getElementById("s1").style.fontSize = 15
document.getElementById("s2").style.fontSize = 15
document.getElementById("nodeSizeRemover").style.display = "none"
}
else{
if(animationActive){
document.getElementById("s1").innerHTML = "–"
document.getElementById("s2").innerHTML = "–"
document.getElementById("s1").style.bottom = "140px"
document.getElementById("s2").style.bottom = "140px"
document.getElementById("s1").style.right = "26px"
document.getElementById("s2").style.right = "98px"
document.getElementById("s1").style.fontFamily = "CenturyGothicPro"
document.getElementById("s2").style.fontFamily = "CenturyGothicPro"
document.getElementById("s1").style.fontSize = 20
document.getElementById("s2").style.fontSize = 20
document.getElementById("nodeSizeRemover").style.display = "block"
}
}
if(edgeColors.length>0 && edgeColors.length>0){
document.getElementById("c1").innerHTML = Number(edgeColorRange[0]).toFixed(2)
document.getElementById("c2").innerHTML = Number(edgeColorRange[1]).toFixed(2)
document.getElementById("c1").style.bottom = "75px"
document.getElementById("c2").style.bottom = "75px"
document.getElementById("c1").style.right = nodeSizeRange[0]<0 ? "80px":"85px"
document.getElementById("c2").style.right = nodeSizeRange[1]<0 ? "10px":"15px"
document.getElementById("c1").style.fontFamily = "CenturyGothicPro"
document.getElementById("c2").style.fontFamily = "CenturyGothicPro"
document.getElementById("c1").style.fontSize = 15
document.getElementById("c2").style.fontSize = 15
document.getElementById("edgeColorRemover").style.display = "none"
}
else{
if(animationActive){
document.getElementById("c1").innerHTML = "–"
document.getElementById("c2").innerHTML = "–"
document.getElementById("c1").style.bottom = "70px"
document.getElementById("c2").style.bottom = "70px"
document.getElementById("c1").style.right = "26px"
document.getElementById("c2").style.right = "98px"
document.getElementById("c1").style.fontFamily = "CenturyGothicPro"
document.getElementById("c2").style.fontFamily = "CenturyGothicPro"
document.getElementById("c1").style.fontSize = 20
document.getElementById("c2").style.fontSize = 20
document.getElementById("edgeColorRemover").style.display = "block"
}
}
if(edgeWeights.length>0 && edgeWeights.length>0){
document.getElementById("w1").innerHTML = Number(edgeWeightRange[0]).toFixed(2)
document.getElementById("w2").innerHTML = Number(edgeWeightRange[1]).toFixed(2)
document.getElementById("w1").style.bottom = "-5px"
document.getElementById("w2").style.bottom = "-5px"
document.getElementById("w1").style.right = edgeWeightRange[0]<0 ? "80px":"85px"
document.getElementById("w2").style.right = edgeWeightRange[1]<0 ? "10px":"15px"
document.getElementById("w1").style.fontFamily = "CenturyGothicPro"
document.getElementById("w2").style.fontFamily = "CenturyGothicPro"
document.getElementById("w1").style.fontSize = 15
document.getElementById("w2").style.fontSize = 15
document.getElementById("edgeWeightRemover").style.display = "none"
}
else{
if(animationActive){
document.getElementById("w1").innerHTML = "–"
document.getElementById("w2").innerHTML = "–"
document.getElementById("w1").style.bottom = "-12x"
document.getElementById("w2").style.bottom = "-12px"
document.getElementById("w1").style.right = "26px"
document.getElementById("w2").style.right = "98px"
document.getElementById("w1").style.fontFamily = "CenturyGothicPro"
document.getElementById("w2").style.fontFamily = "CenturyGothicPro"
document.getElementById("w1").style.fontSize = 20
document.getElementById("w2").style.fontSize = 20
document.getElementById("edgeWeightRemover").style.display = "block"
}
}
}
restOfLegends()
// cross-linking the node objects
finalDataObj.links.forEach(link => {
const a = (finalDataObj.nodes.filter(x => x.id === link.source))[0]
const b = (finalDataObj.nodes.filter(x => x.id === link.target))[0]
!a.neighbors && (a.neighbors = []);
!b.neighbors && (b.neighbors = []);
a.neighbors.push(b);
b.neighbors.push(a);
!a.links && (a.links = []);
!b.links && (b.links = []);
a.links.push(link);
b.links.push(link);
});
/////////////////////////////////////////
////////// GUI CONTROLS ////////////////
////////////////////////////////////////
const fnames = {};
for (const key of file_names) {
fnames[key] = key;
}
const PARAMS = {
Network: file_names[index],
PosL2FC : 0,
NegL2FC : 0,
Background : "#ffffff",
Phosphorylation: "Show",
Labels: "Off"
};
const phosOpt = ["Hide", "Show"];
const labelOpt = ["On", "Off"];
const pane = new Tweakpane.Pane({
container: document.getElementById('guiplace'),
});
pane.registerPlugin(TweakpaneEssentialsPlugin);
const tab = pane.addTab({
pages: [
{title: 'Controls'},
{title: 'Animate & Record'}
],
});
tab.pages[0].addInput(PARAMS, 'Network', {options: fnames, label: 'Network'}).on('change', (ev) => {
changeState();
});
tab.pages[0].addInput(PARAMS, 'PosL2FC', {min: 0, max: nodeColorThreshold, label: 'Pos-Log2FC'}).on('change', (ev) => {
updateHighlight();
});
tab.pages[0].addInput(PARAMS, 'NegL2FC', {min: -nodeColorThreshold, max: 0, label: 'Neg-Log2FC'}).on('change', (ev) => {
updateHighlight();
});
tab.pages[0].addInput(PARAMS, 'Background').on('change', (ev) => {
updateBackground();
});
tab.pages[0].addInput(PARAMS, 'Phosphorylation', {
view: 'radiogrid',
groupName: 'Phosphorylation',
size: [2, 1],
cells: (x, y) => ({
title: phosOpt[y * 3 + x],
value: phosOpt[y * 3 + x],
}),
label: 'Partitions',
}).on('change', (ev) => {
nodeColorLegend(PARAMS.Phosphorylation);
Graph.nodeThreeObject(Graph.nodeThreeObject())
});
tab.pages[0].addInput(PARAMS, 'Labels', {
view: 'radiogrid',
groupName: 'Labels',
size: [2, 1],
cells: (x, y) => ({
title: labelOpt[y * 3 + x],
value: labelOpt[y * 3 + x],
}),
label: 'Labels',
}).on('change', (ev) => {
Graph.nodeThreeObject(Graph.nodeThreeObject())
});
tab.pages[0].addButton({title: 'Enter/Exit Fullscreen'}).on('click',()=>{
fullscreen();
});
tab.pages[0].addButton({title: 'Take a screenshot'}).on('click',()=>{
snapshot();
});
tab.pages[0].addButton({title: 'Reset'}).on('click',()=>{
queryReset();
});
tab.pages[0].addSeparator();
tab.pages[0].addSeparator();
tab.pages[0].addButton({title: 'Switch to 2D'}).on('click',()=>{
window.location.href = 'visualization-2d.html'
});
// Add a new section to your pane for the hyperlink
const geneEnrichSection = tab.pages[0].addFolder({
title: 'Gene Enrichment Analysis',
expanded: true
});
const enrichButton = geneEnrichSection.addButton({title: 'Send genes to Enrichr', disabled: false})
const nodeIDS = finalDataObj["ids"]
let status = checkIDType(nodeIDS)
enrichButton.on('click', async () => {
try {
$('#loader-class').css('display', 'flex');
if(status == "protein"){
const geneMappings = await getGeneIDs(nodeIDS);
// Call the enrich function with the collected genes
const genes = geneMappings.map(mapping => mapping.geneID);
const geneList = genes.join('\n');
enrich({
list: geneList,
description: 'Gene Enrichment Analysis',
popup: true
});
}
else{
const geneList = nodeIDS.join('\n');
enrich({
list: geneList,
description: 'Gene Enrichment Analysis',
popup: true
});
}
// Open Enrichr in a new tab
// window.open('https://maayanlab.cloud/Enrichr/', '_blank');
$('#loader-class').css('display', 'none');
console.log('Enrichr button clicked');
} catch (error) {
console.error('Error fetching gene IDs:', error);
}
});
// geneEnrichSection.add({ link: 'Send Genes to Enrichr' }, 'link')
// .on('click', () => {
// window.open('https://your-enrichment-url.com', '_blank');
// });
const f1 = tab.pages[1].addFolder({
title: 'Animation',
});
const startAnimation = f1.addButton({title: 'Start Animation ▶', disabled: false})
// const pauseAnimation = f1.addButton({title: 'Stop Animation ❚❚', disabled: true})
const stopAnimation =f1.addButton({title: 'Stop Animation ❚❚', disabled: true})
const fileMonitor = f1.addMonitor(PARAMS, 'Network', {
multiline: false,
lineCount: 1,
});
startAnimation.on('click', () => {
if(animate()){
stopAnimation.disabled === true ? stopAnimation.disabled = false : true
startAnimation.disabled === true ? startAnimation.disabled = false : startAnimation.disabled = true
}
});
stopAnimation.on('click', () => {
if(animationActive){
startAnimation.disabled === true ? startAnimation.disabled = false: true
stopAnimation.disabled = !stopAnimation.disabled;
clearInterval(animationInterval)
animationIndex = -1
PARAMS.Network = file_names[localStorage.getItem("idx")]
let newthresholds = thresholdDecider(finalDataObj)
nodeSizes = newthresholds["nodeSizes"]
nodeColors = newthresholds["nodeColors"]
nodeSizeRange = newthresholds["nodeSizeRange"]
nodeColorRange = newthresholds["nodeColorRange"]
nodeColorThreshold = newthresholds["nodeColorThreshold"]
edgeWeights = newthresholds["edgeWeights"]
edgeColors = newthresholds["edgeColors"]
edgeWeightRange = newthresholds["edgeWeightRange"]
edgeColorRange = newthresholds["edgeColorRange"]
restOfLegends();
animationActive = false
resetRows();
if(clickedNode!=null){
let animationFinalClicked = finalDataObj["nodes"].find(x => x.id === clickedNode);
addRows(animationFinalClicked.partitionIDs, animationFinalClicked.nodeColors, animationFinalClicked.pValues)
}
nodeColorLegend(PARAMS.Phosphorylation);
Graph.nodeThreeObject(Graph.nodeThreeObject());
Graph.linkWidth(link => (searchLinks.has(link)) ? 1 : animationActive === true ? linkWidthAnimation(link) : (edgeWeightRange[0]!= undefined && link.edgeWeight != undefined) ? normalized(link.edgeWeight, edgeWeightRange, [0,1])+.5 : .8) // subject to change
}
});
tab.pages[1].addSeparator();
tab.pages[1].addSeparator();
const f2 = tab.pages[1].addFolder({
title: 'Screen Record',
});
const startRecord = f2.addButton({title: 'Start Recording ▶',disabled: false})
const stopRecord =f2.addButton({title: 'Stop Recording ❚❚', disabled: true})
f2.addSeparator();
const downloadRecord = f2.addButton({title: 'Download Recording ↴', disabled: true})
startRecord.on('click', () => {
stopRecord.disabled = !stopRecord.disabled;
startRecord.disabled = !startRecord.disabled;
startRecording()
if(!downloadRecord.disabled){
downloadRecord.disabled = !downloadRecord.disabled;
}
});
stopRecord.on('click', () => {
stopRecord.disabled = !stopRecord.disabled;
startRecord.disabled = !startRecord.disabled;
stopScreen()
downloadRecord.disabled = !downloadRecord.disabled;
});
downloadRecord.on('click', () => {
downloadRecord.disabled = !downloadRecord.disabled;
downloadVideo()
});
/////////////////////////////////////////////////
//////////////// GRAPH CREATION ////////////////
/////////////////////////////////////////////////
const regex = new RegExp('[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}')
var elem = document.getElementById('3d-graph');
var Graph = ForceGraph3D({rendererConfig:{preserveDrawingBuffer : true}})
(elem)
.backgroundColor("#ffffff")
.graphData(finalDataObj)
.linkCurvature('curvature')
.nodeThreeObject(node => animationActive === false ? CreateNode(node): createNodeAnimation(node))
.onNodeClick(node => {
if(doubleclick){
clickedNode = node.id
resetRows();
searchNodes.clear();
searchLinks.clear();
// Aim at node from outside it
const distance = 100;
const distRatio = 1 + distance/Math.hypot(node.x, node.y, node.z);
const newPos = node.x || node.y || node.z