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.php
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<!DOCTYPE html>
<html lang="en">
<head>
<title>SARS-CoV2 Page</title>
<link rel="stylesheet" href="bootstrap.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet"/>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script>
<script src="https://canvasjs.com/assets/script/canvasjs.min.js"></script>
<?php include "./Navigation.php";?>
<style>
.btn
{
margin-top: 25px;
margin-right: 5px;
}
.search-header
{
padding-left: 10px;
}
.search-body
{
background-color: lightgrey;
}
.panel-body
{
background-color: white;
}
.datacontainer {
display: flex;
}
.datacontainer > div {
flex: 1;
}
.datagrid {
height: 500px;
overflow: auto;
display: inline-block;
}
.datagraph {
height: 500px;
padding: 15px;
}
.datagraph.canvasjs-chart-canvas {
width: 100% !important;
border: 1ps solid grey;
}
tr.darkheader th{
background: #333;
color: white;
position: sticky;
top: 0;
box-shadow: 0 2px 2px -1px rgba(0, 0, 0, 0.4);
text-align: center;
}
tr.greyheader th{
background: grey;
color: white;
position: sticky;
top: 33px;
box-shadow: 0 2px 2px -1px rgba(0, 0, 0, 0.4);
text-align: left;
}
tr.grey td{
background: lightgrey;
color: black;
box-shadow: 0 2px 2px -1px rgba(0, 0, 0, 0.4);
text-align: left;
}
.table {
text-align: left;
font-size: 12px;
}
td.rowexpand {
font-weight: bold;
}
/* Style the tab */
.tab {
overflow: hidden;
border-bottom: 1px solid #dee2e6;
margin-bottom: 15px;
}
/* Style the buttons inside the tab */
.tab button {
background-color: inherit;
float: left;
border: none;
outline: none;
cursor: pointer;
padding: 10px 16px;
transition: 0.3s;
font-size: 12px;
}
/* Change background color of buttons on hover */
.tab button:hover {
background-color: #ddd;
}
/* Create an active/current tablink class */
.tab button.active {
background-color: #ccc;
}
</style>
</head>
<body class="search-body">
<h4 class="search-header">Mutations</h4>
<div class="panel-body">
<div id="searchgrid">
<div class="form-group" style="height:10%; width:100%;">
<div class="row">
<fieldset id="Mutations_row">
<!--<div class="col-md-2">
<label for="Reference">Reference Base</label>
<select class = "form-control" id="ReferenceBase">
<option value= "">All</option>
<option value="A">A</option>
<option value="C">C</option>
<option value="G">G</option>
<option value="T">T</option>
</select>
</div>
<div class="col-md-2">
<label for="Alternate">Alternate Base</label>
<select class = "form-control" id="AlternateBase">
<option value= "">All</option>
<option value="A">A</option>
<option value="C">C</option>
<option value="G">G</option>
<option value="T">T</option>
</select>
</div>
<div class="col-md-2">
<label for="Instrument">Instrument</label>
<select class = "form-control" id="Instrument">
<option value= "">All</option>
<option value="Illumina_miseq">Illumina_miseq</option>
<option value="Illumina_novaseq_6000">Illumina_novaseq_6000</option>
<option value="Nextseq_500">Nextseq_500</option>
<option value="Nextseq_550">Nextseq_550</option>
</select>
</div> -->
<div class="col-md-2">
<label for="Start">Start</label>
<input id="Start" type="text" class="form-control"/>
</div>
<div class="col-md-2">
<label for="End">End</label>
<input id="End" type="text" class="form-control" />
</div>
<div class="col-md-2">
<button type="submit" class="btn btn-success" id="submit_btn" name="submit">Submit</button>
<button type="button" onclick="resetForm();" id="clear_btn" class="btn btn-secondary">Clear</button>
</div>
<div class="col-md-2">
<label for="Region">Region</label>
<select class = "form-control" id="Region" >
<option value= "">All</option>
<option value="Nsp1">Nsp1</option>
<option value="Nsp2">Nsp2</option>
<option value="Nsp3">Nsp3</option>
<option value="Nsp4">Nsp4</option>
<option value="Nsp5">Nsp5</option>
<option value="Nsp6">Nsp6</option>
<option value="Nsp7">Nsp7</option>
<option value="Nsp8">Nsp8</option>
<option value="Nsp9">Nsp9</option>
<option value="Nsp10">Nsp10</option>
<option value="Nsp11">Nsp11</option>
<option value="Nsp12">Nsp12</option>
<option value="Nsp13">Nsp13</option>
<option value="Nsp14">Nsp14</option>
<option value="Nsp15">Nsp15</option>
<option value="Nsp16">Nsp16</option>
<option value="Surface Glycoprotein">S Gene</option>
<option value="ORF3a Protein">ORF3a</option>
<option value="Envelope Membrane Protein">E Gene</option>
<option value="Membrane Protein">M Gene</option>
<option value="ORF6a Protein">ORF6a</option>
<option value="ORF7a Protein">ORF7a</option>
<option value="ORF7b Protein">ORF7b</option>
<option value="ORF8 Protein">ORF8</option>
<option value="ORF9 protein">ORF9</option>
<option value="Nucleocapsid proteins">N Gene</option>
<option value="ORF10 Protein">ORF10</option>
</select>
</div>
</fieldset>
<br />
</div>
</div>
</div>
<i id="emptyText">Apply filters and hit submit to start seeing results.</i>
<div id="mutationsData" style="display:none;">
<div class="tab">
<button class="tablinks active" id="summaryTab" onclick="activateMutationsResultTab('summaryTab', 'mutationsSummary')">Summary</button>
<button class="tablinks" id="detailTab" onclick="activateMutationsResultTab('detailTab', 'mutationsDetail')">Detail</button>
</div>
<div id="mutationsSummary" class="datacontainer">
<div id="datagrid" class="datagrid">
</div>
<div id="mutationsChart" class="datagraph"></div>
</div>
</br></br>
<div id="mutationsSummaryFrequency" class="datacontainer">
<div id="mutationsByFreqChart" class="datagraph"></div>
</div>
</br></br>
<div id="mutationsShapeScore" class="datacontainer">
<div id="mutationsShapeScoreChart" class="datagraph"></div>
</div>
<div id="mutationsDetail" class="datacontainer" style="display:none;">
<i>Detail view of the mutations.</i>
</div>
</div>
</div>
<script>
window.onload = function() {
if (localStorage.getItem("start")){
console.log(localStorage.getItem("start"));
document.getElementById("Start").value=parseInt(localStorage.getItem("start"));
document.getElementById("End").value=parseInt(localStorage.getItem("end"));
}
var mutationsChartData = [], mutationsByFreqData=[], mutationsShapeScoreData = [] ;
CanvasJS.addColorSet("greenShades",
[//colorSet Array
"#6d78ad" //--> lavendar
]);
CanvasJS.addColorSet("orangeShades", ['#df7970']);
var mutationsChart = new CanvasJS.Chart("mutationsChart", {
title: {
text: "Mutations by instrument"
},
theme: "light2",
animationEnabled: true,
toolTip:{
shared: true
},
axisY:{
includeZero: true,
labelFontSize: 12,
labelFontColot: "dimGrey"
},
axisX: {
labelFontSize: 12,
labelFontColot: "dimGrey",
interval: 1
},
legend:{
fontSize: 14,
fontColor: "Grey"
},
data: mutationsChartData
});
var mutationsByFreqChart = new CanvasJS.Chart("mutationsByFreqChart", {
title: {
text: "Mutations by frequency"
},
colorSet: 'greenShades',
theme: "light2",
animationEnabled: true,
toolTip:{
shared: true
},
axisY:{
title: 'Frequency',
includeZero: true,
labelFontSize: 12,
labelFontColot: "dimGrey"
},
axisX: {
title: 'Coordinate Intervals',
labelFontSize: 12,
labelFontColot: "dimGrey",
interval: 1
},
legend:{
fontSize: 14,
fontColor: "Grey"
},
toolTip: {
shared: true,
contentFormatter: function (e) {
var content = " ";
for (var i = 0; i < e.entries.length; i++) {
content += "Start - End: " + "<strong>" + e.entries[i].dataPoint.label + "</strong>";
content += "<br/>";
content += "Total: " + "<strong>" + e.entries[i].dataPoint.y + "</strong>";
}
return content;
}
},
data: mutationsByFreqData
});
var mutationsShapeScoreChart = new CanvasJS.Chart("mutationsShapeScoreChart", {
title: {
text: "Mutations Relativity Score"
},
colorSet: 'orangeShades',
theme: "light2",
animationEnabled: true,
toolTip:{
shared: true
},
axisY:{
title: 'Shape Score',
includeZero: true,
labelFontSize: 12,
labelFontColot: "dimGrey"
},
axisX: {
title: 'Coordinate Intervals',
labelFontSize: 12,
labelFontColot: "dimGrey",
interval: 1
},
legend:{
fontSize: 14,
fontColor: "Grey"
},
toolTip: {
shared: true,
contentFormatter: function (e) {
var content = " ";
for (var i = 0; i < e.entries.length; i++) {
content += "Start - End: " + "<strong>" + e.entries[i].dataPoint.label + "</strong>";
content += "<br/>";
content += "Total: " + "<strong>" + e.entries[i].dataPoint.y + "</strong>";
}
return content;
}
},
data: mutationsShapeScoreData
});
var submitButton = document.getElementById("submit_btn");
submitButton.addEventListener("click", submitGetMutationData);
var clearButton = document.getElementById("clear_btn");
clearButton.addEventListener("click", resetForm);
var regionDropDown = document.getElementById("Region");
regionDropDown.addEventListener("change", getMutationsData);
getMutationsData();
function resetForm(){
document.getElementById("Start").value="";
document.getElementById("End").value="";
}
function submitGetMutationData() {
localStorage.clear();
document.getElementById("emptyText").style.display = "none";
document.getElementById("mutationsData").style.display = "block";
var region = document.getElementById("Region").value;
var start = document.getElementById("Start").value;
var end = document.getElementById("End").value;
if( start!= "" || end != ""){
document.getElementById("Region").value = "";
console.log(region)
// region = "";
}
getData(start,end,region)
}
function getMutationsData() {
document.getElementById("emptyText").style.display = "none";
document.getElementById("mutationsData").style.display = "block";
var region = document.getElementById("Region").value;
var start = document.getElementById("Start").value;
var end = document.getElementById("End").value;
console.log(start,end);
console.log(region != "",region)
if( region != "" ) {
start = "";
end = "";
resetForm();
}
// if( start!= "" || end != ""){
// // document.getElementById("Region").value = "";
// region = "";
// }
//var referenceBase = document.getElementById("ReferenceBase").value;
//var alternateBase = document.getElementById("AlternateBase").value;
//var instrument = document.getElementById("Instrument").value;
getData(start,end,region)
}
function getData(start,end,region){
var xmlhttp = new XMLHttpRequest();
xmlhttp.onreadystatechange = function() {
if (this.readyState == 4 && this.status == 200) {
var res = JSON.parse(this.responseText);
for (i = 0; i < res.mutationsByInstrument.length; i++) {
var datagridEle = document.getElementById("datagrid");
datagridEle.innerHTML = res.mutationsByInstrument[i].datagridHTML;
mutationsChartData.splice(0,mutationsChartData.length);
mutationsChartData.push({
type: "stackedColumn",
showInLegend: true,
name: "illumina_miseq",
dataPoints: res.mutationsByInstrument[i].illumina_miseq
},{
type: "stackedColumn",
showInLegend: true,
name: "illumina_novaseq_6000",
dataPoints: res.mutationsByInstrument[i].illumina_novaseq_6000
},{
type: "stackedColumn",
showInLegend: true,
name: "nextseq_500",
dataPoints: res.mutationsByInstrument[i].nextseq_500
},{
type: "stackedColumn",
showInLegend: true,
name: "nextseq_550",
dataPoints: res.mutationsByInstrument[i].nextseq_550
},{
type: "stackedColumn",
showInLegend: true,
name: "illumina_hiseq_2500",
dataPoints: res.mutationsByInstrument[i].illumina_hiseq_2500
},{
type: "stackedColumn",
showInLegend: true,
name: "minion",
dataPoints: res.mutationsByInstrument[i].minion
}
);
mutationsChart.render();
}
for (i = 0; i < res.mutationsByFrequency.length; i++) {
mutationsByFreqData.splice(0,mutationsByFreqData.length);
mutationsByFreqData.push({
type: "column",
dataPoints: res.mutationsByFrequency[i].Total
});
mutationsByFreqChart.render();
}
for (i = 0; i < res.mutationsShapeScore.length; i++) {
mutationsShapeScoreData.splice(0,mutationsShapeScoreData.length);
mutationsShapeScoreData.push({
type: "column",
dataPoints: res.mutationsShapeScore[i].Total
});
mutationsShapeScoreChart.render();
}
}
}
//xmlhttp.open("GET", "MutationsSummary.php?Region="+region+"&ReferenceBase="+referenceBase+"&AlternateBase="+alternateBase+"&Instrument="+instrument+"&Start="+start+"&End="+end, true);
xmlhttp.open("GET", "MutationsSummary.php?Region="+region+"&Start="+start+"&End="+end, true);
xmlhttp.send();
var xmlhttp = new XMLHttpRequest();
xmlhttp.onreadystatechange = function() {
if (this.readyState == 4 && this.status == 200) {
var mutationsDetailEle = document.getElementById("mutationsDetail");
mutationsDetailEle.innerHTML = this.responseText;
}
}
//xmlhttp.open("GET", "MutationsDetail.php?Region="+region+"&ReferenceBase="+referenceBase+"&AlternateBase="+alternateBase+"&Instrument="+instrument+"&Start="+start+"&End="+end, true);
xmlhttp.open("GET", "MutationsDetail.php?Region="+region+"&Start="+start+"&End="+end, true);
xmlhttp.send();
}
}
function showOrHideInstruments(refBaseTotalRowId, instrumentRowsName){
var refBaseTotalRow = document.getElementById(refBaseTotalRowId);
var instrumentRows = document.getElementsByName(instrumentRowsName);
if (refBaseTotalRow.innerHTML == "+") {
refBaseTotalRow.innerHTML = "-";
for (let item of instrumentRows) {
item.style.display = "table-row";
}
} else {
refBaseTotalRow.innerHTML = "+"
for (let item of instrumentRows) {
item.style.display = "none";
}
}
}
function activateMutationsResultTab(tabId, mutationTabId) {
var i, tabcontent, tablinks;
tabcontent = document.getElementsByClassName("datacontainer");
for (i = 0; i < tabcontent.length; i++) {
tabcontent[i].style.display = "none";
}
tablinks = document.getElementsByClassName("tablinks");
for (i = 0; i < tablinks.length; i++) {
tablinks[i].className = tablinks[i].className.replace(" active", "");
}
document.getElementById(mutationTabId).style.display = "flex";
document.getElementById(tabId).className += " active";
if(tabId == 'summaryTab') {
document.getElementById('mutationsSummaryFrequency').style.display = "flex";
document.getElementById('mutationsShapeScore').style.display = 'flex';
}
}
</script>
</body>
</html>