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visualIntragenome.php
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<?php
ini_set('display_errors', 1);
error_reporting(E_ALL);
?>
<!DOCTYPE html>
<html lang="en">
<head>
<title>SARS-CoV-2 intragenome page</title>
<link rel="stylesheet" href="./styles.css" />
<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";?>
<!-- <link rel="stylesheet" href="./styles.css" /> -->
<style>
.header {
position: sticky;
top:0;
}
.datagrid {
width: 100%;
height: 500px;
overflow: auto;
padding-left: 10px;
}
.repeatgrid {
width: 100%;
overflow: auto;
}
tr.dark th{
background: #333;
color: white;
}
th{
position: sticky;
top: 0;
box-shadow: 0 2px 2px -1px rgba(0, 0, 0, 0.4);
}
.table {
text-align: left;
}
.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 {
padding: 15px;
}
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;
}
.comp-table-header {
background-color: #3c3b3b;
color: white;
}
.comp-table-header-td {
padding: 5px;
text-align: center;
font-size: 13px;
padding-right: 5px;
border-right: 1px solid #a7a7a7;
}
.comp-table-row-td {
padding: 5px;
font-size: 12px;
border-right: 1px solid #cecece;
}
.comp-table-row-td-alt {
padding: 5px;
font-size: 12px;
background-color: #efefef;
border-right: 1px solid #cecece;
}
.color-palette {
margin-left: 5px;
border: 1px solid grey;
width: 16px;
height: 16px;
}
#legendRow {
max-width: 900px;
}
</style>
</head>
<?php if (isset($_GET['start']) && isset($_GET['end'])){
// echo "<h4>Test hello</h4>";
$start = $_GET['start'];
$end = $_GET['end'];
$lStart = $_GET['lStart'];
$rStart = $_GET['rStart'];
$lEnd = $_GET['lEnd'];
$rEnd = $_GET['rEnd'];
$q4 = " AND (intraGene.leftStart BETWEEN '" . $start . "' AND '" . $end . "' OR intraGene.leftEnd BETWEEN '" . $start . "' AND '" . $end . "' OR ('" . $start . "' BETWEEN intraGene.leftStart AND intraGene.leftEnd) OR ('" . $end . "' BETWEEN intraGene.leftStart AND intraGene.leftEnd)) OR (intraGene.rightStart BETWEEN '" . $start . "' AND '" . $end . "' OR intraGene.rightEnd BETWEEN '" . $start . "' AND '" . $end . "' OR ('" . $start . "' BETWEEN intraGene.rightStart AND intraGene.rightEnd) OR ('" . $end . "' BETWEEN intraGene.rightStart AND intraGene.rightEnd))";
}else if (isset($_GET['start'])){
$start = $_GET['start'];
$lStart = $_GET['lStart'];
$rStart = $_GET['rStart'];
$lEnd = $_GET['lEnd'];
$rEnd = $_GET['rEnd'];
$stminus = $start-15;
$stplus = $start+15;
$q4 = " AND (intraGene.leftStart BETWEEN '" . $start . "' AND '" . $stminus . "' OR intraGene.leftEnd BETWEEN '" . $start . "' AND '" . $stplus . "') OR ('" . $start . "' BETWEEN intraGene.leftStart AND intraGene.leftEnd) OR ('" . $start . "' BETWEEN intraGene.rightStart AND intraGene.rightEnd) ";
}else if(isset($_GET['end'])){
$end = $_GET['end'];
$lStart = $_GET['lStart'];
$rStart = $_GET['rStart'];
$lEnd = $_GET['lEnd'];
$rEnd = $_GET['rEnd'];
$edminus = $end-15;
$edplus = $end+15;
$q4 = " AND (intraGene.leftStart BETWEEN '" . $end . "' AND '" . $edminus . "' OR intraGene.leftEnd BETWEEN '" . $end . "' AND '" . $edplus . "') OR ('" . $end . "' BETWEEN intraGene.leftStart AND intraGene.leftEnd) OR ('" . $end . "' BETWEEN intraGene.rightStart AND intraGene.rightEnd) ";
}
require_once './connection.php';
// $q4 = " AND (intraGene.leftStart BETWEEN '" . $start . "' AND '" . $end . "' OR intraGene.leftEnd BETWEEN '" . $start . "' AND '" . $end . "' OR ('" . $start . "' BETWEEN intraGene.leftStart AND intraGene.leftEnd) OR ('" . $end . "' BETWEEN intraGene.leftStart AND intraGene.leftEnd)) OR (intraGene.rightStart BETWEEN '" . $start . "' AND '" . $end . "' OR intraGene.rightEnd BETWEEN '" . $start . "' AND '" . $end . "' OR ('" . $start . "' BETWEEN intraGene.rightStart AND intraGene.rightEnd) OR ('" . $end . "' BETWEEN intraGene.rightStart AND intraGene.rightEnd))";
$sqlIntraGene = "SELECT leftStart, rightStart, leftEnd, rightEnd, readSupport FROM intraGene WHERE 1=1 $q4 ORDER BY intraGene.leftStart + 0";
$resultIntragene = $con->query($sqlIntraGene);
if (!$resultIntragene) {
echo $sqlIntraGene;
exit();
}
$result_rowsIntraGene = $resultIntragene->fetch_all(MYSQLI_ASSOC);
$totalIntraGene = $resultIntragene->num_rows;
?>
<body>
<div class="datagraph" >
<h4 class="search-header">Intragenome Interaction Regions</h4>
<div id="coords">
<span>5'</span>
<span>3'</span>
</div>
<div class="repeatDisplay" id="repeatDisplay">
<div id="genehighlight" class="genehighlight"></div>
</div>
<div id="coords">
<span>1</span>
<span>29903</span>
</div>
<div id="textoutput" >
</div>
<div id="container"></div>
<div id="legendRow" ></div>
<script src="./JS/main.js"></script>
<script>
var lStart = <?php echo $lStart; ?>;
var rStart = <?php echo $rStart; ?>;
var lEnd = <?php echo $lEnd; ?>;
var rEnd = <?php echo $rEnd; ?>;
var LRarray = Array(lStart,rEnd,rStart,rEnd);
// console.log(LRarray);
plotrepeats(LRarray);
createLegend();
</script>
</div>
<div class="datagrid">
<table class='table'>
<thead>
<tr class="dark">
<th class="header" width='20%'></th>
<th class="header" width='16%'>Left Hand Start</th>
<th class="header" width='16%'>Left Hand End</th>
<th class="header" width='16%'>Right Hand Start</th>
<th class="header" width='16%'>Right Hand End</th>
<th class="header" width='16%'>Read Support</th>
</tr>
</thead>
<tbody>
<?php
foreach($result_rowsIntraGene as $row) {
$data = '';
// if ($prev_color==$color1){
// $data.= "<tr style=".$color2.">" ;
// $prev_color=$color2;
// } elseif ($prev_color==$color2){
// $data.= "<tr style=".$color1.">" ;
// $prev_color=$color1;
// }\''.$row['leftStart'].'\',\''.$row['leftEnd'].'\',\''.$row['rightStart'].'\',\''.$row['rightEnd'].'\')
$inputArray = "Array(".$row['leftStart'].",".$row['leftEnd'].",".$row['rightStart'].",".$row['rightEnd'].")";
// echo $inputArray;
$data .= '<td><a id="myLink" title="Click to do something" href="#" onclick="plotIntraGenome('.$inputArray.');">Visualize</a></td>';
$data.='<td>'.$row['leftStart'].'</td>';
$data.='<td>'.$row['leftEnd'].'</td>';
$data.='<td>'.$row['rightStart'].'</td>';
$data.='<td>'.$row['rightEnd'].'</td>';
$data.='<td>'.$row['readSupport'].'</td></tr>';
echo $data;
}
?>
</tbody>
</table>
<h5> These data are taken from <a href="https://doi.org/10.1038/s41467-021-25357-1">Yang et al. 2021</a></h5>
</div>
<script>
var lStart = "<?php echo $lStart; ?>";
var rStart = "<?php echo $rStart; ?>";
var lEnd = "<?php echo $lEnd; ?>";
var rEnd = "<?php echo $rEnd; ?>";
var LRarray = Array(lStart,rEnd,rStart,rEnd);
// console.log(LRarray);
plotrepeats(LRarray);
function resetFormGenome(){
// console.log("clicked");
container.innerHTML = '';
var highlights = document.getElementsByClassName("highlight");
var parentNode = document.getElementById("repeatDisplay");
while(highlights.length>0){
parentNode.removeChild(highlights[0]);
// highlights[0]
}}
function plotIntraGenome(array){
resetFormGenome()
// console.log("plotintra");
// console.log(array);
// console.log(typeof(array))
for (let i = 0; i < genests.length; i++) {
var parentNode = document.getElementById("repeatDisplay");
var highlight = document.createElement("div");
highlight.classList.add("genehighlight");
parentNode.appendChild(highlight);
highlight.style.background = "#"+ genecolor[i];
highlight.style.width = map(geneed[i]) - map(genests[i]) +"px";
highlight.style.marginLeft = map(genests[i]) + "px";
// console.log(map(geneed[i]) - map(genests[i]) +"px")
}
// this creates the motifs on the diagram
for (let i = 0; i < array.length; i++) {
var parentNode = document.getElementById("repeatDisplay");
var highlight = document.createElement("div");
highlight.classList.add("highlight");
parentNode.appendChild(highlight);
highlight.style.marginLeft = map(array[i]) + "px";
}
}
</script>
</body>