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<?php
if(!isset($_SESSION)){
session_start();
}
?>
<!DOCTYPE html>
<html lang="en-US">
<head>
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-848D0QR2QW"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-848D0QR2QW');
</script>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
<meta name="description" content="">
<meta name="author" content="">
<title>TOPMed OMICS Progress Report</title>
<!-- Bootstrap CSS -->
<link href="../report/dist/css/bootstrap.min.css" rel="stylesheet">
<link href="data:text/css;charset=utf-8," data-href="../report/dist/css/bootstrap-theme.min.css" rel="stylesheet" id="bs-theme-stylesheet">
<link href="https://cdnjs.cloudflare.com/ajax/libs/tabulator/4.4.3/css/tabulator.min.css" rel="stylesheet">
<link href="../report/css/docs.css" rel="stylesheet">
<link href="../report/css/template.css" rel="stylesheet">
<!-- jquery ui js and css for autocomplete -->
<link href="//code.jquery.com/ui/1.14.1/themes/base/jquery-ui.css" rel="stylesheet"/>
<script src="//code.jquery.com/jquery-3.6.0.js"></script>
<script src="//code.jquery.com/ui/1.14.1/jquery-ui.js" integrity="sha256-9zljDKpE/mQxmaR4V2cGVaQ7arF3CcXxarvgr7Sj8Uc=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/moment.js/2.30.1/moment.min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery-sparklines/2.1.2/jquery.sparkline.js"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.0/js/bootstrap.min.js" integrity="sha384-OgVRvuATP1z7JjHLkuOU7Xw704+h835Lr+6QL9UvYjZE3Ipu6Tp75j7Bh/kR0JKI" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/fetch/2.0.4/fetch.min.js"></script>
<script type="text/javascript" src="https://code.highcharts.com/stock/highstock.js"></script>
<script type="text/javascript" src="https://code.highcharts.com/highcharts-more.js"></script>
<script src="https://code.highcharts.com/modules/histogram-bellcurve.js"></script>
<script src="https://code.highcharts.com/modules/accessibility.js"></script>
<script type="text/javascript" src="https://code.highcharts.com/stock/modules/exporting.js"></script>
<!--script type="text/javascript" src="https://code.highcharts.com/modules/exporting.js"></script-->
<!--script type="text/javascript" src="https://code.highcharts.com/modules/offline-exporting.js"></script-->
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/tabulator/4.4.3/js/tabulator.min.js"></script>
<script type="text/javascript" src="https://oss.sheetjs.com/sheetjs/xlsx.full.min.js"></script>
</head>
<body>
<style>
.container {width: 95%}
div.loading { background-image: url("images/ajax-loader.gif") }
.bs-docs-header { background-image: linear-gradient(to bottom, #0f463c 0, #185f65 100%); }
.bs-docs-header h1 { margin-right: auto }
.bs-docs-footer { height: 30px; margin: 20px 0; padding: 40px 0; background-color: #0f463c; color: #fff;}
.chartheader { text-align: center; color: #1b809e }
.row { padding: 15px; margin: 40px 0 }
p.summary {font-size: 16px;}
p.center {text-align: center }
.right {float: right }
.bs-callout-info h3 { font-weight: normal }
#summary_barchart_rnaseq, #summary_barchart_methylation, #summary_barchart_metabolomics, #timeline_chart, #qc_histogram
{ height: 420px; width: 100% }
.bs-docs-nav .navbar-brand, .bs-docs-nav .navbar-nav>li>a { background: white; }
</style>
<header class="navbar navbar-static-top bs-docs-nav" id="top" role="banner">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">TOPMed IRC</a>
</div>
<div id="navbar" class="collapse navbar-collapse">
<ul class="nav navbar-nav">
<li class="active"><a href ="#">OMICS</a></li>
<li><a href="about.php">About</a></li>
<li><a href="../report/">Whole genomes</a></li>
</ul>
</div>
</div>
</header>
<div class="bs-docs-header" id="content" tabindex="-1">
<div class="container">
<h1 id="subject">TOPMed OMICS Progress Report</h1>
<h4><strong>Last updated</strong> : <?=date("m/d/Y");?></h4>
<p class="lead">This page reports TOPMed Omics data received by the IRC.
</p>
</div>
</div>
<div class="container bs-docs-container">
<div class="bs-callout bs-callout-info">
<h3 id="progress">OMICS sample numbers by study</h3>
</div>
<div class="row loading">
<div class="col-md-3 col-sm-12">
<h3 class="chartheader">RNA-seq</h3>
<div id="summary_barchart_rnaseq"> </div>
</div>
<div class="col-md-3 col-sm-12">
<h3 class="chartheader">Methylation</h3>
<div id="summary_barchart_methylation"> </div>
</div>
<div class="col-md-3 col-sm-12">
<h3 class="chartheader">Metabolomics</h3>
<div id="summary_barchart_metabolomics"> </div>
</div>
<div class="col-md-3 col-sm-12">
<h3 class="chartheader">Proteomics</h3>
<div id="summary_barchart_proteomics"> </div>
</div>
</div>
<div class="bs-callout bs-callout-info">
<h3>RNA-seq progress over time</h3>
</div>
<div class="row loading" id="timeline_div">
<div class="col-lg-12">
<div id="timeline_chart"></div>
</div>
</div>
<div class="row loading">
<div class="col-md-7 col-sm-12">
<h3 class="chartheader">RNA-seq QC metrics</h3>
<p>This table shows aggregates across studies for many metrics of RNA-seq quality.     <button id="download-table-metrics" class="btn btn-primary btn-xs"><span class="glyphicon glyphicon-list-alt"></span> Export table</button></p>
<div>
<div id="qc_metrics_table" style="height: 420px; overflow-y: hidden; overflow-x: hidden" aria-busy="true" role="table"> </div>
</div>
</div>
<div class="col-md-5 col-sm-12">
<h3 class="chartheader">Histogram of QC Measure</h3>
<p id="study_dropdown" class="center hidden">
<label for="sel_study_histogram">1st study: <select id="sel_study_histogram"></select></label>  
<label for="sel_study_two">2nd study: <select id="sel_study_two"></select></label>
</p>
<div id="qc_histogram"><p class="lead center" style="min-height:420px">Cilck rows in the QC metrics table</p></div>
</div>
</div>
<div class="bs-callout bs-callout-info">
<h3>Per sample RNA-seq quality metrics</h3>
<p class="lead">Please log in using Google to download individual level QC results. Email lwkevin@umich.edu if you aren't already on the whole genome sequence whitelist.</p>
<?php if(isset($_SESSION['access_token']) AND isset($_SESSION['omics_user'])) { ?>
<a href="?logout" class="btn btn-warning"><span class="glyphicon glyphicon-lock"></span> Logout <?=$user->email; ?></a>
</div>
<div class="row">
<div class="col-lg-12">
<p class="summary">
<label for="sel_study_table">Filter by study: <select id="sel_study_table"></select></label>    
<label for="sel_size_table">Page size: <select id="sel_size_table">
<option value="100">100</option>
<?php
for($i=1; $i<9; $i++) {
print "<option value='".($i*500)."'>".($i*500)."</option>";
}
?>
</select></label>    
<a id="download-whole-raw" href="lib/datadump.php" class="btn btn-primary btn-sm"><span class="glyphicon glyphicon-download-alt"></span> Download entire QC raw data</a>  
</p>
<div id="sample_raw_table" style="height: 600px; overflow-y: hidden;" aria-busy="true"></div>
</div>
</div>
<?php } else { ?>
<a class="login" href="<?=$authUrl; ?>"><img src="images/google-login-button.png" alt="Login with Google" /></a>
</div>
<div class="row"></div>
<?php } ?>
<div class="bs-callout bs-callout-info">
<h3>OMICS sample numbers by production center</h3>
</div>
<div class="row">
<p class="summary">
<table class="table table-striped">
<thead>
<tr>
<th scope="col"></th>
<th>RNA-seq</td>
<th>Methylation</td>
<th>Metabolomics</td>
<th>Proteomics</th>
<th>Total by Center</th>
</tr>
</thead>
<tbody>
<tr>
<th scope="row">Broad</th>
<td id="broad-rna-seq"> - </td>
<td id ="broad-methylation"> - </td>
<td id="broad-metabolomics"> - </td>
<td id="broad-proteomics"> - </td>
<td id="broad-total"> - </td>
</tr>
<tr>
<th scope="row">NWGC</th>
<td id="nwgc-rna-seq"> - </td>
<td id="nwgc-methylation"> - </td>
<td id="nwgc-metabolomics"> - </td>
<td id="nwgc-proteomics"> - </td>
<td id="nwgc-total"> - </td>
</tr>
<tr>
<th scope="row">NYGC</th>
<td id="nygc-rna-seq"> - </td>
<td id="nygc-methylation"> - </td>
<td id="nygc-metabolomics"> - </td>
<td id="nygc-proteomics"> - </td>
<td id="nygc-total"> - </td>
</tr>
<tr>
<th scope="row">USC</th>
<td id="usc-rna-seq"> - </td>
<td id="usc-methylation"> - </td>
<td id="usc-metabolomics"> - </td>
<td id="usc-proteomics"> - </td>
<td id="usc-total"> - </td>
</tr>
<tr>
<th scope="row">Baylor</th>
<td id="baylor-rna-seq"> - </td>
<td id="baylor-methylation"> - </td>
<td id="baylor-metabolomics"> - </td>
<td id="baylor-proteomics"> - </td>
<td id="baylor-total"> - </td>
</tr>
<tr>
<th scope="row">Total by Type</th>
<td id="total-rna-seq"> - </td>
<td id="total-methylation"> - </td>
<td id="total-metabolomics"> - </td>
<td id="total-proteomics"> - </td>
<td id="total-all"></td>
</tr>
</tbody>
</table>
</p>
<p> </p>
<p class="summary">
<strong>Technical:</strong><br/>
Stranded, poly-A-selected RNA, 101 bp paired end NovaSeq, target 75 M reads per sample for blood samples, 50 M reads per sample for tissue, cell sorted or globin-depleted blood samples.<br/>
Illumina EPIC methylation array, ~850 k sites.<br/>
Four metabolomics assay types: C8-pos, C-18-neg, HILIC-pos (all untargeted), plus Amide-neg with multiple reaction monitoring for ~200 target metabolites.
</p>
</div>
</div>
<footer class="bs-docs-footer">
<div class="container">
<p>© <?=date("Y"); ?> All Rights Reserved </p>
</div>
</footer>
<script type="text/javascript" src="js/main.js.php"></script>
<script>$(function() { $('pre').addClass('prettyprint'); $('.loading').removeClass('loading');
})</script>
</body>
</html>