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gene.html
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<!DOCTYPE html>
<html lang="en">
<head>
<!-- Global site tag (gtag.js) - Google Analytics - Personal -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-176192306-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-176192306-1');
</script>
<!-- Global site tag (gtag.js) - Google Analytics - SBRG -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-176090948-2"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-176090948-2');
</script>
<title>iModulonDB</title>
<!-- Metadata -->
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link rel="icon" href="favicon.ico" type="image/x-icon"/>
<!-- Bootstrap CDN -->
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.0/css/bootstrap.min.css"
integrity="sha384-9aIt2nRpC12Uk9gS9baDl411NQApFmC26EwAOH8WgZl5MYYxFfc+NcPb1dKGj7Sk" crossorigin="anonymous">
<!-- FontAwesome Icons -->
<script src="https://kit.fontawesome.com/a27dabf34d.js" crossorigin="anonymous"></script>
<!-- Font -->
<link href="https://fonts.googleapis.com/css2?family=Roboto:wght@100;300;400;500;700&display=swap" rel="stylesheet">
<!-- CSS -->
<style>
* {
font-family: 'Roboto', 'Helvetica', 'Segoe UI', sans-serif;
}
.header {
background-color: #5D5C61;
color: white;
margin-bottom: 0rem;
padding: 0.4rem;
padding-left: 0.7rem;
}
.subheader {
background-color: lightgray;
color: black;
margin-top: 2rem;
margin-bottom: 1rem;
border-radius: 8px;
padding-top: 8px;
}
.header a {
color: white;
}
.header a:hover {
color: #A8D0E6;
}
.dropdown-menu {
background-color: #5D5C61;
}
.dropdown-item {
color: white;
}
#left_col {
background-color: #A8D0E6;
padding: 1rem;
height: unset;
min-height: 100vh;
}
#left_col_content {
position: sticky;
top: 4.5rem;
}
.card {
background-color: #5D5C61;
}
.im_head_meta_cat {
margin-bottom: 0rem;
font-size: 12px;
font-weight: bold;
color: white;
}
.im_head_meta_val {
color: white;
}
.im_head_meta_val a {
color: #A8D0E6;
}
.bd-lead {
overflow-wrap: break-word;
word-wrap: break-word;
-webkit-hyphens: auto;
-ms-hyphens: auto;
-moz-hyphens: auto;
hyphens: auto;
}
</style>
</head>
<body>
<!-- Page Content -->
<div class="container-fluid" style="min-width: 650px; max-width: 1600px">
<!-- Navbar -->
<div class="header row navbar-dark sticky-top">
<div class="navbar-header">
<a class="navbar-brand" href="index.html">
<img src="images/modulytics_logo.png" width="30" height="30" class="d-inline-block align-top" alt=""
loading="lazy">
iModulonDB
</a>
</div>
<ul class="nav navbar-dark">
<li class="nav-item">
<a id="im_list" class="nav-link navbar-dark" href="dataset.html">Dataset Page</a>
</li>
<li class="nav-item">
<a id="gene_search_link" class="nav-link" href="search.html">Search</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" data-toggle="dropdown" href="#" role="button" aria-haspopup="true"
aria-expanded="false">Download</a>
<div class="dropdown-menu">
<a id="gene_table_download" class="dropdown-item" href="#">Gene Table</a>
<a id="expression_download" class="dropdown-item" href="#">Gene Expression</a>
<div class="dropdown-divider"></div>
<a id="data_download" class="dropdown-item" href="e_coli/precise1/data_files.zip">Full Dataset</a>
<a id="gene_download" class="dropdown-item" href="e_coli/annotation/gene_files.zip">Gene Annotations
& TRN</a>
<a id="meta_download" class="dropdown-item" href="e_coli/precise1/sample_metadata.csv">Experimental
Conditions</a>
</div>
</li>
<li class="nav-item">
<a class="nav-link" href="about.html">About</a>
</li>
</ul>
</div>
<div class="row">
<!-- Left column: Header -->
<div id="left_col" class="col-md-3">
<div id="left_col_content">
<h1 id="gene_name" class="bd-title bd-lead"></h1>
<div class="card p-2 bd-lead" id="gene_head_text"></div>
</div>
</div>
<!-- Main body -->
<div class="col-md-9 p-3">
<!-- Gene header & gene table -->
<div class="row">
<div class="col-md-12">
<div class="row mx-auto justify-content-center">
<h5>Gene Relationship to iModulons</h5>
</div>
<div id="gene_table" style="width: 100%;height:275px;"></div>
</div>
</div>
<hr/>
<!-- Activity plot -->
<div class="row mx-auto justify-content-center">
<h5>Gene Expression</h5>
</div>
<div class="row">
<div class="col-md-12">
<div id="bar" style="width: 100%;height: 250px;"></div> <!-- width = 900px -->
</div>
</div>
<hr id="reg_hr" class="d-none"/>
<!-- Footer -->
<hr/>
<footer>
<div class="container">
<div class="row">
<div class="col-sm-3">
<a href="http://systemsbiology.ucsd.edu/">
<img class="img-fluid" src="images/sbrg-logo.png">
</a>
</div>
<div class="col-sm-9 m-auto">
<p class="copyright text-muted small">
iModulonDB is maintained by the Systems Biology Research Group at the University of
California, San Diego. <br/>
</p>
</div>
</div>
</div>
</footer>
</div>
</div>
</div>
<!-- Scripts for Bootstrap: jQuery, Popper.js, Bootstrap JS-->
<script src="https://code.jquery.com/jquery-3.5.1.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/umd/popper.min.js"
integrity="sha384-Q6E9RHvbIyZFJoft+2mJbHaEWldlvI9IOYy5n3zV9zzTtmI3UksdQRVvoxMfooAo"
crossorigin="anonymous"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.0/js/bootstrap.min.js"
integrity="sha384-OgVRvuATP1z7JjHLkuOU7Xw704+h835Lr+6QL9UvYjZE3Ipu6Tp75j7Bh/kR0JKI"
crossorigin="anonymous"></script>
<!-- Required CDNs: Highcharts, Papa Parse, Tabulator -->
<script src="https://code.highcharts.com/stock/highstock.js"></script>
<script src="https://code.highcharts.com/modules/data.src.js"></script>
<script src="https://code.highcharts.com/modules/exporting.src.js"></script>
<script src="https://code.highcharts.com/modules/venn.src.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/PapaParse/5.1.0/papaparse.min.js"></script>
<link href="https://unpkg.com/[email protected]/dist/css/tabulator_simple.min.css" rel="stylesheet"/>
<script src="https://unpkg.com/[email protected]/dist/js/tabulator.min.js"></script>
<!-- Custom scripts -->
<script src="js/gene_activity_bar.js"></script>
<!-- Populate the HTML page -->
<script>
//helper for querystring params
function qs(key) {
key = key.replace(/[*+?^$.\[\]{}()|\\\/]/g, "\\$&"); // escape RegEx meta chars
var match = location.search.match(new RegExp("[?&]" + key + "=([^&]+)(&|$)"));
return match && decodeURIComponent(match[1].replace(/\+/g, " "));
}
</script>
<script>
// Determine which gene this is
var gene_id = qs('gene_id');
var org_folder = "organisms/" + qs('organism') + "/" + qs('dataset') + "/";
var data_prefix = org_folder + "gene_page_files/" + gene_id + "/" + gene_id + "_";
var link_suffix = "?organism=" + qs('organism') + "&dataset=" + qs('dataset');
// add links specific to this dataset
document.getElementById("im_list").setAttribute('href', "dataset.html" + link_suffix);
document.getElementById("gene_search_link").setAttribute('href', "search.html" + link_suffix);
if (qs('dataset') == 'precise1k') {
document.getElementById('data_download').setAttribute('href', 'https://www.dropbox.com/s/p9wfadei4heup1v/p1k_data_files.zip?dl=0');
} else {
document.getElementById('data_download').setAttribute('href', org_folder + 'data_files.zip');
}
document.getElementById('gene_download').setAttribute('href', 'organisms/' + qs('organism') + '/annotation/gene_files.zip');
document.getElementById('meta_download').setAttribute('href', org_folder + 'sample_metadata.csv');
// read in the gene metadata
$.get(data_prefix + "meta.csv", function (gene_metaCSV) {
var gene_meta = Papa.parse(gene_metaCSV, {dynamicTyping: true}).data;
// populate the dataset info
$.get(org_folder + 'dataset_meta.csv', function (meta) {
var metadata = Papa.parse(meta).data;
// dataset title
var title = metadata[0][1] + ': Gene Dashboard';
$('#title_org').append(title);
// add header
$('#gene_name').append("Gene: " + gene_meta[2][1]);
$('#gene_head_text').append('<p class="im_head_meta_cat">DATASET</p>');
$('#gene_head_text').append('<p class="im_head_meta_val">' + metadata[1][1] + '</p>');
$('#gene_head_text').append('<p class="im_head_meta_cat">GENE ID</p>');
$('#gene_head_text').append('<p class="im_head_meta_val">' + gene_meta[1][1] + '</p>');
if (qs('organism') == 's_acidocaldarius') {
$('#gene_head_text').append('<p class="im_head_meta_cat">OLD LOCUS TAG</p>');
$('#gene_head_text').append('<p class="im_head_meta_val">' + gene_meta[8][1] + '</p>');
}
$('#gene_head_text').append('<p class="im_head_meta_cat">PRODUCT</p>');
if (gene_meta[2][1] == gene_meta[4][1]) {
$('#gene_head_text').append('<p class="im_head_meta_val"><i>Not Available</i></p>');
} else {
$('#gene_head_text').append('<p class="im_head_meta_val">' + gene_meta[4][1] + '</p>');
}
$('#gene_head_text').append('<p class="im_head_meta_cat">OPERON</p>');
$('#gene_head_text').append('<p class="im_head_meta_val">' + gene_meta[3][1] + '</p>');
$('#gene_head_text').append('<p class="im_head_meta_cat">CATEGORY</p>');
$('#gene_head_text').append('<p class="im_head_meta_val">' + gene_meta[5][1] + '</p>');
var regulator_name = gene_meta[6][1]
if (regulator_name != null) {
$('#gene_head_text').append('<p class="im_head_meta_cat">REGULATOR</p>');
$('#gene_head_text').append('<p class="im_head_meta_val">' + regulator_name + '</p>');
}
if (gene_meta[7][1] != '<i>Not Available</i>') {
$('#gene_head_text').append('<p class="im_head_meta_cat">ADDITIONAL INFORMATION</p>');
$('#gene_head_text').append('<p class="im_head_meta_val">' + gene_meta[7][1] + '</p>');
}
// change page title
document.title = 'iModulonDB: ' + gene_meta[1][1];
});
// add download links specific to this imodulon
document.getElementById("gene_table_download").setAttribute('href', data_prefix + 'perGene_table.csv');
document.getElementById("expression_download").setAttribute('href', data_prefix + 'expression.csv');
});
// generate activity (expression) plot
$.get(org_folder + 'data_files/sample_table.csv', function (metadata) {
$.get(data_prefix + 'activity_bar.csv', function (activity_bar_data) {
generateGeneActivityBar(metadata, activity_bar_data, 'bar');
});
});
// Generate table
$.get(data_prefix + 'perGene_table.csv', function (table_data) {
// get the data, convert to objects
var data = Papa.parse(table_data, {dynamicTyping: true}).data;
var tabledata = []
for (i = 1; i < data.length - 1; i++) { //rows, excluding header
var obj = {};
for (j = 0; j < data[0].length; j++) { //cols
if (typeof data[i][j] === 'string') {
if (data[i][j].includes('<a')) {
data[i][j] = data[i][j].split('<a')[0]
}
}
obj[data[0][j]] = data[i][j];
}
tabledata.push(obj);
}
// columns object
var columns = [
{title: "iModulon Name", field: "name", frozen: true},
{
title: "Gene in iModulon?", field: "in_iM",
formatter: "tickCross"
},
{
title: "M<sub>i</sub>", field: "gene_weight",
formatter: "money", formatterParams: {precision: 4}
},
{
title: "iM Regulator", field: "regulator",
width: 150
},
{title: "iM Function", field: "function"},
{
title: "iM Category", field: "category"
}
]
// generate the tableS
var table = new Tabulator('#gene_table', {
layout: "fitDataStretch",
data: tabledata,
columns: columns,
initialSort: [
{column: "in_iM", dir: "desc"}
],
rowClick: function (e, row) { //link to the page in a database
var link = 'iModulon.html?';
link += 'organism=' + qs('organism') + '&';
link += 'dataset=' + qs('dataset') + '&';
link += 'k=' + row.getData().k;
window.open(link);
},
tooltips: function (cell) {
return "Click to view iModulon dashboard";
}
});
});
</script>
</body>
</html>