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about.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="Network analysis of Oomycete Effectors">
<meta name="author" content="Jamie McGowan">
<title>Oomycete Effectors - About</title>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<link href="css/styles.css" rel="stylesheet">
<link href="css/network_pages.css" rel="stylesheet">
<link href="css/ie10-viewport-bug-workaround.css" rel="stylesheet">
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-106391473-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-106391473-1');
</script>
</head>
<body>
<!-- Have modal at top level -->
<div class="modal fade" id="modal" tabindex="-1" role="dialog" aria-labelledby="modal-label">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>
<h4 class="modal-title" id="modal-label">Protein ID</h4>
</div>
<div class="modal-body">
<p><span class="popup-label">Protein ID: </span><span id="protein-id"></span><p>
<p><span class="popup-label">Species: </span><span id="species"></span><p>
<p><span class="popup-label">Genus: </span><span id="genus"></span><p>
<p><span class="popup-label">Order: </span><span id="order"></span><p>
<hr>
<p><span class="popup-label" title="Node degree is the number of edges a node has (i.e. the number of homologs a protein has in the network).">Node Degree: </span><span id="degree"></span><p>
<p><span class="popup-label">Protein Length: </span><span id="protein-length"></span><p>
<p><span class="popup-label">Sequence: </span><span id="sequence"></span><p>
</div>
<div class="modal-footer">
<button id="blast" type="button" class="btn btn-primary" title="BLAST this sequence against the NCBI databases">BLAST</button>
<button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- Modal for help/info popup -->
<div class="modal fade" id="modal-help" tabindex="-1" role="dialog" aria-labelledby="modal-label">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<button id="button-close_help-modal1" type="button" class="close"><span aria-hidden="true">×</span></button>
<h4 class="modal-title" id="modal-label">Help</h4>
</div>
<div class="modal-body">
<p>This is a sequence similarty network. Each node represents a protein. An edge/line joining two nodes represents shared sequence similarity between the two proteins. Proteins are coloured according to their genus.</p>
<p>Click on a protein/node to view information about it.</p>
<p>The network can be filtered to hide/show particular proteins (e.g. by Genus or Order) using the buttons on the right.</p>
<hr>
<h4>Usage</h4>
<p><img src="./images/help_screenshot.png" width="50%"></p>
<p>
<ol>
<li><strong>Left to right</strong>:
<ul>
<li><span class="glyphicon glyphicon-zoom-in"></span> Zoom in</li>
<li><span class="glyphicon glyphicon-zoom-out"></span> Zoom out</li>
<li><span class="glyphicon glyphicon-home"></span> Center view on network</li>
</ul>
</li>
<li><strong>Toggle Edges:</strong> hides/shows all edges in the network. Hiding edges improves performance</li>
<li><strong>Toggle Labels:</strong> hides/shows labels for all nodes in the network. Hiding labels improves performance </li>
<li><strong>Filter box:</strong> type a query here to filter by Protein ID, Species, Genus or Order</li>
</ol>
</p>
<div class="modal-footer">
<button id="button-close_help-modal2" type="button" class="btn btn-default">Close</button>
</div>
</div>
</div>
</div>
</div>
<nav class="navbar navbar-default navbar-fixed-top">
<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="index.html">Oomycete Effectors</a>
</div>
<div id="navbar" class="collapse navbar-collapse">
<ul class="nav navbar-nav">
<li><a href="index.html">Home</a></li>
<li class="active"><a href="#">About</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Networks <span class="caret"></span></a>
<ul class="dropdown-menu">
<li class="active"><a href="chitinases.html">Chitinases</a></li>
<li><a href="nlps.html">Necrosis-inducing Proteins</a></li>
<li><a href="rxlrs.html">RxLRs</a></li>
</ul>
</li>
</ul>
</div>
</div>
</nav>
<div class="container">
<div class="page-header">
<h2>About</h2>
</div>
<p>This site contains supplementary interative sequence similarity networks for <q><a target="_blank" href="http://msphere.asm.org/content/2/6/e00408-17">Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal</a></q>.</p>
<p>In a sequence similarty network, each node represents a protein. An edge/line joining two nodes represents shared sequence similarity between the two proteins. Proteins are coloured according to their genus. Significant sequence similarity is detected using all-vs-all BLASTp homology searches.</p>
<p>Clicking on a protein shows information about it (e.g. Species, Order, Sequence Length, etc.)</p>
<p>The network can be filtered to hide/show particular proteins (e.g. by Genus or Order) using the buttons to the right of the network.</p>
<h4>Usage</h4>
<p><img src="./images/help_screenshot.png" width="20%"></p>
<p>
<ol>
<li><strong>Left to right</strong>:
<ul>
<li><span class="glyphicon glyphicon-zoom-in"></span> Zoom in</li>
<li><span class="glyphicon glyphicon-zoom-out"></span> Zoom out</li>
<li><span class="glyphicon glyphicon-home"></span> Center view on network</li>
</ul>
</li>
<li><strong>Toggle Edges:</strong> hides/shows all edges in the network. Hiding edges improves performance</li>
<li><strong>Toggle Labels:</strong> hides/shows labels for all nodes in the network. Hiding labels improves performance </li>
<li><strong>Filter box:</strong> type a query here to filter by Protein ID, Species, Genus or Order</li>
</ol>
</p><br>
<p>Additionally, for RxLR effectors, it is possible to filter according to the method that identified the candidate RxLR or if they contain a WYL motif. The methods used to identify putative RxLRs include: Win method <a href="http://www.plantcell.org/content/19/8/2349" target="_blank">(Win et al., 2007)</a>, Regex method <a href="http://www.nature.com/nature/journal/v450/n7166/abs/nature06203.html" target="_blank">(Whisson et al., 2007)</a>, HMM method using HMMsearch for <code>cropped.hmm</code> <a href="http://www.nature.com/nature/journal/v450/n7166/abs/nature06203.html" target="_blank">(Whisson et al., 2007)</a> and identifying homologs to previously reported RxLRs using BLAST <a href="https://www.nature.com/nature/journal/v461/n7262/full/nature08358.html" target="_blank">(Haas et al. 2009)</a>.</p>
<br>
<p>The source code for this site is available on <a href="https://github.com/oomycetes/oomycetes.github.io" target="_blank">GitHub</a> along with <a href="https://github.com/oomycetes/oomycetes.github.io/tree/master/SupplementaryMaterial" target="_blank">additional supplementary materials</a>.</p>
<hr>
<h4>Reference:</h4>
<p>McGowan, J. and Fitzpatrick, D. (2017). Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal. mSphere, 2(6), pp.e00408-17.</p>
</div>
<footer class="footer" style="z-index:50">
<div class="container">
<p class="text-muted">Genome Evolution Lab, <a href="https://www.maynoothuniversity.ie/biology" target="_blank">Department of Biology</a>, <a href="https://www.maynoothuniversity.ie" target="_blank">Maynooth University</a> - 2017.</p>
</div>
</footer>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
<script src="js/main.js"></script>
<script src="js/ie10-viewport-bug-workaround.js"></script>
<!-- JS to load the network file -->
<script>
var graph;
var default_zoom;
sigma.parsers.json(
"./data/chitinases.json",
{
container: 'network-container',
settings: {
defaultLabelSize: 12
}
},
function(s) {
// Save reference to network for later
graph = s;
graph.bind('clickNode', nodeClicked);
// Gephi and SigmaJS use difference coordinate systems
// Invert Y-coordinates of all nodes to match Gephi figures
nodes = graph.graph.nodes()
for (var i = 0; i < nodes.length; i++) {
console.log(nodes[i].y);
nodes[i].y = nodes[i].y * -1;
console.log(nodes[i].y);
}
graph.refresh();
// Fixes bug where node labels aren't shown on hover when drawLabels = false
//graph.settings('drawLabels', false);
//graph.refresh();
default_zoom = graph.camera.ratio;
// Hide the loading icon
$('.loading').hide();
$('#button-in').click(function() {
graph.camera.goTo({
ratio: graph.camera.ratio / graph.camera.settings('zoomingRatio')
});
});
$('#button-out').click(function() {
graph.camera.goTo({
ratio: graph.camera.ratio * graph.camera.settings('zoomingRatio')
});
});
$('#button-home').click(function() {
graph.camera.goTo({
ratio: default_zoom,
x: 0,
y: 0
});
});
$('#button-edges').click(function() {
graph.settings('drawEdges', !graph.settings('drawEdges'));
graph.refresh({ skipIndexation: true});
});
$('#button-labels').click(function() {
graph.settings('drawLabels', !graph.settings('drawLabels'));
graph.refresh({ skipIndexation: true});
})
});
</script>
</body>
</html>