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tmpl.html
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<html>
<head>
<!-- Plotly.js and Datatables.js -->
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.16/css/jquery.dataTables.min.css">
<style type="text/css" class="init">
</style>
<script src="https://code.jquery.com/jquery-1.12.4.min.js"></script>
<script src="https://cdn.datatables.net/1.10.16/js/jquery.dataTables.min.js"></script>
<script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
<title>pathoscore</title>
</head>
<body>
<pre>
date: $date
created with <a href=https://github.com/quinlan-lab/pathoscore>pathoscore</a> version: $version
</pre>
<p><i>pathoscore</i> evaluates pathogenicity tools and scores.</p>
In this evaluation, there were <b>$n_pathogenic pathogenic</b> ($path_indel_pct% indels) and <b>$n_benign benign</b>
($benign_indel_pct% indels) variants that could be scored.
<h3>Distribution of variants scored</h3>
<div id="scored-plot-div"><!-- Plotly chart will be drawn inside this DIV --></div>
<h3>Receiver Operating Characteristic Curves</h3>
<div id="roc-plot-div"><!-- Plotly chart will be drawn inside this DIV --></div>
<h3>Precision-Recall Curves</h3>
<div id="pr-plot-div"><!-- Plotly chart will be drawn inside this DIV --></div>
<h3>Youden's J Statistic</h3>
<div id="J-barplot-div"><!-- Plotly chart will be drawn inside this DIV --></div>
<h3>Youden's J Distribution</h3>
<div id="J-distplot-div"><!-- Plotly chart will be drawn inside this DIV --></div>
<h3>Distribution of Scores for Pathogenic and Benign</h3>
$score_step_divs
<hr />
<h3>Clinical Utility for Genes of Interest</h3>
<div class="content">
<table id="clinical-utility" class="display" width="100%"></table>
</div>
<h3>command</h3>
<pre>$command</pre>
<script>
var trace1 = {
x: $methods,
y: $scored_pathogenic,
name: 'scored pathogenic',
type: 'bar',
marker: { color: 'rgb(76, 114, 176)'},
};
var trace2 = {
x: $methods,
y: $scored_benign,
name: 'scored benign',
marker: { color: 'rgb(64, 96, 149)'},
type: 'bar'
};
var trace3 = {
x: $methods,
y: $unscored_pathogenic,
name: 'unscored pathogenic',
marker: { color: 'rgb(229, 229, 229)' },
type: 'bar'
};
var trace4 = {
x: $methods,
y: $unscored_benign,
name: 'unscored benign',
marker: { color: 'rgb(204, 204, 204)'},
type: 'bar'
}
var data = [trace1, trace2, trace3, trace4];
var layout = {
barmode: 'stack',
yaxis: {title: 'Count'},
}
Plotly.newPlot('scored-plot-div', data, layout);
var roc_layout = {
hovermode: 'closest',
width: 900,
height: 900,
xaxis: {title: 'FPR', domain: [0, 1]},
yaxis: {title: 'TPR', domain: [0, 1]},
legend: {
x: 0.7,
y: 0.1
},
}
Plotly.newPlot('roc-plot-div', $roc_data, roc_layout);
var pr_layout = {
hovermode: 'closest',
width: 900,
height: 900,
xaxis: {title: 'Recall', domain: [0, 1]},
yaxis: {title: 'Precision', domain: [0, 1]},
legend: {
x: 0.1,
y: 0.1
},
}
Plotly.newPlot('pr-plot-div', $pr_data, pr_layout);
var Jbar_layout = {
yaxis: {title: 'J-index'},
}
Plotly.newPlot('J-barplot-div', $Jbar_data, Jbar_layout);
var Jdist_layout = {
hovermode: 'closest',
width: 1100,
height: 900,
yaxis: {title: 'J-score'},
xaxis: {title: 'Normalized score'},
}
Plotly.newPlot('J-distplot-div', $Jdist_data, Jdist_layout);
$plotly_score_steps
jQuery(document).ready(function() {
jQuery('#clinical-utility').DataTable( {
data: $culist,
columns: $header
} );
} );
</script>
</body>
</html>