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lda.php
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lda.php
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<?php
$type = urldecode($_GET["type"]);
$bioproject = urldecode($_GET["bioproject"]);
$dp = urldecode($_GET["dp"]);
$at = urldecode($_GET["at"]);
$biome = urldecode($_GET["biome"]);
$is = urldecode($_GET["is"]);
// echo $type."<br/>".$bioproject."<br/>".$dp."<br/>".$at."<br/>".$is."<br/>".$biome."<br/>";
?>
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<title>LDA - MDPD</title>
<link rel = "stylesheet" type = "text/css" href = "css/main.css" />
<script type = "text/javascript" src = "js/plot_lda.js"></script>
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js" type="text/javascript"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery-csv/1.0.8/jquery.csv.min.js"></script>
<script type = "text/javascript" src = "https://cdn.plot.ly/plotly-latest.min.js"></script>
</head>
<body>
<div class = "section_header">
<center><p class="title">MDPD - Microbiome Database of Pulmonary Diseases</p></center>
</div>
<div class = "section_menu">
<center>
<table cellpadding="3px">
<tr class="nav">
<td class="nav"><a href="index.php" class="side_nav">Home</a></td>
<td class="nav"><a href="browse.php" class="side_nav">Browse</a></td>
<td class="nav"><a href="statistics.php" class="side_nav">Statistics</a></td>
<td class="nav"><a href="about.php" class="side_nav">About</a></td>
<td class="nav"><a href="help.html" class="side_nav">Help</a></td>
<td class="nav"><a href="team.html" class="side_nav">Team</a></td>
</tr>
</table>
</center>
</div>
<!--<div class = "section_left"></div>-->
<div class = "section_middle">
<center><p id="display_text"></p></center>
<div id="download_div" style="width:100%; text-align:center; margin-bottom:20px;"></div>
<div style="width:100%" id="plot_container">
<p>
<b><i>N.B.</i></b> - <b>1)</b> To view all the differential markers, please hover on the bars of the plot
or download the data using the <i>"Download data"</i> button. located at the top of the page <b>2)</b> A
cutoff of <i>log<sub>10</sub> (LDA score) ≥ 2</i> was used to determine the differential markers.
<b>3)</b> All differential markers in the LDA plot were found to be statistically significant. <b>4)</b>
The statistical significance cutoff used was: <i>p-value < 0.01</i> (Kruskal-Wallis test). <b>5)</b>
To check the p-values for each differential marker, please download the data using the "Download data"
button. <b>6)</b> The downloaded data shows Kruskal-Wallis <i>p</i>-value. <b>7)</b> The LDA plot can be
downloaded as a SVG image by clicking on the <i>"Export as SVG"</i>
<svg xmlns="http://www.w3.org/2000/svg" height="1em" viewBox="0 0 512 512">
<path d="M288 32c0-17.7-14.3-32-32-32s-32 14.3-32 32V274.7l-73.4-73.4c-12.5-12.5-32.8-12.5-45.3 0s-12.5 32.8 0 45.3l128 128c12.5 12.5 32.8 12.5 45.3 0l128-128c12.5-12.5 12.5-32.8 0-45.3s-32.8-12.5-45.3 0L288 274.7V32zM64 352c-35.3 0-64 28.7-64 64v32c0 35.3 28.7 64 64 64H448c35.3 0 64-28.7 64-64V416c0-35.3-28.7-64-64-64H346.5l-45.3 45.3c-25 25-65.5 25-90.5 0L165.5 352H64zm368 56a24 24 0 1 1 0 48 24 24 0 1 1 0-48z"/>
</svg>
button in the menubar located at the top right corner of the plot.
</p>
</div>
<script>
function getLDAData(queryType, bioproject, diseasePair, assayType, biome, isolationSource, score) {
var prefix = 'input/LDA/';
if(queryType == 'DISEASE') {
var folder = prefix + assayType + '/';
var file = folder + 'LDA_' + diseasePair.replace(/ /g,"_") + '_' + isolationSource.replace(/ /g,"_") + '.csv';
var display = diseasePair.replace(/_/g," - ") + ' | ' + assayType + ' | ' + biome + ' | ' + isolationSource;
} else if(queryType == 'BIOPROJECT') {
var folder = prefix + 'Bioproject/' ;
var file = folder + 'LDA_' + bioproject + '_' + isolationSource.replace(/ /g,"_") + '_' + assayType.replace(/ /g,"_") + '.csv';
var display = 'BioProject ID: ' + bioproject + ' | ' + assayType + ' | ' + isolationSource;
}
// alert(queryType+'<br/>'+bioproject+'<br/>'+diseasePair+'<br/>'+assayType+'<br/>'+isolationSource+'<br/>'+'\n'+file);
var xmlhttp = new XMLHttpRequest();
xmlhttp.onreadystatechange = function() {
if (this.readyState == 4 && this.status == 200) {
document.getElementById('display_text').innerHTML = '<h3>' + display + '</h3>';
document.getElementById('download_div').innerHTML = '<a href="' + file + '"><button type="button" style="margin:2px;">Download data</button></a>';
plotLDA('plot_container', this.responseText, diseasePair.replace(/_/g,"-"), assayType, biome, isolationSource.replace(/ /g,"_"), score);
}
};
xmlhttp.open('GET', file, true);
xmlhttp.setRequestHeader("Content-type", "text/csv");
xmlhttp.send();
}
<?php echo "getLDAData('".$type."','".$bioproject."','".$dp."','".$at."','".$biome."','".$is."',0);"; ?>
</script>
<br/><hr/>
<p style="font-size:0.9em;text-align:center;">
© 2023 Bose Institute. All rights reserved. For queries, please contact Dr. Sudipto Saha
(<a style="color:#003325;" href="mailto:[email protected]">[email protected]</a>,
<a style="color:#003325;" href="mailto:[email protected]">[email protected]</a>).
</p>
</div>
</body>
</html>