mdpd/dynamic_taxonomic_analysis.php at main · PulmonomicsLab/mdpd · GitHub

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<?php
    include 'db.php';

    $disease = (isset($_POST['taxonomic_ds'])) ? $_POST['taxonomic_ds'] : "";
    $subgroups = (isset($_POST['taxonomic_sg'])) ? $_POST['taxonomic_sg'] : array();
    $isolationSources = (isset($_POST['taxonomic_is'])) ? $_POST['taxonomic_is'] : array();
    $at = (isset($_POST['taxonomic_at'])) ? $_POST['taxonomic_at'] : "";
    $libs = (isset($_POST['taxonomic_lib'])) ? $_POST['taxonomic_lib'] : array();
    $bioprojects = (isset($_POST['taxonomic_bp'])) ? $_POST['taxonomic_bp'] : array();
    $runs = array();

//     echo $disease."<br/>";
//     echo implode(', ', $subgroups)."<br/>";
//     echo implode(', ', $isolationSources)."<br/>";
//     echo $at."<br/>";
//     echo implode(', ', $libs)."<br/>";
//     echo implode(', ', $bioprojects)."<br/>";

    function getSGPlaceholder() {
        global $subgroups;
        return str_repeat("?,", count($subgroups) - 1) . "?";
    }

    function getISPlaceholder() {
        global $isolationSources;
        return str_repeat("?,", count($isolationSources) - 1) . "?";
    }

    function getLibPlaceholder() {
        global $libs;
        return str_repeat("?,", count($libs) - 1) . "?";
    }

    function getBPPlaceholder() {
        global $bioprojects;
        return str_repeat("?,", count($bioprojects) - 1) . "?";
    }

    function getParamString() {
        global $subgroups;
        global $isolationSources;
        global $libs;
        global $bioprojects;
        return "ss" . str_repeat("s", count($subgroups)) . str_repeat("s", count($isolationSources)) . str_repeat("s", count($libs)) . str_repeat("s", count($bioprojects));
    }

    function getValues() {
        global $disease;
        global $at;
        global $libs;
        global $subgroups;
        global $isolationSources;
        global $bioprojects;
        $values = array($disease, $at);
        foreach ($subgroups as $sg)
            array_push($values, $sg);
        foreach ($isolationSources as $is)
            array_push($values, $is);
        foreach ($libs as $lib)
            array_push($values, $lib);
        foreach ($bioprojects as $bp)
            array_push($values, $bp);
        return $values;
    }

    function refValues($arr){
        $refs = array();
        for($i=0; $i<count($arr); ++$i)
            $refs[$i] = &$arr[$i];
        return $refs;
    }

    if (isset($_POST['taxonomic_sg']) && isset($_POST['taxonomic_is']) && isset($_POST['taxonomic_lib']) && isset($_POST['taxonomic_bp'])) {
        $query = "select Run from run inner join disease on run.SubGroup = disease.SubGroup where disease.Grp=? and AssayType=? and run.SubGroup in (".getSGPlaceholder().") and IsolationSource in (".getISPlaceholder().") and LibraryLayout in (".getLibPlaceholder().") and BioProject in (".getBPPlaceholder().");";
        $paramString = getParamString();
        $values = getValues();

        $conn = connect();
        $stmt = $conn->prepare($query);

        array_unshift($values, $paramString);
        call_user_func_array(
            array($stmt, "bind_param"),
            refValues($values)
        );
        $stmt->execute();
        $rows = execute_and_fetch_assoc($stmt);
//         echo count($rows)."<br/>";

        $stmt->close();
        closeConnection($conn);

        foreach ($rows as $row)
            array_push($runs, $row["Run"]);
    }

    $heading1 = "<b>Group:</b> ".$disease;
    $heading2 = "<b>Assay type:</b> ".$at;
    $heading3 = "<b>Isolation sources:</b> [".implode(", ", $isolationSources)."]";
    $heading4 = "<b>Subgroups:</b> [".implode(", ", $subgroups)."]";
    $heading5 = "<b>BioProjects:</b> [".implode(", ", $bioprojects)."]";
    $heading6 = "<b>Library layouts:</b> [".implode(", ", $libs)."]";
    $heading7 = "Number of runs found in database: ".count($runs);

    $dataJSON = json_encode(
        array(
            "at" => $at,
            "bioprojects" => $bioprojects,
            "runs" => $runs
        )
    );
?>

<!DOCTYPE html>
<html>
    <head>
        <meta charset="UTF-8">
        <title>Taxonomic analysis - MDPD</title>
        <link rel="icon" href="resource/pulmonomics_lab_logo.png" type="image/x-icon">
        <link rel = "stylesheet" type = "text/css" href = "css/main.css" />
        <link rel = "stylesheet" type = "text/css" href = "css/browse.css" />
        <script type = "text/javascript" src = "js/plot_dynamic_taxonomic.js"></script>
        <script type = "text/javascript" src = "https://cdn.plot.ly/plotly-latest.min.js"></script>
        <script>
            function showDiv(divId){
                document.getElementById(divId).style.display = 'block';
            }
            function hideDiv(divId){
                document.getElementById(divId).style.display = 'none';
            }
        </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="analysis.php" class="side_nav">Analysis</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="submission.php" class="side_nav">Submit data</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">
            <p style="margin:0; font-size:1.2em; font-weight:bold; text-align:center;">Taxonomic analysis result</p>

            <center><button type="button" style="margin:5px;" onclick="showDiv('query_display_div')">Show query</button></center>
            <div class="browse-result" id="query_display_div" style="margin:10px 0 10px 0; font-size:1em; display:none;">
                <center><button type="button" class="round" style="margin:3px;" onclick="hideDiv('query_display_div')">&#10005;</button></center>
                <p style="margin:0 5px;">
                    <?php
                        echo $heading1."<br/>";
                        echo $heading2."<br/>";
                        echo $heading3."<br/>";
                        echo $heading4."<br/>";
                        echo $heading5."<br/>";
                        echo $heading6;
                    ?>
                </p>
            </div>
            <p style="margin:10px 0 10px 0; font-size:1em; font-weight:bold; text-align:center;"><?php echo $heading7; ?></p>

            <div id="download_div" style="width:100%; text-align:center; display:none;">
                <a id="download_button" download="taxonomic_analysis_figure_data.csv">
                    <button type="button" style="margin:2px;">Download figure data</button>
                </a>
            </div>

            <div id="analysis_plot_div" style="width:90%; margin:0 5% 0 5%;">
                <center><img style="height:300px;" src="resource/loading.gif" /></center>
            </div>
            <p id="taxa_button_group_heading" style="margin:3px; font-weight:bold; display:none;">Taxa details</p>
            <div id="taxa_button_group" style="width:100%; background-color:#fff9e6; border:1px dashed #004d99; display:none;"></div>
            <p id="heatmap_legend" style="font-size: 0.9em; display:none;">
                <b>Heatmap</b> shows the taxonomic signatures of top 25
                abundant taxa of the group with respect to the BioProjects,
                isolation sources, subgroups for the given assay type and
                library layouts. The blank cells denote the absence of taxa.
                <b>Click</b> on the <b>"Show query"</b> option to get the
                query parameters. <b>Hover mouse</b> on each cell to highlight
                the taxa name and the relative abundance values. <b>Click on
                the buttons</b> below the plot to get the information of the
                respective taxa. The plot can be downloaded as SVG by clicking
                on the <b>"
                <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>
                "</b> button in the figure menu bar at the top right corner. The
                data can be downloaded using the <b>"Download figure data"</b>
                button.
            </p>

            <br/><hr/>
            <p style="font-size:0.9em;text-align:center;">
                &#169; 2025 Bose Institute. All rights reserved. For queries, please contact Dr. Sudipto Saha
                (<a style="color:#003325;" href="mailto:ssaha4@jcbose.ac.in">ssaha4@jcbose.ac.in</a>,
                <a style="color:#003325;" href="mailto:ssaha4@gmail.com">ssaha4@gmail.com</a>).
            </p>
        </div>
    </body>
    <script>
        <?php echo "getHeatmapData('analysis_plot_div', '".$dataJSON."');"; ?>
    </script>
</html>