<title>KODAMA</title> <style> /* Font Family and Size */ body, .navbar-nav .nav-link {color: #ffffff; .navbar-nav .nav-link { font-family: "Source Sans Pro", Arial, sans-serif; font-size: 16px; color: #ffffff; background-color: ; }}

    /* Navbar Styles */
    .navbar {
        position: fixed;
        top: 0;
        left: 0cm;
        right: 0;
        z-index: 500;
        background-color: #333333;
        padding-top: 0;
        padding-bottom: 0;
        height: 50px;
        width: calc(100%);
    }

    .navbar-brand {
        margin-top: -5px;
    }

    .navbar-nav .nav-item {
        margin-bottom: 04px;
        display: flex;
        align-items: center;
        justify-content: space-between;
        box-shadow: 0 109px 109px rgba(0, 0, 0, 0);
    }

    .navbar-nav .nav-link {
        white-space: nowrap;
        overflow: hidden;
        text-overflow: ellipsis;
    }

    .navbar-nav .nav-item:nth-child(1) {
        margin-top: 20px;
    }

    .navbar-nav .nav-item:nth-child(2) {
        margin-top: 20px;
    }

    .navbar-nav .nav-item:nth-child(3) {
        margin-top: 20px;
    }

    .navbar-nav .nav-item:nth-child(4) {
        margin-top: 20px;
        margin-right: 10cm;
        margin-left: auto;
    }

    .navbar-nav .source-code-link {
        margin-top: 40px;
    }

    .container {
        padding-left: 7.3cm;
    }

    .navbar-brand,
    .navbar-nav .nav-link {
        padding: 0.1px 1rem;
        text-decoration: none;
        display: inline-block;
    }

    .navbar-brand {
        font-size: 20px;
        margin-right: 5px;
        position: relative;
        display: block;
    }

    .navbar-brand:hover,
    .navbar-nav .nav-link:hover {
        text-decoration: none;
    }

    .navbar-nav {
        display: flex;
        align-items: center;
        margin-left: 05px;
    }

    /* Body padding to compensate for fixed navbar */
    body {
        padding-top: 0cm;
        background-color: #ffffff;
        color: #333;
        margin: 0;
    }

    /* Sidebar Styles */
    #sidebar {
        position: fixed;
        top: 2.9cm;
        bottom: 2cm;
        left: 9.5cm;
        width: 180%;
        max-width: 260px;
        max-height: 19%;
        overflow-y: auto;
        box-shadow: 0px 0px 5px rgba(0, 0, 0, 0.0);
        padding: 5px;
        line-height: 20px;
        border-radius: 6px;
        border: 1px solid #ccc;
    }

    #sidebar ul {
        list-style: none;
        padding: 0;
        margin: 0;
    }

    #sidebar ul li {
        padding: 5px;
        transition: background-color 0.3s;
        cursor: pointer;
    }

    #sidebar ul li:hover {
        background-color: #none;
    }

    #sidebar ul li a {
        color: #000000;
        text-decoration: none;
        font-size: 16px;
        font-family: "Source Sans Pro", Arial, sans-serif;
    }

    #sidebar ul li a i {
        font-size: 10px;
    }

    /* Main Content Styles */
    .container {
        margin-left: 1.5cm;
    }

    /* Sections Styles */
    .data-section {
        margin-bottom: 20px;
    }

    /* Adjusting margin for Introduction */
    .navbar-nav .nav-item:first-child {
        margin-top: 20px;
    }

    /* Active link styles */
    .active-link {
        background-color: #2780e3 !important;
    }

    .active-link a {
        color: white !important;
    }

    /* Code container styles */
    .code-container {
        position: relative;
        background-color: #f8f9fa;
        border: 1px solid #ccc;
        padding: 10px;
        margin-top: 10px;
        border-radius: 6px;
        overflow: hidden;
    }

    pre {
        margin: 0;
        padding: 0;
        overflow-x: auto;
    }

    button {
        position: absolute;
        top: 5px;
        right: 5px;
        background-color: transparent;
        border: none;
        color: #007bff;
        cursor: pointer;
    }

    button:hover {
        color: #0056b3;
    }

    button.copied {
        color: #28a745;
    }

    button.copied:hover {
        color: #218838;
    }


</style>

KODAMA

        <div class="collapse navbar-collapse" id="navbarSupportedContent">
            <ul class="navbar-nav mr-auto">
                <li class="nav-item">
                    <a class="nav-link" href="https://moussakassim.github.io/KODAMA1/">Introduction</a>
                </li>
                <li class="nav-item">
                    <a class="nav-link" href="#software-tutorial">Software Tutorial</a>
                </li>
                <li class="nav-item">
                    <a class="nav-link" href="#simulation">Simulation</a>
                </li>
                <li class="nav-item dropdown">
                    <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button"
                        data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
                        Data Analyses
                    </a>
                    <div class="dropdown-menu" aria-labelledby="navbarDropdown">
                        <a class="dropdown-item"
                            href="https://moussakassim.github.io/Metabolomic-data/">Metabolomic
                            data</a>
                        <a class="dropdown-item"
                            href="https://moussakassim.github.io/Single-cell-Data/">Single
                            cell RNA seq data</a>
                        <a class="dropdown-item"
                            href="https://moussakassim.github.io/Spatial-Transcriptomics/">Spatial
                            Transcriptomic data</a>
                    </div>
                </li>
            </ul>
            <ul class="navbar-nav">
                <li class="nav-item">
                    <a class="nav-link" href="https://github.com/tkcaccia/KODAMA">
                        <span class="fab fa-github"></span>
                        Source code
                    </a>
                </li>
            </ul>
        </div>
    </div>
</nav>

<!-- Sidebar -->
<div id="sidebar">
    <ul>
        <li id="TutorialLink" data-toggle="tooltip" data-placement="right" title="Tutorial">
            <a href="#Tutorial">
                <i class="fas fa-book-open"></i>
                <span>Tutorial</span>
            </a>
        </li>
        <li id="MDS, tSNE and UMAPLink" data-toggle="tooltip" data-placement="right" title="MDS, tSNE and UMAP">
            <a href="#MDS, tSNE and UMAP">
                <i class="fas fa-newspaper"></i>
                <span>MDS, tSNE and UMAP</span>
            </a>
        </li>
        <li id="KODAMALink" data-toggle="tooltip" data-placement="right" title="KODAMA">
            <a href="#KODAMA">
                <i class="fas fa-tools"></i>
                <span>KODAMA</span>
            </a>
        </li>
        <li id="Visualize the different clustering algorithmsLink" data-toggle="tooltip" data-placement="right" title="Visualize the different clustering algorithms">
            <a href="#Visualize the different clustering algorithms">
                <i class="fas fa-tasks"></i>
                <span>Visualize the different clustering algorithms</span>
            </a>
        </li>
    </ul>
</div>
 <script>
    // Fonction pour changer le style de l'élément actif
    function setActiveLink(linkId) {
        // Supprimer la classe active-link de tous les éléments
        var links = document.querySelectorAll('#sidebar ul li');
        links.forEach(function (item) {
            item.classList.remove('active-link');
        });

        // Ajouter la classe active-link à l'élément sélectionné
        var selectedLink = document.getElementById(linkId);
        selectedLink.classList.add('active-link');
    }

    // Ajouter un écouteur d'événement pour chaque élément de la barre latérale
    var sidebarLinks = document.querySelectorAll('#sidebar ul li');
    sidebarLinks.forEach(function (link) {
        link.addEventListener('click', function (event) {
            // Empêcher le comportement par défaut du lien
            event.preventDefault();
            
            // Récupérer l'ID de l'élément cliqué
            var linkId = event.currentTarget.id;
            
            // Appeler la fonction pour définir l'élément actif
            setActiveLink(linkId);
        });
    });
</script>

Metabolomic Data

The data belong to a cohort of 22 healthy donors (11 male and 11 female) where each provided about 40 urine samples over the time course of approximately 2 months, for a total of 873 samples. Each sample was analysed by Nuclear Magnetic Resonance Spectroscopy. Each spectrum was divided in 450 spectral bins.

Tutorial

Here, we load the MetRef dataset. Columns with only zero values are removed.

data(MetRef)
u = MetRef$data
u = u[,-which(colSums(u) == 0)]

We apply the Probabilistic Quotient Normalization

u = normalization(u)$newXtrain

We mean-center and univariate scaling the data set.

u = scaling(u)$newXtrain

Two classification vectors are created

class = as.numeric(as.factor(MetRef$gender))
class2 = as.numeric(as.factor(MetRef$donor))

<!-- MDS, tSNE and UMAP Section -->

MDS, tSNE and UMAP

Different algorithms for dimensionality reduction are applied

res_MDS = cmdscale(dist(u))
res_tSNE = Rtsne(u)$Y
res_UMAP = umap(u)$layout

<!-- KODAMA Section -->

KODAMA

We apply KODAMA with Partial Least Square Discriminant Analysis (PLS-DA) as classifier with 50 components to drive the accuracy maximization. The KODAMA dissimilarity matrix is converted in a low dimensionality space using three different methods (i.e., MDS, t-SNE, and UMAP).

kk = KODAMA.matrix(u, f.par = 50)
res_KODAMA_MDS = KODAMA.visualization(kk, method = "MDS")
res_KODAMA_tSNE = KODAMA.visualization(kk, method = "t-SNE")
res_KODAMA_UMAP = KODAMA.visualization(kk, method = "UMAP")

<!-- Visualize the different clustering algorithms Section -->

Visualize the different clustering algorithms:

a) Labelled by the gender

par(mfrow = c(2, 3))
plot(res_MDS, pch = 21, bg = rainbow(2)[class], main = "MDS")
plot(res_tSNE, pch = 21, bg = rainbow(2)[class], main = "tSNE")
plot(res_UMAP, pch = 21, bg = rainbow(2)[class], main = "UMAP")
plot(res_KODAMA_MDS, pch = 21, bg = rainbow(2)[class], main = "KODAMA_MDS")
plot(res_KODAMA_tSNE, pch = 21, bg = rainbow(2)[class], main = "KODAMA_tSNE")
plot(res_KODAMA_UMAP, pch = 21, bg = rainbow(2)[class], main = "KODAMA_UMAP")

    <p>b) Labelled by the donor</p>
    <div class="code-container">
        <button class="copyButton"><i class="far fa-copy"></i></button>
        <pre><code>plot(res_MDS, pch = 21, bg = rainbow(22)[class2], main = "MDS")

plot(res_tSNE, pch = 21, bg = rainbow(22)[class2], main = "tSNE") plot(res_UMAP, pch = 21, bg = rainbow(22)[class2], main = "UMAP") plot(res_KODAMA_MDS, pch = 21, bg = rainbow(22)[class2], main = "KODAMA_MDS") plot(res_KODAMA_tSNE, pch = 21, bg = rainbow(22)[class2], main = "KODAMA_tSNE") plot(res_KODAMA_UMAP, pch = 21, bg = rainbow(22)[class2], main = "KODAMA_UMAP")

<!-- Bootstrap Scripts -->
<script src="https://code.jquery.com/jquery-3.5.1.slim.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/@popperjs/[email protected]/dist/umd/popper.min.js"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js"></script>

<!-- Font Awesome Script -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/js/all.min.js"></script>

<!-- JavaScript for interactive functionality -->
<script>
// Fonction pour déplacer la page vers l'élément correspondant

function scrollToSection(sectionId) { var section = document.getElementById(sectionId); section.scrollIntoView({ behavior: 'smooth', block: 'start' }); }

// Ajouter un écouteur d'événement pour chaque élément de la barre latérale var sidebarLinks = document.querySelectorAll('#sidebar ul li'); sidebarLinks.forEach(function (link) { link.addEventListener('click', function (event) { // Empêcher le comportement par défaut du lien event.preventDefault();

    // Récupérer l'ID de la section correspondante
    var sectionId = link.querySelector('a').getAttribute('href').replace('#', '');

    // Défiler jusqu'à la section correspondante
    scrollToSection(sectionId);
});

});

    // Fonction pour ajouter la classe de couleur de fond au survol
    function addBackgroundOnHover(element) {
        element.addEventListener('mouseenter', function () {
            element.classList.add('bg-color');
        });
        element.addEventListener('mouseleave', function () {
            element.classList.remove('bg-color');
        });
    }

    // Fonction pour gérer le clic sur un élément de la liste
    function handleItemClick(element) {
        element.addEventListener('click', function () {
            // Supprimer la classe de couleur de fond de tous les éléments
            var listItems = document.querySelectorAll('.nav-item');
            listItems.forEach(function (item) {
                item.classList.remove('bg-color');
            });

            // Ajouter la classe de couleur de fond à l'élément cliqué
            element.classList.add('bg-color');
        });
    }

    // Sélectionnez tous les éléments de la liste du menu
    var menuItems = document.querySelectorAll('.nav-item');

    // Ajouter la logique d'interaction pour chaque élément de la liste du menu
    menuItems.forEach(function (item) {
        handleItemClick(item);
        addBackgroundOnHover(item);
    });
   
var copyButton = document.getElementById('copyButton');
var codeBlock = document.querySelector('.code-container pre code');

document.getElementById('copyButton1').addEventListener('click', function() {
var codeBlock = document.getElementById('codeBlock1');
var textToCopy = codeBlock.querySelector('code').innerText;
navigator.clipboard.writeText(textToCopy)
    .then(function() {
        // Changement de couleur du bouton pour indiquer que la copie a réussi
        document.getElementById('copyButton1').classList.add('copied');
        setTimeout(function() {
            document.getElementById('copyButton1').classList.remove('copied');
        }, 1000);
    })
    .catch(function(err) {
        console.error('Failed to copy: ', err);
    });

});

     </script>