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index.html

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   <a href="./ui.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">The user interface</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./first.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">First use</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item">
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@@ -191,7 +197,7 @@ <h1 class="title">iSEETheBook</h1>
 
 <section id="preface" class="level1 unnumbered">
 <h1 class="unnumbered">Preface</h1>
-<p>This book compiles essential knowledge about <a href="https://bioconductor.org/packages/iSEE/"><em>iSEE</em></a>, an R package released through the Bioconductor project.</p>
+<p>This book compiles essential knowledge about <a href="https://bioconductor.org/packages/iSEE/"><em>iSEE</em></a>, an <em>R</em> package released through the Bioconductor project.</p>
 <p>This book caters for three main groups of users:</p>
 <ul>
 <li>End users interacting with the graphical user interface in their web browser.</li>

intro.html

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   <a href="./ui.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">The user interface</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./first.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">First use</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item">
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references.html

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-<link href="./ui.html" rel="prev">
+<link href="./first.html" rel="prev">
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 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
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   <a href="./ui.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">The user interface</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./first.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">First use</span></span></a>
+  </div>
 </li>
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@@ -415,8 +421,8 @@ <h1 class="title">References</h1>
 </script>
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-      <a href="./ui.html" class="pagination-link">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">The user interface</span></span>
+      <a href="./first.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">First use</span></span>
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search.json

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     "section": "2.4 Collapsible boxes of parameters",
     "text": "2.4 Collapsible boxes of parameters\n\n2.4.1 Data parameters\nThe Data parameters collapsible box contains interactive elements that control the nature of the observations displayed in each panel.\nFor plots, that is typically the choice of variables shown along each axis.\nFor tables, that is typically the subset of columns hidden in the panel.\n\n\n\nFigure 2.7: The Data parameters box of the Reduced dimension plot panel, expanded to reveal its contents.\n\n\n\n\n2.4.2 Visual parameters\nThe Visual parameters collapsible box contains interactive elements that control the appearance of data points and non-data elements of panels that produce a plot.\nThat is typically the color, shape, size, and opacity of data points. It may also include the possibility of faceting the plot by discrete variables along each axis, and further customisation of non-data elements of the plot such as axis labels and the plot legend.\n\n\n\nFigure 2.8: The Visual parameters box of the Reduced dimension plot panel, expanded and configured to reveal the ‘Color’, ‘Shape’, ‘Size’, and ‘Facet’ sections of its contents.\n\n\n\n\n2.4.3 Selection parameters\nThe Selection parameters collapsible box contains interactive elements that control the transmission and usage of selections in each panel.\nThat is typically the name of another panel to receive a selection from and whether to restrict data points in the current panel to those selected in the other panel It may also include the possibility of saving and deleting saved selections made in the current panel.\n\n\n\nFigure 2.9: The Selection parameters box of the Reduced dimension plot panel, expanded to reveal its contents."
   },
+  {
+    "objectID": "first.html#quick-start",
+    "href": "first.html#quick-start",
+    "title": "3  First use",
+    "section": "3.1 Quick start",
+    "text": "3.1 Quick start\nThe iSEE package is built around the iSEE() function.\nIn the simplest case, given nothing more than a SummarizedExperiment object, the iSEE() function automatically scans the object for information stored in standard components and returns a shiny app object. If the shiny app object is not assigned to an object name, the app is immediately launched in a new window.\nThe code chunk below illustrate conceptually how:\n\nPackages are attached to the R session.\nA SummarizedExperiment object is produced.\nA SummarizedExperiment object is given to the iSEE() function.\n\nlibrary(SummarizedExperiment)\nlibrary(iSEE)\nse <- SummarizedExperiment(...)\niSEE(se)\n\n\n\n\n\n\nWarning\n\n\n\nIn the code chunk above, SummarizedExperiment(...) is pseudo-code that represents the creation of SummarizedExperiment; do not run that code! In practice, you will produce those objects through your own scripts and workflows."
+  },
   {
     "objectID": "references.html",
     "href": "references.html",

ui.html

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 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./references.html" rel="next">
+<link href="./first.html" rel="next">
 <link href="./intro.html" rel="prev">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
@@ -116,6 +116,12 @@
   <a href="./ui.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">The user interface</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./first.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">First use</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item">
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       </a>          
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-      <a href="./references.html" class="pagination-link">
-        <span class="nav-page-text">References</span> <i class="bi bi-arrow-right-short"></i>
+      <a href="./first.html" class="pagination-link">
+        <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">First use</span></span> <i class="bi bi-arrow-right-short"></i>
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