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+          <a href="interactive.html">Interactive Utilities</a>
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+        <li>
+          <a href="importingdata.html">Importing Spatial Data</a>
+        </li>
+        <li>
+          <a href="voltronobjects.html">Working with VoltRon Objects</a>
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+
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+
+<h1 class="title toc-ignore">Interactive</h1>
+
+</div>
+
+
+<style>
+.title{
+  display: none;
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+  text-align: justify
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+.center {
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+</style>
+<style type="text/css">
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+</style>
+<p><br></p>
+<div id="interactive-annotation" class="section level1">
+<h1>Interactive Annotation</h1>
+<p><strong>VoltRon</strong> includes interactive applications to select
+and manually label spatial points by drawing polygons and circles. As an
+example, we will use a Spot-based spatial transcriptomic assay,
+specifically the <strong>Mouse Brain Serial Section 1/2</strong>
+datasets, analyzed in the <a href="nicheclustering.html">Niche
+Clustering</a> tutorial. You can find the already analyzed data stored
+as a VoltRon object <a
+href="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/NicheClustering/Visium&amp;Visium_data_decon_analyzed.rds">here</a></p>
+<pre class="r watch-out"><code>MBrain_Sec &lt;- readRDS(&quot;Visium&amp;Visium_data_decon_analyzed.rds&quot;)</code></pre>
+<p>We can start annotating the spatial assay. By passing arguments used
+by the <strong>vrSpatialPlot</strong> function to visualize labels
+(e.g. clusters), we can better select regions within tissue sections for
+annotation.</p>
+<pre class="r watch-out"><code>MBrain_Sec &lt;- annotateSpatialData(MBrain_Sec, assay = &quot;Assay1&quot;, 
+                                  group.by = &quot;clusters&quot;, label = &quot;annotation&quot;)</code></pre>
+<p><img width="100%" height="100%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/interactive_annotation.png" class="center"></p>
+<p><br></p>
+<p>Here, <strong>annotateSpatialData</strong> function not only labels
+spots with within regions of interests (ROIs) selected by the user, but
+also records these regions in ROI assays within the same layer of the
+annotated Visium assay. The new assay type will be given the name
+<strong>ROIAnnotations</strong> if otherwise not specified using the
+<strong>annotation_assay</strong> arguement in the function.</p>
+<pre class="r watch-out"><code>MBrain_Sec </code></pre>
+<pre><code>VoltRon Object 
+Anterior: 
+  Layers: Section1 Section2 
+Posterior: 
+  Layers: Section1 Section2 
+Assays: Visium_decon(Main) Visium ROIAnnotation </code></pre>
+<pre class="r watch-out"><code>MBrain_Sec@sample.metadata </code></pre>
+<pre><code>&gt; MBrain_Sec@sample.metadata
+               Assay    Layer    Sample
+Assay1        Visium Section1  Anterior
+Assay2        Visium Section2  Anterior
+Assay3        Visium Section1 Posterior
+Assay4        Visium Section2 Posterior
+Assay5 ROIAnnotation Section1  Anterior</code></pre>
+<p>The new annotations are available in the metadata of the spot assay
+(default assay in this object) and can be visualized if wanted.</p>
+<pre class="r watch-out"><code>head(Metadata(MBrain_Sec))</code></pre>
+<pre><code>                          Count        Assay    Layer   Sample clusters annotation
+AAACAAGTATCTCCCA-1_Assay1     1 Visium_decon Section1 Anterior        1   Region 3
+AAACACCAATAACTGC-1_Assay1     1 Visium_decon Section1 Anterior        3  undefined
+AAACAGAGCGACTCCT-1_Assay1     1 Visium_decon Section1 Anterior        4  undefined
+AAACAGCTTTCAGAAG-1_Assay1     1 Visium_decon Section1 Anterior        5   Region 1
+AAACAGGGTCTATATT-1_Assay1     1 Visium_decon Section1 Anterior        5   Region 1
+AAACATGGTGAGAGGA-1_Assay1     1 Visium_decon Section1 Anterior        3  undefined</code></pre>
+<pre class="r watch-out"><code>vrSpatialPlot(MBrain_Sec, assay = &quot;Assay1&quot;, group.by = &quot;annotation&quot;)</code></pre>
+<p><img width="80%" height="80%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/interactive_annotation_plot.png" class="center"></p>
+<p><br></p>
+<p>You can also overlay the ROI annotations with the clustered spots to
+visualize multiple assays in the same time.</p>
+<pre class="r watch-out"><code>library(ggnewscale)
+vrSpatialPlot(MBrain_Sec, assay = &quot;Assay1&quot;, group.by = &quot;clusters&quot;) |&gt; 
+  addSpatialLayer(MBrain_Sec, assay = &quot;Assay5&quot;, group.by = &quot;annotation&quot;, alpha = 0.7)</code></pre>
+<p><img width="80%" height="80%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/interactive_annotation_example_overlay_plot.png" class="center"></p>
+<p><br></p>
+</div>
+<div id="interactive-visualization" class="section level1">
+<h1>Interactive Visualization</h1>
+<p>VoltRon incorporates utilities</p>
+<ul>
+<li><strong>(i)</strong> to convert VoltRon objects into other spatial
+data objects and files that could be used platforms, and</li>
+<li><strong>(ii)</strong> to incorporate wrapper functions to call
+methods from package that achieves interactive visualization</li>
+</ul>
+<p><br></p>
+<div id="vitessce" class="section level2">
+<h2>Vitessce</h2>
+<p>We will transform VoltRon objects of Xenium data into zarr arrays,
+and use them for interactive visualization in <a
+href="http://vitessce.io/">Vitessce</a>. We should first download the
+vitessceR package which incorporates wrapper function to visualize zarr
+arrays interactively in R.</p>
+<pre class="r watch-out"><code>if (!require(&quot;devtools&quot;, quietly = TRUE))
+    install.packages(&quot;devtools&quot;)
+if (!require(&quot;vitessceR&quot;, quietly = TRUE))
+    devtools::install_github(&quot;Artur-man/vitessceR&quot;)</code></pre>
+<p>We can convert the VoltRon object into an anndata object and save it
+as a a zarr array using the <strong>as.AnnData</strong> function which
+will create the array in the specified location. We use the
+<strong>flip_coordinates=TRUE</strong> argument to flip the coordinates
+of cells vertically, hence match it with the top to bottom system of the
+background DAPI image. Also, we can save an OMETIFF file of the DAPI
+image using <strong>create.ometiff</strong> arguement to be used by
+vitessceR later.</p>
+<pre class="r watch-out"><code>xenium_data &lt;- as.AnnData(xenium_data, file = &quot;xenium_data.zarr&quot;, assay = &quot;Xenium&quot;, 
+                          flip_coordinates = TRUE, create.ometiff = TRUE)</code></pre>
+<p><br></p>
+<p>We can use the zarr file directly in the
+<strong>vrSpatialPlot</strong> function to visualize the zarr array
+interactively in Rstudio viewer. The <strong>reduction</strong>
+arguement allows the umap of the Xenium data to be visualized alongside
+with the spatial coordinates of the Xenium cells (thus associated cell
+segmentations).</p>
+<pre class="r watch-out"><code>vrSpatialPlot(&quot;xenium_data.zarr&quot;, group.by = &quot;clusters&quot;, reduction = &quot;umap&quot;)</code></pre>
+<p><img width="90%" height="90%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/interactive_vitessce.png" class="center"></p>
+<p><br></p>
+<p>The vitessce application in the viewer pane allows visualizing
+background DAPI image and segmentations simultaneously while allowing
+users to zoom in and control the pane for advanced visualization.</p>
+<p><img width="90%" height="90%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/interactive_vitessce_zoom.png" class="center"></p>
+<p><br></p>
+</div>
+<div id="tissuumaps" class="section level2">
+<h2>TissUUmaps</h2>
+<p>To use <strong>TissUUmaps</strong> for interactive investigation of
+your spatial omic data, we first need to convert the VoltRon object into
+an anndata object. However, this time we save the anndata object as an
+h5ad array using again the <strong>as.AnnData</strong> function which
+will create the array in the specified location. We use the
+<strong>flip_coordinates=TRUE</strong> argument to flip the coordinates
+of cells vertically, hence match it with the top to bottom system of the
+background DAPI image.</p>
+<pre class="r watch-out"><code>as.AnnData(xenium_data, file = &quot;xenium_data.h5ad&quot;, assay = &quot;Xenium&quot;, flip_coordinates = TRUE)</code></pre>
+<p>To use <strong>TissUUmaps</strong>, you can follow the instructions
+<a href="https://tissuumaps.github.io/installation/">here</a>. Once
+installed and executed, simply drag and drop the h5ad file to the main
+panel of the application</p>
+<p><img width="100%" height="100%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/interactive_tissuumaps.png" class="center"></p>
+<p><br></p>
+</div>
+<div id="voltron" class="section level2">
+<h2>VoltRon</h2>
+<p>You can also use the built-in Shiny-based interactive visualizers of
+the VoltRon package by calling <strong>interactive=TRUE</strong>. You
+can zoom in by drawing a box on the plot and double-clicking in the
+selected area.</p>
+<pre class="r watch-out"><code>vrSpatialPlot(xenium_data, group.by = &quot;clusters&quot;, plot.segments = TRUE, interactive = TRUE)</code></pre>
+<p><img width="85%" height="85%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/interactive_voltron.png" class="center"></p>
+<p><br></p>
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+    $(this).parent().toggleClass('nav-tabs-open');
+  });
+});
+</script>
+
+<!-- code folding -->
+
+<script>
+$(document).ready(function ()  {
+
+    // temporarily add toc-ignore selector to headers for the consistency with Pandoc
+    $('.unlisted.unnumbered').addClass('toc-ignore')
+
+    // move toc-ignore selectors from section div to header
+    $('div.section.toc-ignore')
+        .removeClass('toc-ignore')
+        .children('h1,h2,h3,h4,h5').addClass('toc-ignore');
+
+    // establish options
+    var options = {
+      selectors: "h1,h2,h3",
+      theme: "bootstrap3",
+      context: '.toc-content',
+      hashGenerator: function (text) {
+        return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
+      },
+      ignoreSelector: ".toc-ignore",
+      scrollTo: 0
+    };
+    options.showAndHide = false;
+    options.smoothScroll = false;
+
+    // tocify
+    var toc = $("#TOC").tocify(options).data("toc-tocify");
+});
+</script>
+
+<!-- dynamically load mathjax for compatibility with self-contained -->
+<script>
+  (function () {
+    var script = document.createElement("script");
+    script.type = "text/javascript";
+    script.src  = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
+    document.getElementsByTagName("head")[0].appendChild(script);
+  })();
+</script>
+
+</body>
+</html>