diff --git a/404.html b/404.html
index 8311290..5668a41 100644
--- a/404.html
+++ b/404.html
@@ -35,6 +35,9 @@
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
 <li><a class="dropdown-item" href="http://jef.works/scatterbar/articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="http://jef.works/scatterbar/articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="http://jef.works/scatterbar/articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="http://jef.works/scatterbar/articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="http://jef.works/scatterbar/articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul>
 </li>
 <li class="nav-item"><a class="nav-link" href="http://jef.works/scatterbar/news/index.html">Changelog</a></li>
diff --git a/LICENSE.html b/LICENSE.html
index af034a0..6b223b6 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -20,6 +20,9 @@
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
diff --git a/articles/customizing_scatterbar.html b/articles/customizing_scatterbar.html
index 5adb233..8bd3917 100644
--- a/articles/customizing_scatterbar.html
+++ b/articles/customizing_scatterbar.html
@@ -35,6 +35,9 @@
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
 <li><a class="dropdown-item" href="../articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="../articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="../articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul>
 </li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
@@ -61,7 +64,7 @@ <h1>Customizing scatterbar</h1>
                         <h4 data-toc-skip class="author">Jean Fan and
 Dee Velazquez</h4>
             
-            <h4 data-toc-skip class="date">2024-10-16</h4>
+            <h4 data-toc-skip class="date">2024-10-18</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/JEFworks-Lab/scatterbar/blob/main/vignettes/customizing_scatterbar.Rmd" class="external-link"><code>vignettes/customizing_scatterbar.Rmd</code></a></small>
       <div class="d-none name"><code>customizing_scatterbar.Rmd</code></div>
@@ -69,6 +72,9 @@ <h4 data-toc-skip class="date">2024-10-16</h4>
 
     
     
+<div class="section level2">
+<h2 id="customizing-scatterbar">Customizing scatterbar<a class="anchor" aria-label="anchor" href="#customizing-scatterbar"></a>
+</h2>
 <p>Below, we will simulate some data for demo purposes. We will create a
 small dataset to demonstrate the <code>scatterbar</code> function.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
@@ -255,6 +261,7 @@ <h4 data-toc-skip class="date">2024-10-16</h4>
 <span>                  padding_x <span class="op">=</span> <span class="fl">0.1</span>, padding_y <span class="op">=</span> <span class="fl">0.1</span>, legend_title<span class="op">=</span> <span class="st">"Animals"</span>, colors<span class="op">=</span><span class="va">custom_colors</span><span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_bw</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">'y'</span><span class="op">)</span> <span class="op">+</span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title<span class="op">=</span><span class="st">"Favorite Animals Among Classrooms"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="customizing_scatterbar_files/figure-html/test-9.png" width="700"></p>
+</div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside>
 </div>
diff --git a/articles/getting-started-with-scatterbars.html b/articles/getting-started-with-scatterbars.html
index 94ac237..62abdf6 100644
--- a/articles/getting-started-with-scatterbars.html
+++ b/articles/getting-started-with-scatterbars.html
@@ -35,6 +35,9 @@
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
 <li><a class="dropdown-item" href="../articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="../articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="../articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul>
 </li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
@@ -61,7 +64,7 @@ <h1>Getting started with scatterbars</h1>
                         <h4 data-toc-skip class="author">Jean Fan and
 Dee Velazquez</h4>
             
-            <h4 data-toc-skip class="date">2024-10-16</h4>
+            <h4 data-toc-skip class="date">2024-10-18</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/JEFworks-Lab/scatterbar/blob/main/vignettes/getting-started-with-scatterbars.Rmd" class="external-link"><code>vignettes/getting-started-with-scatterbars.Rmd</code></a></small>
       <div class="d-none name"><code>getting-started-with-scatterbars.Rmd</code></div>
@@ -69,6 +72,9 @@ <h4 data-toc-skip class="date">2024-10-16</h4>
 
     
     
+<div class="section level2">
+<h2 id="getting-started-with-scatterbars">Getting started with scatterbars<a class="anchor" aria-label="anchor" href="#getting-started-with-scatterbars"></a>
+</h2>
 <p>Below is how to use scatterbar from the provided spatial
 transcriptomic data from the mouse olfactory bulb tissue sample.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
@@ -78,34 +84,45 @@ <h4 data-toc-skip class="date">2024-10-16</h4>
 <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mOB</span><span class="op">$</span><span class="va">xy</span><span class="op">)</span></span></code></pre></div>
 <p><img src="getting-started-with-scatterbars_files/figure-html/setup-1.png" width="700"></p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">mOB</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span>
-<span><span class="co">#&gt;                            1          2         3          4         5</span></span>
-<span><span class="co">#&gt; ACAACTATGGGTTGGCGG 0.1420916 0.05540521 0.2902388 0.00000000 0.1657935</span></span>
-<span><span class="co">#&gt; ACACAGATCCTGTTCTGA 0.0000000 0.77541118 0.0000000 0.00000000 0.0000000</span></span>
-<span><span class="co">#&gt; ACATCACCTGCGCGCTCT 0.3360811 0.00000000 0.0000000 0.32262562 0.3412932</span></span>
-<span><span class="co">#&gt; ACATTTAAGGCGCATGAT 0.2239877 0.00000000 0.0000000 0.55189741 0.2241149</span></span>
-<span><span class="co">#&gt; ACCACTGTAATCTCCCAT 0.1373168 0.08529107 0.2204332 0.00000000 0.0000000</span></span>
-<span><span class="co">#&gt; ACCAGAGCCGTTGAGCAA 0.1364591 0.37986322 0.1499492 0.06702756 0.2147332</span></span>
-<span><span class="co">#&gt;                             6         7          8</span></span>
-<span><span class="co">#&gt; ACAACTATGGGTTGGCGG 0.00000000 0.1329341 0.21353679</span></span>
-<span><span class="co">#&gt; ACACAGATCCTGTTCTGA 0.14536750 0.0000000 0.07922131</span></span>
-<span><span class="co">#&gt; ACATCACCTGCGCGCTCT 0.00000000 0.0000000 0.00000000</span></span>
-<span><span class="co">#&gt; ACATTTAAGGCGCATGAT 0.00000000 0.0000000 0.00000000</span></span>
-<span><span class="co">#&gt; ACCACTGTAATCTCCCAT 0.00000000 0.1876818 0.36927715</span></span>
-<span><span class="co">#&gt; ACCAGAGCCGTTGAGCAA 0.05196769 0.0000000 0.00000000</span></span>
-<span></span>
-<span><span class="fu">scatterbar</span><span class="fu">::</span><span class="fu"><a href="../reference/scatterbar.html">scatterbar</a></span><span class="op">(</span><span class="va">mOB</span><span class="op">$</span><span class="va">data</span>, <span class="va">mOB</span><span class="op">$</span><span class="va">xy</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">mOB</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">##                            1          2         3          4         5</span></span>
+<span><span class="co">## ACAACTATGGGTTGGCGG 0.1420916 0.05540521 0.2902388 0.00000000 0.1657935</span></span>
+<span><span class="co">## ACACAGATCCTGTTCTGA 0.0000000 0.77541118 0.0000000 0.00000000 0.0000000</span></span>
+<span><span class="co">## ACATCACCTGCGCGCTCT 0.3360811 0.00000000 0.0000000 0.32262562 0.3412932</span></span>
+<span><span class="co">## ACATTTAAGGCGCATGAT 0.2239877 0.00000000 0.0000000 0.55189741 0.2241149</span></span>
+<span><span class="co">## ACCACTGTAATCTCCCAT 0.1373168 0.08529107 0.2204332 0.00000000 0.0000000</span></span>
+<span><span class="co">## ACCAGAGCCGTTGAGCAA 0.1364591 0.37986322 0.1499492 0.06702756 0.2147332</span></span>
+<span><span class="co">##                             6         7          8</span></span>
+<span><span class="co">## ACAACTATGGGTTGGCGG 0.00000000 0.1329341 0.21353679</span></span>
+<span><span class="co">## ACACAGATCCTGTTCTGA 0.14536750 0.0000000 0.07922131</span></span>
+<span><span class="co">## ACATCACCTGCGCGCTCT 0.00000000 0.0000000 0.00000000</span></span>
+<span><span class="co">## ACATTTAAGGCGCATGAT 0.00000000 0.0000000 0.00000000</span></span>
+<span><span class="co">## ACCACTGTAATCTCCCAT 0.00000000 0.1876818 0.36927715</span></span>
+<span><span class="co">## ACCAGAGCCGTTGAGCAA 0.05196769 0.0000000 0.00000000</span></span></code></pre>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">start.time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="fu">scatterbar</span><span class="fu">::</span><span class="fu"><a href="../reference/scatterbar.html">scatterbar</a></span><span class="op">(</span><span class="va">mOB</span><span class="op">$</span><span class="va">data</span>, <span class="va">mOB</span><span class="op">$</span><span class="va">xy</span><span class="op">)</span> <span class="op">+</span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/coord_fixed.html" class="external-link">coord_fixed</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <p><img src="getting-started-with-scatterbars_files/figure-html/setup-2.png" width="700"></p>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">end.time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">end.time</span> <span class="op">-</span> <span class="va">start.time</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Time difference of 0.2757623 secs</span></span></code></pre>
 <p>We can change the order of how each bar is laid out by changing the
 order of the cell-type proportion matrix of spatial transcriptomic data.
 We can also combine scatterbar with other ggplot geoms and
 customization!</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
+<span><span class="va">start.time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="fu">scatterbar</span><span class="fu">::</span><span class="fu"><a href="../reference/scatterbar.html">scatterbar</a></span><span class="op">(</span><span class="va">mOB</span><span class="op">$</span><span class="va">data</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>,<span class="fl">3</span>,<span class="fl">4</span>,<span class="fl">5</span>,<span class="fl">6</span>,<span class="fl">7</span>,<span class="fl">8</span>,<span class="fl">1</span><span class="op">)</span><span class="op">]</span>, <span class="va">mOB</span><span class="op">$</span><span class="va">xy</span>, size_x <span class="op">=</span> <span class="fl">1</span>, size_y <span class="op">=</span> <span class="fl">1</span>, padding_x <span class="op">=</span> <span class="fl">0.1</span>, padding_y <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></span><span class="op">(</span>data<span class="op">=</span><span class="va">mOB</span><span class="op">$</span><span class="va">xy</span>, mapping<span class="op">=</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x<span class="op">=</span><span class="va">x</span>, y<span class="op">=</span><span class="va">y</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_bw</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">'y'</span><span class="op">)</span> </span></code></pre></div>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_bw</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">'y'</span><span class="op">)</span> <span class="op">+</span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/coord_fixed.html" class="external-link">coord_fixed</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <p><img src="getting-started-with-scatterbars_files/figure-html/shiftorder-1.png" width="700"></p>
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">end.time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">end.time</span> <span class="op">-</span> <span class="va">start.time</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Time difference of 0.3487422 secs</span></span></code></pre>
+</div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside>
 </div>
diff --git a/articles/getting-started-with-scatterbars_files/figure-html/setup-2.png b/articles/getting-started-with-scatterbars_files/figure-html/setup-2.png
index 043e746..ad851a2 100644
Binary files a/articles/getting-started-with-scatterbars_files/figure-html/setup-2.png and b/articles/getting-started-with-scatterbars_files/figure-html/setup-2.png differ
diff --git a/articles/getting-started-with-scatterbars_files/figure-html/shiftorder-1.png b/articles/getting-started-with-scatterbars_files/figure-html/shiftorder-1.png
index 78c3511..112dd42 100644
Binary files a/articles/getting-started-with-scatterbars_files/figure-html/shiftorder-1.png and b/articles/getting-started-with-scatterbars_files/figure-html/shiftorder-1.png differ
diff --git a/articles/index.html b/articles/index.html
index f5b67e1..b8c01ed 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -20,6 +20,9 @@
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="../articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="../articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
@@ -44,6 +47,12 @@ <h3>All vignettes</h3>
         <dd>
         </dd><dt><a href="getting-started-with-scatterbars.html">Getting started with scatterbars</a></dt>
         <dd>
+        </dd><dt><a href="using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></dt>
+        <dd>
+        </dd><dt><a href="using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></dt>
+        <dd>
+        </dd><dt><a href="visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></dt>
+        <dd>
       </dd></dl></div>
   </main></div>
 
diff --git a/articles/using-scatterbar-with-spatial-experiment.html b/articles/using-scatterbar-with-spatial-experiment.html
new file mode 100644
index 0000000..b8cc670
--- /dev/null
+++ b/articles/using-scatterbar-with-spatial-experiment.html
@@ -0,0 +1,343 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Using scatterbar with a SpatialExperiment object • scatterbar</title>
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
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+      <h1>Using scatterbar with a SpatialExperiment object</h1>
+                        <h4 data-toc-skip class="author">Jean Fan and
+Dee Velazquez</h4>
+            
+            <h4 data-toc-skip class="date">2024-10-18</h4>
+      
+      <small class="dont-index">Source: <a href="https://github.com/JEFworks-Lab/scatterbar/blob/main/vignettes/using-scatterbar-with-spatial-experiment.Rmd" class="external-link"><code>vignettes/using-scatterbar-with-spatial-experiment.Rmd</code></a></small>
+      <div class="d-none name"><code>using-scatterbar-with-spatial-experiment.Rmd</code></div>
+    </div>
+
+    
+    
+<div class="section level2">
+<h2 id="using-scatterbar-with-a-spatialexperiment-object">Using <code>scatterbar</code> with a <code>SpatialExperiment</code>
+object<a class="anchor" aria-label="anchor" href="#using-scatterbar-with-a-spatialexperiment-object"></a>
+</h2>
+<p>This tutorial demonstrates how to visualize cell-type proportions
+with <code>scatterbar</code> from a <code>SpatialExperiment</code>
+object. <code>SpatialExperiment</code> is a class from Bioconductor that
+stores information from spatial-omics experiments, which we can use to
+visualize the cell types found in certain spots. We will use
+<code>SEraster</code> to rasterize cell-type counts and calculate their
+proportions within pixels, when can then be utilized by
+<code>scatterbar</code>.</p>
+<p>For more information on <code>SpatialExperiment</code>, click [here]
+(<a href="https://www.bioconductor.org/packages/release/bioc/vignettes/SpatialExperiment/inst/doc/SpatialExperiment.html" class="external-link uri">https://www.bioconductor.org/packages/release/bioc/vignettes/SpatialExperiment/inst/doc/SpatialExperiment.html</a>).</p>
+<div class="section level3">
+<h3 id="load-libraries">Load libraries<a class="anchor" aria-label="anchor" href="#load-libraries"></a>
+</h3>
+<p>First, we need to loading the necessary libraries and load in the
+dataset provided by <code>SEraster</code>. It is a preprocessed MERFISH
+dataset of the mouse preoptic area (POA) from a female naive animal. For
+more information, please refer to the original work, <a href="https://www.science.org/doi/10.1126/science.aau5324" class="external-link">Moffitt J.
+and Bambah-Mukku D. et al. (2018), “Molecular, spatial, and functional
+single-cell profiling of the hypothalamic preoptic region”, <em>Science
+Advances</em></a>.</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Load required libraries</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/drighelli/SpatialExperiment" class="external-link">SpatialExperiment</a></span><span class="op">)</span></span>
+<span><span class="co">#&gt; Loading required package: SingleCellExperiment</span></span>
+<span><span class="co">#&gt; Loading required package: SummarizedExperiment</span></span>
+<span><span class="co">#&gt; Loading required package: MatrixGenerics</span></span>
+<span><span class="co">#&gt; Loading required package: matrixStats</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; Attaching package: 'MatrixGenerics'</span></span>
+<span><span class="co">#&gt; The following objects are masked from 'package:matrixStats':</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt;     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,</span></span>
+<span><span class="co">#&gt;     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,</span></span>
+<span><span class="co">#&gt;     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,</span></span>
+<span><span class="co">#&gt;     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,</span></span>
+<span><span class="co">#&gt;     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,</span></span>
+<span><span class="co">#&gt;     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,</span></span>
+<span><span class="co">#&gt;     colWeightedMeans, colWeightedMedians, colWeightedSds,</span></span>
+<span><span class="co">#&gt;     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,</span></span>
+<span><span class="co">#&gt;     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,</span></span>
+<span><span class="co">#&gt;     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,</span></span>
+<span><span class="co">#&gt;     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,</span></span>
+<span><span class="co">#&gt;     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,</span></span>
+<span><span class="co">#&gt;     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,</span></span>
+<span><span class="co">#&gt;     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,</span></span>
+<span><span class="co">#&gt;     rowWeightedSds, rowWeightedVars</span></span>
+<span><span class="co">#&gt; Loading required package: GenomicRanges</span></span>
+<span><span class="co">#&gt; Loading required package: stats4</span></span>
+<span><span class="co">#&gt; Loading required package: BiocGenerics</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; Attaching package: 'BiocGenerics'</span></span>
+<span><span class="co">#&gt; The following objects are masked from 'package:stats':</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt;     IQR, mad, sd, var, xtabs</span></span>
+<span><span class="co">#&gt; The following objects are masked from 'package:base':</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt;     anyDuplicated, aperm, append, as.data.frame, basename, cbind,</span></span>
+<span><span class="co">#&gt;     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,</span></span>
+<span><span class="co">#&gt;     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,</span></span>
+<span><span class="co">#&gt;     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,</span></span>
+<span><span class="co">#&gt;     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,</span></span>
+<span><span class="co">#&gt;     tapply, union, unique, unsplit, which.max, which.min</span></span>
+<span><span class="co">#&gt; Loading required package: S4Vectors</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; Attaching package: 'S4Vectors'</span></span>
+<span><span class="co">#&gt; The following object is masked from 'package:utils':</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt;     findMatches</span></span>
+<span><span class="co">#&gt; The following objects are masked from 'package:base':</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt;     expand.grid, I, unname</span></span>
+<span><span class="co">#&gt; Loading required package: IRanges</span></span>
+<span><span class="co">#&gt; Loading required package: GenomeInfoDb</span></span>
+<span><span class="co">#&gt; Loading required package: Biobase</span></span>
+<span><span class="co">#&gt; Welcome to Bioconductor</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt;     Vignettes contain introductory material; view with</span></span>
+<span><span class="co">#&gt;     'browseVignettes()'. To cite Bioconductor, see</span></span>
+<span><span class="co">#&gt;     'citation("Biobase")', and for packages 'citation("pkgname")'.</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; Attaching package: 'Biobase'</span></span>
+<span><span class="co">#&gt; The following object is masked from 'package:MatrixGenerics':</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt;     rowMedians</span></span>
+<span><span class="co">#&gt; The following objects are masked from 'package:matrixStats':</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt;     anyMissing, rowMedians</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/JEFworks-Lab/SEraster" class="external-link">SEraster</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/JEFworks-Lab/scatterbar" class="external-link">scatterbar</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Load the MERFISH dataset from mouse POA (Preoptic Area)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"merfish_mousePOA"</span><span class="op">)</span></span></code></pre></div>
+<p>We can see that this data is in the form of a
+<code>SpatialExperiment</code>.</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Check the class of the dataset</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/class.html" class="external-link">class</a></span><span class="op">(</span><span class="va">merfish_mousePOA</span><span class="op">)</span></span>
+<span><span class="co">#&gt; [1] "SpatialExperiment"</span></span>
+<span><span class="co">#&gt; attr(,"package")</span></span>
+<span><span class="co">#&gt; [1] "SpatialExperiment"</span></span></code></pre></div>
+</div>
+<div class="section level3">
+<h3 id="rasterize-cell-type-counts">Rasterize Cell-Type Counts<a class="anchor" aria-label="anchor" href="#rasterize-cell-type-counts"></a>
+</h3>
+<p>To aggregate cell-type data into spatial pixels, we use the
+<code>rasterizeCellType</code> function from <code>SEraster</code>. This
+function takes the <code>SpatialExperiment</code> object and generates a
+rasterized view of cell-type counts. We will rasterize at a resolution
+of 55 micrometers (µm) and use the “sum” function to aggregate the
+number of cells.</p>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Rasterize the cell-type data at 55um resolution</span></span>
+<span><span class="va">rastCt</span> <span class="op">&lt;-</span> <span class="fu">SEraster</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/SEraster/man/rasterizeCellType.html" class="external-link">rasterizeCellType</a></span><span class="op">(</span></span>
+<span>  <span class="va">merfish_mousePOA</span>,  <span class="co"># SpatialExperiment object</span></span>
+<span>  col_name <span class="op">=</span> <span class="st">"celltype"</span>,  <span class="co"># Column with cell-type information</span></span>
+<span>  resolution <span class="op">=</span> <span class="fl">55</span>,  <span class="co"># Set resolution to 55 micrometers</span></span>
+<span>  fun <span class="op">=</span> <span class="st">"sum"</span>,  <span class="co"># Sum up the cells within each pixel</span></span>
+<span>  square <span class="op">=</span> <span class="cn">TRUE</span>  <span class="co"># Use square-shaped pixels for rasterization</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Visualize the rasterized result (total number of cells per pixel)</span></span>
+<span><span class="fu">SEraster</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/SEraster/man/plotRaster.html" class="external-link">plotRaster</a></span><span class="op">(</span><span class="va">rastCt</span>, name <span class="op">=</span> <span class="st">"Total cells"</span><span class="op">)</span></span></code></pre></div>
+<p><img src="using-scatterbar-with-spatial-experiment_files/figure-html/rasterize-1.png" width="700"></p>
+</div>
+<div class="section level3">
+<h3 id="calculate-cell-type-proportions">Calculate Cell-Type Proportions<a class="anchor" aria-label="anchor" href="#calculate-cell-type-proportions"></a>
+</h3>
+<p>Next, we calculate the proportions of each cell type within each
+pixel. We first retrieve the list of cell IDs for each pixel and the
+corresponding cell types. We then calculate the proportions for each
+cell type by dividing the number of cells of a given type by the total
+number of cells in each pixel.</p>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Extract the list of cell IDs for each pixel</span></span>
+<span><span class="va">cellids_perpixel</span> <span class="op">&lt;-</span> <span class="fu">colData</span><span class="op">(</span><span class="va">rastCt</span><span class="op">)</span><span class="op">$</span><span class="va">cellID_list</span></span>
+<span></span>
+<span><span class="co"># Retrieve the cell-type information</span></span>
+<span><span class="va">ct</span> <span class="op">&lt;-</span> <span class="va">merfish_mousePOA</span><span class="op">$</span><span class="va">celltype</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ct</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">merfish_mousePOA</span><span class="op">)</span></span>
+<span><span class="va">ct</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">ct</span><span class="op">)</span>  <span class="co"># Ensure cell types are factors</span></span>
+<span></span>
+<span><span class="co"># Calculate proportions for each pixel</span></span>
+<span><span class="va">prop</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/do.call.html" class="external-link">do.call</a></span><span class="op">(</span><span class="va">rbind</span>, <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">cellids_perpixel</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span></span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">ct</span><span class="op">[</span><span class="va">x</span><span class="op">]</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
+<span><span class="op">}</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Set rownames to match the pixel IDs in the raster object</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">prop</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="fu">colData</span><span class="op">(</span><span class="va">rastCt</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">prop</span><span class="op">)</span>  <span class="co"># Display the first few rows of the proportions matrix</span></span>
+<span><span class="co">#&gt;         Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3 Ependymal</span></span>
+<span><span class="co">#&gt; pixel21 0.2000000 0.0000000     0.0000000             0             0         0</span></span>
+<span><span class="co">#&gt; pixel22 0.0000000 0.0000000     0.5000000             0             0         0</span></span>
+<span><span class="co">#&gt; pixel23 0.0000000 0.3333333     0.0000000             0             0         0</span></span>
+<span><span class="co">#&gt; pixel24 0.0000000 0.0000000     0.3333333             0             0         0</span></span>
+<span><span class="co">#&gt; pixel25 0.6666667 0.0000000     0.0000000             0             0         0</span></span>
+<span><span class="co">#&gt; pixel26 0.0000000 0.3333333     0.0000000             0             0         0</span></span>
+<span><span class="co">#&gt;         Excitatory Inhibitory Microglia OD Immature 1 OD Immature 2 OD Mature 1</span></span>
+<span><span class="co">#&gt; pixel21  0.2000000  0.6000000         0     0.0000000             0           0</span></span>
+<span><span class="co">#&gt; pixel22  0.0000000  0.5000000         0     0.0000000             0           0</span></span>
+<span><span class="co">#&gt; pixel23  0.0000000  0.3333333         0     0.3333333             0           0</span></span>
+<span><span class="co">#&gt; pixel24  0.6666667  0.0000000         0     0.0000000             0           0</span></span>
+<span><span class="co">#&gt; pixel25  0.3333333  0.0000000         0     0.0000000             0           0</span></span>
+<span><span class="co">#&gt; pixel26  0.6666667  0.0000000         0     0.0000000             0           0</span></span>
+<span><span class="co">#&gt;         OD Mature 2 OD Mature 3 OD Mature 4 Pericytes</span></span>
+<span><span class="co">#&gt; pixel21           0           0           0         0</span></span>
+<span><span class="co">#&gt; pixel22           0           0           0         0</span></span>
+<span><span class="co">#&gt; pixel23           0           0           0         0</span></span>
+<span><span class="co">#&gt; pixel24           0           0           0         0</span></span>
+<span><span class="co">#&gt; pixel25           0           0           0         0</span></span>
+<span><span class="co">#&gt; pixel26           0           0           0         0</span></span></code></pre></div>
+</div>
+<div class="section level3">
+<h3 id="retrieve-pixel-coordinates">Retrieve Pixel Coordinates<a class="anchor" aria-label="anchor" href="#retrieve-pixel-coordinates"></a>
+</h3>
+<p>For <code>scatterbar</code>, we also need the x and y coordinates of
+the pixels from the <code>rastCt</code> object. These spatial
+coordinates correspond to the positions of each pixel in the rasterized
+grid.</p>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Extract the spatial coordinates of the pixels (x, y)</span></span>
+<span><span class="va">pos</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/SpatialExperiment/man/SpatialExperiment-methods.html" class="external-link">spatialCoords</a></span><span class="op">(</span><span class="va">rastCt</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">pos</span><span class="op">)</span>  <span class="co"># Display the first few rows of the spatial coordinates</span></span>
+<span><span class="co">#&gt;              x    y</span></span>
+<span><span class="co">#&gt; pixel21 1099.5 -0.5</span></span>
+<span><span class="co">#&gt; pixel22 1154.5 -0.5</span></span>
+<span><span class="co">#&gt; pixel23 1209.5 -0.5</span></span>
+<span><span class="co">#&gt; pixel24 1264.5 -0.5</span></span>
+<span><span class="co">#&gt; pixel25 1319.5 -0.5</span></span>
+<span><span class="co">#&gt; pixel26 1374.5 -0.5</span></span></code></pre></div>
+</div>
+<div class="section level3">
+<h3 id="filter-pixels-with-more-than-one-cell">Filter Pixels with More than One Cell<a class="anchor" aria-label="anchor" href="#filter-pixels-with-more-than-one-cell"></a>
+</h3>
+<p>We only want to visualize pixels that contain more than one cell, so
+we filter out pixels that do not meet this criterion.</p>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Filter for pixels that only contain more than one cell for visualization</span></span>
+<span><span class="va">vi</span> <span class="op">&lt;-</span> <span class="fu">colData</span><span class="op">(</span><span class="va">rastCt</span><span class="op">)</span><span class="op">$</span><span class="va">num_cell</span> <span class="op">&gt;</span> <span class="fl">1</span></span>
+<span><span class="va">pos</span> <span class="op">&lt;-</span> <span class="va">pos</span><span class="op">[</span><span class="va">vi</span>, <span class="op">]</span>  <span class="co"># Filter spatial coordinates</span></span>
+<span><span class="va">prop</span> <span class="op">&lt;-</span> <span class="va">prop</span><span class="op">[</span><span class="va">vi</span>, <span class="op">]</span>  <span class="co"># Filter proportions matrix</span></span>
+<span></span>
+<span><span class="co"># Check dimensions to ensure filtering was successful</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">pos</span><span class="op">)</span></span>
+<span><span class="co">#&gt; [1] 1035    2</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">prop</span><span class="op">)</span></span>
+<span><span class="co">#&gt; [1] 1035   16</span></span></code></pre></div>
+</div>
+<div class="section level3">
+<h3 id="visualize-cell-type-proportions-using-scatterbar">Visualize Cell-Type Proportions Using <code>scatterbar</code><a class="anchor" aria-label="anchor" href="#visualize-cell-type-proportions-using-scatterbar"></a>
+</h3>
+<p>Now that we have both the cell-type proportions and pixel position
+coordinates, we can visualize the data using <code>scatterbar</code>. We
+pass the proportions and coordinates, along with custom colors, to
+create a <code>scatterbar</code> plot. Remember that both the
+proportions and position data must be data frames in order to be passed
+into scatterbar.</p>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># Generate custom colors for the cell types</span></span>
+<span><span class="va">custom_colors</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/grDevices/palettes.html" class="external-link">rainbow</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/levels.html" class="external-link">levels</a></span><span class="op">(</span><span class="va">ct</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Visualize the cell-type proportions using scatterbar</span></span>
+<span><span class="va">start.time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="fu">scatterbar</span><span class="fu">::</span><span class="fu"><a href="../reference/scatterbar.html">scatterbar</a></span><span class="op">(</span></span>
+<span>  <span class="va">prop</span>,  <span class="co"># Proportions matrix</span></span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="va">pos</span><span class="op">)</span>,  <span class="co"># Spatial coordinates</span></span>
+<span>  colors <span class="op">=</span> <span class="va">custom_colors</span>,  <span class="co"># Custom colors for each cell type</span></span>
+<span>  padding_x <span class="op">=</span> <span class="fl">10</span>,  <span class="co"># Add padding to the x-axis</span></span>
+<span>  padding_y <span class="op">=</span> <span class="fl">10</span>, <span class="co"># Add padding to the y-axis</span></span>
+<span>  legend_title <span class="op">=</span> <span class="st">"Cell Types"</span> <span class="co"># Legend title</span></span>
+<span>  <span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/coord_fixed.html" class="external-link">coord_fixed</a></span><span class="op">(</span><span class="op">)</span>  <span class="co"># Maintain aspect ratio</span></span></code></pre></div>
+<p><img src="using-scatterbar-with-spatial-experiment_files/figure-html/scatterbar-1.png" width="700"></p>
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">end.time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">end.time</span> <span class="op">-</span> <span class="va">start.time</span><span class="op">)</span></span>
+<span><span class="co">#&gt; Time difference of 0.349581 secs</span></span></code></pre></div>
+<p>This plot shows the proportion of each cell type within each pixel,
+with bars stacked to represent the composition of cell types. The colors
+correspond to different cell types, as defined by the custom color
+vector.</p>
+</div>
+</div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside>
+</div>
+
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Dee Velazquez, Jean Fan.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer>
+</div>
+
+
+
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+
+  </body>
+</html>
diff --git a/articles/using-scatterbar-with-spatial-experiment_files/figure-html/rasterize-1.png b/articles/using-scatterbar-with-spatial-experiment_files/figure-html/rasterize-1.png
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new file mode 100644
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--- /dev/null
+++ b/articles/using-scatterbar-with-visium.html
@@ -0,0 +1,168 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Using scatterbar with Visium data • scatterbar</title>
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Using scatterbar with Visium data">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">scatterbar</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+<li><a class="dropdown-item" href="../articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
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+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="../articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
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+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/JEFworks-Lab/scatterbar/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Using scatterbar with Visium data</h1>
+                        <h4 data-toc-skip class="author">Jean Fan and
+Dee Velazquez</h4>
+            
+            <h4 data-toc-skip class="date">2024-10-18</h4>
+      
+      <small class="dont-index">Source: <a href="https://github.com/JEFworks-Lab/scatterbar/blob/main/vignettes/using-scatterbar-with-visium.Rmd" class="external-link"><code>vignettes/using-scatterbar-with-visium.Rmd</code></a></small>
+      <div class="d-none name"><code>using-scatterbar-with-visium.Rmd</code></div>
+    </div>
+
+    
+    
+<div class="section level2">
+<h2 id="using-scatterbar-with-visium-data">Using scatterbar with Visium data<a class="anchor" aria-label="anchor" href="#using-scatterbar-with-visium-data"></a>
+</h2>
+<p>Below is how to use <code>scatterbar</code> from the provided Visium
+dataset of an FFPE preserved adult mouse brain partial coronal section
+from 10X Genomics.</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/JEFworks-Lab/scatterbar" class="external-link">scatterbar</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"adult_mouse_brain_ffpe"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">pos</span><span class="op">)</span></span></code></pre></div>
+<p><img src="using-scatterbar-with-visium_files/figure-html/setup-1.png" width="700"></p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">prop</span><span class="op">)</span></span>
+<span><span class="co">#&gt;                            1          2         3         4         5         6</span></span>
+<span><span class="co">#&gt; AAACAGAGCGACTCCT-1 0.1264103 0.00000000 0.0000000 0.2183626 0.0000000 0.0000000</span></span>
+<span><span class="co">#&gt; AAACCCGAACGAAATC-1 0.0000000 0.00000000 0.0000000 0.0000000 0.1612265 0.7494948</span></span>
+<span><span class="co">#&gt; AAACCGGGTAGGTACC-1 0.2881994 0.32242398 0.0000000 0.3893766 0.0000000 0.0000000</span></span>
+<span><span class="co">#&gt; AAACCGTTCGTCCAGG-1 0.3040547 0.27785934 0.2535515 0.0000000 0.0000000 0.0000000</span></span>
+<span><span class="co">#&gt; AAACGAAGAACATACC-1 0.1585737 0.09403518 0.0000000 0.3510139 0.0000000 0.0000000</span></span>
+<span><span class="co">#&gt; AAACGAGACGGTTGAT-1 0.0000000 0.00000000 0.2962469 0.0000000 0.0000000 0.0000000</span></span>
+<span><span class="co">#&gt;                            7 8          9 10         11         12</span></span>
+<span><span class="co">#&gt; AAACAGAGCGACTCCT-1 0.1865617 0 0.07496736  0 0.39369799 0.00000000</span></span>
+<span><span class="co">#&gt; AAACCCGAACGAAATC-1 0.0000000 0 0.00000000  0 0.00000000 0.08927876</span></span>
+<span><span class="co">#&gt; AAACCGGGTAGGTACC-1 0.0000000 0 0.00000000  0 0.00000000 0.00000000</span></span>
+<span><span class="co">#&gt; AAACCGTTCGTCCAGG-1 0.0768548 0 0.00000000  0 0.08767969 0.00000000</span></span>
+<span><span class="co">#&gt; AAACGAAGAACATACC-1 0.2808292 0 0.00000000  0 0.11554800 0.00000000</span></span>
+<span><span class="co">#&gt; AAACGAGACGGTTGAT-1 0.0000000 0 0.00000000  0 0.00000000 0.70375311</span></span>
+<span></span>
+<span><span class="va">start.time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="fu"><a href="../reference/scatterbar.html">scatterbar</a></span><span class="op">(</span></span>
+<span>  <span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">prop</span>,</span>
+<span>  <span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">pos</span>,</span>
+<span>  size_x <span class="op">=</span> <span class="fl">220</span>,</span>
+<span>  size_y <span class="op">=</span> <span class="fl">220</span>,</span>
+<span>  legend_title <span class="op">=</span> <span class="st">"Cell Types"</span></span>
+<span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/coord_fixed.html" class="external-link">coord_fixed</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+<p><img src="using-scatterbar-with-visium_files/figure-html/setup-2.png" width="700"></p>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span></span>
+<span><span class="va">end.time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">end.time</span> <span class="op">-</span> <span class="va">start.time</span><span class="op">)</span></span>
+<span><span class="co">#&gt; Time difference of 0.5269275 secs</span></span></code></pre></div>
+<p>Just like with the mOB data, we can change the order of how each bar
+is laid out by changing the order of the cell-type proportion matrix and
+combine <code>scatterbar</code> with other ggplot geoms and
+customization.</p>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">start.time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="va">custom_colors</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'1'</span><span class="op">=</span> <span class="st">'#5d6f99'</span>,</span>
+<span>    <span class="st">'2'</span> <span class="op">=</span> <span class="st">'#985a39'</span>,</span>
+<span>    <span class="st">'3'</span> <span class="op">=</span>  <span class="st">'#d6589a'</span>,</span>
+<span>    <span class="st">'4'</span> <span class="op">=</span> <span class="st">'#4d1395'</span>,</span>
+<span>    <span class="st">'5'</span> <span class="op">=</span> <span class="st">'#b5ef27'</span>,</span>
+<span>    <span class="st">'6'</span> <span class="op">=</span> <span class="st">'#77d5bc'</span>,</span>
+<span>    <span class="st">'7'</span> <span class="op">=</span> <span class="st">'#7830d2'</span>,</span>
+<span>    <span class="st">'8'</span> <span class="op">=</span><span class="st">'#b43b59'</span>,</span>
+<span>    <span class="st">'9'</span> <span class="op">=</span> <span class="st">'#1c40b1'</span>,</span>
+<span>    <span class="st">'10'</span> <span class="op">=</span> <span class="st">"#FF5733"</span>,</span>
+<span>    <span class="st">'11'</span> <span class="op">=</span> <span class="st">'#FFFF00'</span>,</span>
+<span>    <span class="st">'12'</span> <span class="op">=</span> <span class="st">'#f4a6f1'</span><span class="op">)</span></span>
+<span><span class="fu">scatterbar</span><span class="fu">::</span><span class="fu"><a href="../reference/scatterbar.html">scatterbar</a></span><span class="op">(</span><span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">prop</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>,<span class="fl">3</span>,<span class="fl">4</span>,<span class="fl">11</span>,<span class="fl">5</span>,<span class="fl">6</span>,<span class="fl">10</span>,<span class="fl">7</span>,<span class="fl">8</span>,<span class="fl">1</span>,<span class="fl">9</span>, <span class="fl">12</span><span class="op">)</span><span class="op">]</span>, <span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">pos</span>, size_x <span class="op">=</span> <span class="fl">220</span>, size_y <span class="op">=</span> <span class="fl">220</span>, padding_x <span class="op">=</span> <span class="fl">0.1</span>, padding_y <span class="op">=</span> <span class="fl">0.1</span>, legend_title <span class="op">=</span> <span class="st">'Cell Type'</span>, colors <span class="op">=</span> <span class="va">custom_colors</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html" class="external-link">geom_point</a></span><span class="op">(</span>data<span class="op">=</span><span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">pos</span>, mapping<span class="op">=</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x<span class="op">=</span><span class="va">x</span>, y<span class="op">=</span><span class="va">y</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_bw</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">'y'</span><span class="op">)</span> <span class="op">+</span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/coord_fixed.html" class="external-link">coord_fixed</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+<p><img src="using-scatterbar-with-visium_files/figure-html/shiftorder-1.png" width="700"></p>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">end.time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">end.time</span> <span class="op">-</span> <span class="va">start.time</span><span class="op">)</span></span>
+<span><span class="co">#&gt; Time difference of 0.4268332 secs</span></span></code></pre></div>
+</div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside>
+</div>
+
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Dee Velazquez, Jean Fan.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer>
+</div>
+
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+
+
+
+  </body>
+</html>
diff --git a/articles/using-scatterbar-with-visium_files/figure-html/setup-1.png b/articles/using-scatterbar-with-visium_files/figure-html/setup-1.png
new file mode 100644
index 0000000..eae4396
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diff --git a/articles/using-scatterbar-with-visium_files/figure-html/setup-2.png b/articles/using-scatterbar-with-visium_files/figure-html/setup-2.png
new file mode 100644
index 0000000..997a0ce
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diff --git a/articles/using-scatterbar-with-visium_files/figure-html/shiftorder-1.png b/articles/using-scatterbar-with-visium_files/figure-html/shiftorder-1.png
new file mode 100644
index 0000000..36df513
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diff --git a/articles/visualizing-multiple-datasets.html b/articles/visualizing-multiple-datasets.html
new file mode 100644
index 0000000..7e84944
--- /dev/null
+++ b/articles/visualizing-multiple-datasets.html
@@ -0,0 +1,122 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Visualizing multiple datasets with scatterbar • scatterbar</title>
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Visualizing multiple datasets with scatterbar">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">scatterbar</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
+
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+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
+    <li><a class="dropdown-item" href="../articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="../articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
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+</form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/JEFworks-Lab/scatterbar/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Visualizing multiple datasets with scatterbar</h1>
+                        <h4 data-toc-skip class="author">Jean Fan and
+Dee Velazquez</h4>
+            
+            <h4 data-toc-skip class="date">2024-10-18</h4>
+      
+      <small class="dont-index">Source: <a href="https://github.com/JEFworks-Lab/scatterbar/blob/main/vignettes/visualizing-multiple-datasets.Rmd" class="external-link"><code>vignettes/visualizing-multiple-datasets.Rmd</code></a></small>
+      <div class="d-none name"><code>visualizing-multiple-datasets.Rmd</code></div>
+    </div>
+
+    
+    
+<div class="section level2">
+<h2 id="visualizing-multiple-datasets-with-scatterbar">Visualizing multiple datasets with scatterbar<a class="anchor" aria-label="anchor" href="#visualizing-multiple-datasets-with-scatterbar"></a>
+</h2>
+<p>This tutorial demonstrates how to visualize multiple datasets
+together, utilizing the package <code>patchwork</code>.</p>
+<p>Below we can load in our datasets provided by <code>scatterbar</code>
+and create the respective scatterbars using those datasets and save them
+to a variable.</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/JEFworks-Lab/scatterbar" class="external-link">scatterbar</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"mOB"</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"adult_mouse_brain_ffpe"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Basic scatterbar plot with default settings</span></span>
+<span><span class="va">p1</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/scatterbar.html">scatterbar</a></span><span class="op">(</span><span class="va">mOB</span><span class="op">$</span><span class="va">data</span>, <span class="va">mOB</span><span class="op">$</span><span class="va">xy</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/coord_fixed.html" class="external-link">coord_fixed</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="va">p2</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/scatterbar.html">scatterbar</a></span><span class="op">(</span><span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">prop</span>, <span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">pos</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/coord_fixed.html" class="external-link">coord_fixed</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+<p>We can then load in <code>patchwork</code> and visualize both
+scatterbars in one plot.</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://patchwork.data-imaginist.com" class="external-link">patchwork</a></span><span class="op">)</span></span>
+<span><span class="va">p1</span> <span class="op">+</span> <span class="va">p2</span></span></code></pre></div>
+<p><img src="visualizing-multiple-datasets_files/figure-html/patchwork-1.png" width="700"></p>
+</div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside>
+</div>
+
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Dee Velazquez, Jean Fan.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer>
+</div>
+
+
+
+
+
+  </body>
+</html>
diff --git a/articles/visualizing-multiple-datasets_files/figure-html/patchwork-1.png b/articles/visualizing-multiple-datasets_files/figure-html/patchwork-1.png
new file mode 100644
index 0000000..2eaed76
Binary files /dev/null and b/articles/visualizing-multiple-datasets_files/figure-html/patchwork-1.png differ
diff --git a/authors.html b/authors.html
index 8305f60..b471d76 100644
--- a/authors.html
+++ b/authors.html
@@ -20,6 +20,9 @@
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
diff --git a/index.html b/index.html
index 3158500..1b454a1 100644
--- a/index.html
+++ b/index.html
@@ -37,6 +37,9 @@
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
 <li><a class="dropdown-item" href="articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul>
 </li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
@@ -86,6 +89,9 @@ <h2 id="tutorials">Tutorials<a class="anchor" aria-label="anchor" href="#tutoria
 <ul>
 <li><a href="https://jef.works/scatterbar/articles/customizing_scatterbar.html" class="external-link">Customizing Scatterbar</a></li>
 <li><a href="https://jef.works/scatterbar/articles/getting-started-with-scatterbars.html" class="external-link">Getting Started With Scatterbar</a></li>
+<li><a href="https://jef.works/scatterbar/articles/using-scatterbar-with-spatial-experiment.html" class="external-link">Using Scatterbar With <code>SpatialExperiment</code></a></li>
+<li><a href="https://jef.works/scatterbar/articles/using-scatterbar-with-visium.html" class="external-link">Using Scatterbar With Visium Files</a></li>
+<li><a href="https://jef.works/scatterbar/articles/visualizing-multiple-datasets.html" class="external-link">Visualizing Multiple Datasets</a></li>
 </ul>
 </div>
 <div class="section level2">
diff --git a/news/index.html b/news/index.html
index 55a48a5..c98ef10 100644
--- a/news/index.html
+++ b/news/index.html
@@ -20,6 +20,9 @@
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="../articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="../articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul></li>
 <li class="active nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
diff --git a/pkgdown.yml b/pkgdown.yml
index 62109bb..42312f1 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,7 +4,10 @@ pkgdown_sha: ~
 articles:
   customizing_scatterbar: customizing_scatterbar.html
   getting-started-with-scatterbars: getting-started-with-scatterbars.html
-last_built: 2024-10-16T22:05Z
+  using-scatterbar-with-spatial-experiment: using-scatterbar-with-spatial-experiment.html
+  using-scatterbar-with-visium: using-scatterbar-with-visium.html
+  visualizing-multiple-datasets: visualizing-multiple-datasets.html
+last_built: 2024-10-18T01:58Z
 urls:
   reference: http://jef.works/scatterbar/reference
   article: http://jef.works/scatterbar/articles
diff --git a/reference/adult_mouse_brain_ffpe.html b/reference/adult_mouse_brain_ffpe.html
index fba6f67..a73d2da 100644
--- a/reference/adult_mouse_brain_ffpe.html
+++ b/reference/adult_mouse_brain_ffpe.html
@@ -20,6 +20,9 @@
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="../articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="../articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
diff --git a/reference/index.html b/reference/index.html
index 0099e00..6a03fff 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -20,6 +20,9 @@
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="../articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="../articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
diff --git a/reference/mOB.html b/reference/mOB.html
index f255724..ad2bc86 100644
--- a/reference/mOB.html
+++ b/reference/mOB.html
@@ -20,6 +20,9 @@
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="../articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="../articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
diff --git a/reference/scatterbar-2.png b/reference/scatterbar-2.png
new file mode 100644
index 0000000..301a032
Binary files /dev/null and b/reference/scatterbar-2.png differ
diff --git a/reference/scatterbar.html b/reference/scatterbar.html
index f861be8..145cd0a 100644
--- a/reference/scatterbar.html
+++ b/reference/scatterbar.html
@@ -22,6 +22,9 @@
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/customizing_scatterbar.html">Customizing scatterbar</a></li>
     <li><a class="dropdown-item" href="../articles/getting-started-with-scatterbars.html">Getting started with scatterbars</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-spatial-experiment.html">Using scatterbar with a SpatialExperiment object</a></li>
+    <li><a class="dropdown-item" href="../articles/using-scatterbar-with-visium.html">Using scatterbar with Visium data</a></li>
+    <li><a class="dropdown-item" href="../articles/visualizing-multiple-datasets.html">Visualizing multiple datasets with scatterbar</a></li>
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
@@ -111,6 +114,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="fu">scatterbar</span><span class="op">(</span><span class="va">mOB</span><span class="op">$</span><span class="va">data</span>, <span class="va">mOB</span><span class="op">$</span><span class="va">xy</span>, padding_x <span class="op">=</span> <span class="fl">0.3</span>, padding_y <span class="op">=</span> <span class="fl">0.3</span>, legend_title <span class="op">=</span> <span class="st">"Cell Types"</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="scatterbar-1.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">adult_mouse_brain_ffpe</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">scatterbar</span><span class="op">(</span></span></span>
+<span class="r-in"><span><span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">prop</span>,</span></span>
+<span class="r-in"><span><span class="va">adult_mouse_brain_ffpe</span><span class="op">$</span><span class="va">pos</span>,</span></span>
+<span class="r-in"><span>size_x <span class="op">=</span> <span class="fl">220</span>,</span></span>
+<span class="r-in"><span>size_y <span class="op">=</span> <span class="fl">220</span>,</span></span>
+<span class="r-in"><span>legend_title <span class="op">=</span> <span class="st">"Cell Types"</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="scatterbar-2.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/search.json b/search.json
index 0948240..58496fd 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"http://jef.works/scatterbar/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"http://jef.works/scatterbar/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"http://jef.works/scatterbar/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. 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Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"http://jef.works/scatterbar/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"http://jef.works/scatterbar/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"http://jef.works/scatterbar/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Dee Velazquez. Author, maintainer. Jean Fan. Author, reviewer.","code":""},{"path":"http://jef.works/scatterbar/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Velazquez D, Fan J (2024). scatterbar: Scattered Stacked Bar Chart Plots. R package version 0.1.0, http://jef.works/scatterbar/, https://github.com/JEFworks-Lab/scatterbar.","code":"@Manual{,   title = {scatterbar: Scattered Stacked Bar Chart Plots},   author = {Dee Velazquez and Jean Fan},   year = {2024},   note = {R package version 0.1.0, http://jef.works/scatterbar/},   url = {https://github.com/JEFworks-Lab/scatterbar}, }"},{"path":"http://jef.works/scatterbar/index.html","id":"scatterbar","dir":"","previous_headings":"","what":"Scattered Stacked Bar Chart Plots","title":"Scattered Stacked Bar Chart Plots","text":"scatterbar open-source R package displaying proportional data across spatially resolved contexts. scatterbar R documentation website. Questions, suggestions, problems submitted GitHub issues.","code":""},{"path":"http://jef.works/scatterbar/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Scattered Stacked Bar Chart Plots","text":"combining concepts scatter plots stacked bar charts, scatterbar allows users visualize variations proportional data data compare across different spatial locations.","code":""},{"path":"http://jef.works/scatterbar/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Scattered Stacked Bar Chart Plots","text":"install scatterbarfrom GitHub, recommend using remotes:","code":"require(remotes) remotes::install_github('JEFworks-Lab/scatterbar')"},{"path":"http://jef.works/scatterbar/index.html","id":"tutorials","dir":"","previous_headings":"","what":"Tutorials","title":"Scattered Stacked Bar Chart Plots","text":"Customizing Scatterbar Getting Started Scatterbar","code":""},{"path":"http://jef.works/scatterbar/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Scattered Stacked Bar Chart Plots","text":"preprint describing scatterbar available bioRxiv: Velazquez D. et al. (2024), “scatterbar: R package visualizing proportional data across spatially resolved coordinates”, bioRxiv","code":""},{"path":"http://jef.works/scatterbar/reference/adult_mouse_brain_ffpe.html","id":null,"dir":"Reference","previous_headings":"","what":"Deconvolved cell-type proportions from STdeconvolve for a Visium data from the adult mouse brain along with the positions of their respective spots — adult_mouse_brain_ffpe","title":"Deconvolved cell-type proportions from STdeconvolve for a Visium data from the adult mouse brain along with the positions of their respective spots — adult_mouse_brain_ffpe","text":"Deconvolved cell-type proportions STdeconvolve Visium data adult mouse brain along positions respective spots","code":""},{"path":"http://jef.works/scatterbar/reference/adult_mouse_brain_ffpe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deconvolved cell-type proportions from STdeconvolve for a Visium data from the adult mouse brain along with the positions of their respective spots — adult_mouse_brain_ffpe","text":"","code":"data(adult_mouse_brain_ffpe)"},{"path":"http://jef.works/scatterbar/reference/adult_mouse_brain_ffpe.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deconvolved cell-type proportions from STdeconvolve for a Visium data from the adult mouse brain along with the positions of their respective spots — adult_mouse_brain_ffpe","text":"list 2 objects, 2264 rows 2 columns: prop, contains 12 deconvolved cell-types proportions 2264 spots/pixels spatial transcriptomics experiment performed adult mouse brain tissue tissue pos, contains x y-coordinates 2264 spots/pixels adult mouse brain tissue slide.","code":""},{"path":"http://jef.works/scatterbar/reference/adult_mouse_brain_ffpe.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Deconvolved cell-type proportions from STdeconvolve for a Visium data from the adult mouse brain along with the positions of their respective spots — adult_mouse_brain_ffpe","text":"https://www.10xgenomics.com/datasets/adult-mouse-brain-ffpe-1-standard-1-3-0","code":""},{"path":"http://jef.works/scatterbar/reference/mOB.html","id":null,"dir":"Reference","previous_headings":"","what":"Deconvolved cell-type proportions from STdeconvolve for a Spatial Transcriptomic dataset of the mouse olfactory bulb along with the positions of their respective spots — mOB","title":"Deconvolved cell-type proportions from STdeconvolve for a Spatial Transcriptomic dataset of the mouse olfactory bulb along with the positions of their respective spots — mOB","text":"Deconvolved cell-type proportions STdeconvolve Spatial Transcriptomic dataset mouse olfactory bulb along positions respective spots","code":""},{"path":"http://jef.works/scatterbar/reference/mOB.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deconvolved cell-type proportions from STdeconvolve for a Spatial Transcriptomic dataset of the mouse olfactory bulb along with the positions of their respective spots — mOB","text":"","code":"data(mOB)"},{"path":"http://jef.works/scatterbar/reference/mOB.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deconvolved cell-type proportions from STdeconvolve for a Spatial Transcriptomic dataset of the mouse olfactory bulb along with the positions of their respective spots — mOB","text":"list 2 objects, 260 rows 2 columns: data, contains 8 deconvolved cell-types proportions 260 spots/pixels spatial transcriptomics experiment performed mouse olfactory bulb tissue xy, contains x y-coordinates 260 spots/pixels mouse olfactory bulb tissue slide.","code":""},{"path":"http://jef.works/scatterbar/reference/mOB.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Deconvolved cell-type proportions from STdeconvolve for a Spatial Transcriptomic dataset of the mouse olfactory bulb along with the positions of their respective spots — mOB","text":"https://science.sciencemag.org/content/353/6294/78","code":""},{"path":"http://jef.works/scatterbar/reference/scatterbar.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a scattered stacked bar chart plot — scatterbar","title":"Create a scattered stacked bar chart plot — scatterbar","text":"function creates scatterbar plot using ggplot2, bars stacked based different proportions groups 2-D location/spot. scatterbar plot combination scatter plot stacked bar chart, allowing visualization proportional data across spatial coordinates. function allows customized scaling factors padding creating plot. scaling factors specified, function automatically determines optimal scaling factors based data.","code":""},{"path":"http://jef.works/scatterbar/reference/scatterbar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a scattered stacked bar chart plot — scatterbar","text":"","code":"scatterbar(   data,   xy,   size_x = NULL,   size_y = NULL,   padding_x = 0,   padding_y = 0,   show_legend = TRUE,   legend_title = \"Group\",   colors = NULL )"},{"path":"http://jef.works/scatterbar/reference/scatterbar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a scattered stacked bar chart plot — scatterbar","text":"data data frame containing proportions different categories location. row represents location, column (except row names) represents category. xy data frame containing positional information location. data frame includes x y coordinates location/spot (respective row names). size_x X-axis scaling factor (default NULL). provided, automatically calculated based data. size_y Y-axis scaling factor (default NULL). provided, automatically calculated based data. padding_x Padding x-axis (default 0). padding_y Padding y-axis (default 0). show_legend Boolean indicating whether display plot legend (default TRUE). legend_title Custom title legend (default \"Group\"). colors Optional vector colors use category (default NULL). provided, default palette used.","code":""},{"path":"http://jef.works/scatterbar/reference/scatterbar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a scattered stacked bar chart plot — scatterbar","text":"ggplot object representing scattered stacked bar chart plot.","code":""},{"path":"http://jef.works/scatterbar/reference/scatterbar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a scattered stacked bar chart plot — scatterbar","text":"","code":"data(mOB) scatterbar(mOB$data, mOB$xy, padding_x = 0.3, padding_y = 0.3, legend_title = \"Cell Types\")"},{"path":"http://jef.works/scatterbar/news/index.html","id":"scatterbar-010","dir":"Changelog","previous_headings":"","what":"scatterbar 0.1.0","title":"scatterbar 0.1.0","text":"Initial CRAN submission.","code":""}]
+[{"path":"http://jef.works/scatterbar/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"http://jef.works/scatterbar/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. 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Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Protecting Users’ Legal Rights From Anti-Circumvention Law","title":"GNU General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"http://jef.works/scatterbar/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"http://jef.works/scatterbar/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. 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END TERMS CONDITIONS","code":""},{"path":"http://jef.works/scatterbar/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"http://jef.works/scatterbar/articles/customizing_scatterbar.html","id":"customizing-scatterbar","dir":"Articles","previous_headings":"","what":"Customizing scatterbar","title":"Customizing scatterbar","text":", simulate data demo purposes. create small dataset demonstrate scatterbar function. , create scatterbar plots using scatterbar function demonstrate various customization options using ggplot2.          proportions don’t add 1?","code":"# Load the scatterbar library library(scatterbar)  # Define positional data: coordinates (x, y) for each spot pos <- data.frame(x = c(1,1,2,2),                   y = c(1,2,1,2))  # Define proportional data: proportions of different categories (p1, p2, p3, p4) at each spot prop <- matrix(c(0.5, 0.5,  0,   0,                  0.5, 0,    0,   0.5,                  0,   0.5,  0.5, 0,                  0,   0,    0.5, 0.5), nrow=4)  # Assign row names to both positional and proportional data, representing the spot identifiers rownames(pos) <- rownames(prop) <- c('a','b','c','d')  # Assign column names to the proportional data, representing the categories/groups colnames(prop) <- c('Dogs', 'Cats', 'Fish', 'Snakes')  # Print out the positional data print(pos) ##   x y ## a 1 1 ## b 1 2 ## c 2 1 ## d 2 2 # Print out the positional data print(prop) ##   Dogs Cats Fish Snakes ## a  0.5  0.5  0.0    0.0 ## b  0.5  0.0  0.5    0.0 ## c  0.0  0.0  0.5    0.5 ## d  0.0  0.5  0.0    0.5 # Basic scatterbar plot with default settings scatterbar(prop, pos) # Scatterbar plot with a black-and-white theme and customized y-axis label scatterbar(prop, pos) +   ggplot2::theme_bw() + ggplot2::ylab('y') # Scatterbar plot with fixed x and y scale factors of 1 (size_x and size_y) scatterbar(prop, pos,                    size_x = 1, size_y = 1) +   ggplot2::theme_bw() + ggplot2::ylab('y') # Scatterbar plot with padding applied to the x and y axes, making the tiles slightly smaller scatterbar(prop, pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1) +   ggplot2::theme_bw() + ggplot2::ylab('y') # Scatterbar plot with flipped coordinates, so that x and y axes are interchanged scatterbar(prop, pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1) +   ggplot2::theme_bw() + ggplot2::ylab('y') +    ggplot2::coord_flip() # Scatterbar plot with customized legend title scatterbar(prop, pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1, legend_title= \"Animals\") +   ggplot2::theme_bw() + ggplot2::ylab('y') # Scatterbar plot using the custom colors # Define a custom set of colors for the categories custom_colors <- c(\"#FF0000\",  # Red                    \"#00FF00\",  # Green                    \"#0000FF\",  # Blue                    \"#A020F0\")  # Purple scatterbar(prop, pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1, legend_title= \"Animals\", colors=custom_colors) +   ggplot2::theme_bw() + ggplot2::ylab('y') # Scatterbar plot with title scatterbar(prop, pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1, legend_title= \"Animals\", colors=custom_colors) +   ggplot2::theme_bw() + ggplot2::ylab('y') + ggplot2::labs(title=\"Favorite Animals Among Classrooms\") # Scatterbar plot modifying the order of categories plotted  scatterbar(prop[, c(\"Fish\", \"Snakes\", \"Cats\", \"Dogs\")], pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1, legend_title= \"Animals\", colors=custom_colors) +   ggplot2::theme_bw() + ggplot2::ylab('y') + ggplot2::labs(title=\"Favorite Animals Among Classrooms\") # Define a new proportional data matrix where proportions do not sum to 1 prop <- matrix(c(0.1, 0.2,  0,   0,                  0.1, 0,    0,   0.4,                  0,   0.2,  0.3, 0,                  0,   0,    0.3, 0.4), nrow=4)  # Assign row names representing the spots rownames(prop) <- c('a','b','c','d')  # Assign column names representing the categories/groups colnames(prop) <- c('Dogs', 'Cats', 'Fish', 'Snakes')  # Print the new proportional data print(prop) ##   Dogs Cats Fish Snakes ## a  0.1  0.1  0.0    0.0 ## b  0.2  0.0  0.2    0.0 ## c  0.0  0.0  0.3    0.3 ## d  0.0  0.4  0.0    0.4 # Create a scatterbar plot with the new data scatterbar(prop, pos) # Customize the scatterbar plot using a black-and-white theme and customized y-axis label scatterbar(prop, pos) +   ggplot2::theme_bw() + ggplot2::ylab('y') # Create a scatterbar plot with fixed x and y scales and customized theme scatterbar(prop, pos,                    size_x = 1, size_y = 1) +   ggplot2::theme_bw() + ggplot2::ylab('y') # Apply padding to the scatterbar plot to make the tiles smaller scatterbar(prop, pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1) +   ggplot2::theme_bw() + ggplot2::ylab('y') # Scatterbar plot with flipped coordinates scatterbar(prop, pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1) +   ggplot2::theme_bw() + ggplot2::ylab('y') +    ggplot2::coord_flip() # Scatterbar plot with customized legend title scatterbar(prop, pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1, legend_title= \"Animals\") +   ggplot2::theme_bw() + ggplot2::ylab('y') # Scatterbar plot using the custom colors # Define a custom set of colors for the categories custom_colors <- c(\"#FF0000\",  # Red                    \"#00FF00\",  # Green                    \"#0000FF\",  # Blue                    \"#A020F0\")  # Purple scatterbar(prop, pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1, legend_title= \"Animals\", colors=custom_colors) +   ggplot2::theme_bw() + ggplot2::ylab('y') # Scatterbar plot with title scatterbar(prop, pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1, legend_title= \"Animals\", colors=custom_colors) +   ggplot2::theme_bw() + ggplot2::ylab('y') + ggplot2::labs(title=\"Favorite Animals Among Classrooms\") # Scatterbar plot modifying the order of categories plotted  scatterbar(prop[, c(\"Fish\", \"Snakes\", \"Cats\", \"Dogs\")], pos,                    size_x = 1, size_y = 1,                    padding_x = 0.1, padding_y = 0.1, legend_title= \"Animals\", colors=custom_colors) +   ggplot2::theme_bw() + ggplot2::ylab('y') + ggplot2::labs(title=\"Favorite Animals Among Classrooms\")"},{"path":"http://jef.works/scatterbar/articles/getting-started-with-scatterbars.html","id":"getting-started-with-scatterbars","dir":"Articles","previous_headings":"","what":"Getting started with scatterbars","title":"Getting started with scatterbars","text":"use scatterbar provided spatial transcriptomic data mouse olfactory bulb tissue sample.   can change order bar laid changing order cell-type proportion matrix spatial transcriptomic data. can also combine scatterbar ggplot geoms customization!","code":"library(scatterbar) data(\"mOB\")  plot(mOB$xy) head(mOB$data) ##                            1          2         3          4         5 ## ACAACTATGGGTTGGCGG 0.1420916 0.05540521 0.2902388 0.00000000 0.1657935 ## ACACAGATCCTGTTCTGA 0.0000000 0.77541118 0.0000000 0.00000000 0.0000000 ## ACATCACCTGCGCGCTCT 0.3360811 0.00000000 0.0000000 0.32262562 0.3412932 ## ACATTTAAGGCGCATGAT 0.2239877 0.00000000 0.0000000 0.55189741 0.2241149 ## ACCACTGTAATCTCCCAT 0.1373168 0.08529107 0.2204332 0.00000000 0.0000000 ## ACCAGAGCCGTTGAGCAA 0.1364591 0.37986322 0.1499492 0.06702756 0.2147332 ##                             6         7          8 ## ACAACTATGGGTTGGCGG 0.00000000 0.1329341 0.21353679 ## ACACAGATCCTGTTCTGA 0.14536750 0.0000000 0.07922131 ## ACATCACCTGCGCGCTCT 0.00000000 0.0000000 0.00000000 ## ACATTTAAGGCGCATGAT 0.00000000 0.0000000 0.00000000 ## ACCACTGTAATCTCCCAT 0.00000000 0.1876818 0.36927715 ## ACCAGAGCCGTTGAGCAA 0.05196769 0.0000000 0.00000000 start.time <- Sys.time() scatterbar::scatterbar(mOB$data, mOB$xy) + ggplot2::coord_fixed() end.time <- Sys.time() print(end.time - start.time) ## Time difference of 0.2757623 secs library(ggplot2) start.time <- Sys.time() scatterbar::scatterbar(mOB$data[, c(2,3,4,5,6,7,8,1)], mOB$xy, size_x = 1, size_y = 1, padding_x = 0.1, padding_y = 0.1) +   geom_point(data=mOB$xy, mapping=aes(x=x, y=y)) +   theme_bw() + ylab('y') + ggplot2::coord_fixed() end.time <- Sys.time() print(end.time - start.time) ## Time difference of 0.3487422 secs"},{"path":"http://jef.works/scatterbar/articles/using-scatterbar-with-spatial-experiment.html","id":"using-scatterbar-with-a-spatialexperiment-object","dir":"Articles","previous_headings":"","what":"Using scatterbar with a SpatialExperiment object","title":"Using scatterbar with a SpatialExperiment object","text":"tutorial demonstrates visualize cell-type proportions scatterbar SpatialExperiment object. SpatialExperiment class Bioconductor stores information spatial-omics experiments, can use visualize cell types found certain spots. use SEraster rasterize cell-type counts calculate proportions within pixels, can utilized scatterbar. information SpatialExperiment, click [] (https://www.bioconductor.org/packages/release/bioc/vignettes/SpatialExperiment/inst/doc/SpatialExperiment.html).","code":""},{"path":"http://jef.works/scatterbar/articles/using-scatterbar-with-spatial-experiment.html","id":"load-libraries","dir":"Articles","previous_headings":"Using scatterbar with a SpatialExperiment object","what":"Load libraries","title":"Using scatterbar with a SpatialExperiment object","text":"First, need loading necessary libraries load dataset provided SEraster. preprocessed MERFISH dataset mouse preoptic area (POA) female naive animal. information, please refer original work, Moffitt J. Bambah-Mukku D. et al. (2018), “Molecular, spatial, functional single-cell profiling hypothalamic preoptic region”, Science Advances. can see data form SpatialExperiment.","code":"# Load required libraries library(SpatialExperiment) #> Loading required package: SingleCellExperiment #> Loading required package: SummarizedExperiment #> Loading required package: MatrixGenerics #> Loading required package: matrixStats #>  #> Attaching package: 'MatrixGenerics' #> The following objects are masked from 'package:matrixStats': #>  #>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, #>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums, #>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, #>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, #>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, #>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, #>     colWeightedMeans, colWeightedMedians, colWeightedSds, #>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, #>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, #>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, #>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, #>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, #>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, #>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians, #>     rowWeightedSds, rowWeightedVars #> Loading required package: GenomicRanges #> Loading required package: stats4 #> Loading required package: BiocGenerics #>  #> Attaching package: 'BiocGenerics' #> The following objects are masked from 'package:stats': #>  #>     IQR, mad, sd, var, xtabs #> The following objects are masked from 'package:base': #>  #>     anyDuplicated, aperm, append, as.data.frame, basename, cbind, #>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, #>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, #>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, #>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, #>     tapply, union, unique, unsplit, which.max, which.min #> Loading required package: S4Vectors #>  #> Attaching package: 'S4Vectors' #> The following object is masked from 'package:utils': #>  #>     findMatches #> The following objects are masked from 'package:base': #>  #>     expand.grid, I, unname #> Loading required package: IRanges #> Loading required package: GenomeInfoDb #> Loading required package: Biobase #> Welcome to Bioconductor #>  #>     Vignettes contain introductory material; view with #>     'browseVignettes()'. To cite Bioconductor, see #>     'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'. #>  #> Attaching package: 'Biobase' #> The following object is masked from 'package:MatrixGenerics': #>  #>     rowMedians #> The following objects are masked from 'package:matrixStats': #>  #>     anyMissing, rowMedians library(SEraster) library(scatterbar) library(ggplot2)  # Load the MERFISH dataset from mouse POA (Preoptic Area) data(\"merfish_mousePOA\") # Check the class of the dataset class(merfish_mousePOA) #> [1] \"SpatialExperiment\" #> attr(,\"package\") #> [1] \"SpatialExperiment\""},{"path":"http://jef.works/scatterbar/articles/using-scatterbar-with-spatial-experiment.html","id":"rasterize-cell-type-counts","dir":"Articles","previous_headings":"Using scatterbar with a SpatialExperiment object","what":"Rasterize Cell-Type Counts","title":"Using scatterbar with a SpatialExperiment object","text":"aggregate cell-type data spatial pixels, use rasterizeCellType function SEraster. function takes SpatialExperiment object generates rasterized view cell-type counts. rasterize resolution 55 micrometers (µm) use “sum” function aggregate number cells.","code":"# Rasterize the cell-type data at 55um resolution rastCt <- SEraster::rasterizeCellType(   merfish_mousePOA,  # SpatialExperiment object   col_name = \"celltype\",  # Column with cell-type information   resolution = 55,  # Set resolution to 55 micrometers   fun = \"sum\",  # Sum up the cells within each pixel   square = TRUE  # Use square-shaped pixels for rasterization )  # Visualize the rasterized result (total number of cells per pixel) SEraster::plotRaster(rastCt, name = \"Total cells\")"},{"path":"http://jef.works/scatterbar/articles/using-scatterbar-with-spatial-experiment.html","id":"calculate-cell-type-proportions","dir":"Articles","previous_headings":"Using scatterbar with a SpatialExperiment object","what":"Calculate Cell-Type Proportions","title":"Using scatterbar with a SpatialExperiment object","text":"Next, calculate proportions cell type within pixel. first retrieve list cell IDs pixel corresponding cell types. calculate proportions cell type dividing number cells given type total number cells pixel.","code":"# Extract the list of cell IDs for each pixel cellids_perpixel <- colData(rastCt)$cellID_list  # Retrieve the cell-type information ct <- merfish_mousePOA$celltype names(ct) <- colnames(merfish_mousePOA) ct <- as.factor(ct)  # Ensure cell types are factors  # Calculate proportions for each pixel prop <- do.call(rbind, lapply(cellids_perpixel, function(x) {   table(ct[x]) / length(x) }))  # Set rownames to match the pixel IDs in the raster object rownames(prop) <- rownames(colData(rastCt)) head(prop)  # Display the first few rows of the proportions matrix #>         Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3 Ependymal #> pixel21 0.2000000 0.0000000     0.0000000             0             0         0 #> pixel22 0.0000000 0.0000000     0.5000000             0             0         0 #> pixel23 0.0000000 0.3333333     0.0000000             0             0         0 #> pixel24 0.0000000 0.0000000     0.3333333             0             0         0 #> pixel25 0.6666667 0.0000000     0.0000000             0             0         0 #> pixel26 0.0000000 0.3333333     0.0000000             0             0         0 #>         Excitatory Inhibitory Microglia OD Immature 1 OD Immature 2 OD Mature 1 #> pixel21  0.2000000  0.6000000         0     0.0000000             0           0 #> pixel22  0.0000000  0.5000000         0     0.0000000             0           0 #> pixel23  0.0000000  0.3333333         0     0.3333333             0           0 #> pixel24  0.6666667  0.0000000         0     0.0000000             0           0 #> pixel25  0.3333333  0.0000000         0     0.0000000             0           0 #> pixel26  0.6666667  0.0000000         0     0.0000000             0           0 #>         OD Mature 2 OD Mature 3 OD Mature 4 Pericytes #> pixel21           0           0           0         0 #> pixel22           0           0           0         0 #> pixel23           0           0           0         0 #> pixel24           0           0           0         0 #> pixel25           0           0           0         0 #> pixel26           0           0           0         0"},{"path":"http://jef.works/scatterbar/articles/using-scatterbar-with-spatial-experiment.html","id":"retrieve-pixel-coordinates","dir":"Articles","previous_headings":"Using scatterbar with a SpatialExperiment object","what":"Retrieve Pixel Coordinates","title":"Using scatterbar with a SpatialExperiment object","text":"scatterbar, also need x y coordinates pixels rastCt object. spatial coordinates correspond positions pixel rasterized grid.","code":"# Extract the spatial coordinates of the pixels (x, y) pos <- spatialCoords(rastCt) head(pos)  # Display the first few rows of the spatial coordinates #>              x    y #> pixel21 1099.5 -0.5 #> pixel22 1154.5 -0.5 #> pixel23 1209.5 -0.5 #> pixel24 1264.5 -0.5 #> pixel25 1319.5 -0.5 #> pixel26 1374.5 -0.5"},{"path":"http://jef.works/scatterbar/articles/using-scatterbar-with-spatial-experiment.html","id":"filter-pixels-with-more-than-one-cell","dir":"Articles","previous_headings":"Using scatterbar with a SpatialExperiment object","what":"Filter Pixels with More than One Cell","title":"Using scatterbar with a SpatialExperiment object","text":"want visualize pixels contain one cell, filter pixels meet criterion.","code":"# Filter for pixels that only contain more than one cell for visualization vi <- colData(rastCt)$num_cell > 1 pos <- pos[vi, ]  # Filter spatial coordinates prop <- prop[vi, ]  # Filter proportions matrix  # Check dimensions to ensure filtering was successful dim(pos) #> [1] 1035    2 dim(prop) #> [1] 1035   16"},{"path":"http://jef.works/scatterbar/articles/using-scatterbar-with-spatial-experiment.html","id":"visualize-cell-type-proportions-using-scatterbar","dir":"Articles","previous_headings":"Using scatterbar with a SpatialExperiment object","what":"Visualize Cell-Type Proportions Using scatterbar","title":"Using scatterbar with a SpatialExperiment object","text":"Now cell-type proportions pixel position coordinates, can visualize data using scatterbar. pass proportions coordinates, along custom colors, create scatterbar plot. Remember proportions position data must data frames order passed scatterbar.  plot shows proportion cell type within pixel, bars stacked represent composition cell types. colors correspond different cell types, defined custom color vector.","code":"# Generate custom colors for the cell types custom_colors <- sample(rainbow(length(levels(ct))))  # Visualize the cell-type proportions using scatterbar start.time <- Sys.time() scatterbar::scatterbar(   prop,  # Proportions matrix   data.frame(pos),  # Spatial coordinates   colors = custom_colors,  # Custom colors for each cell type   padding_x = 10,  # Add padding to the x-axis   padding_y = 10, # Add padding to the y-axis   legend_title = \"Cell Types\" # Legend title   ) + coord_fixed()  # Maintain aspect ratio end.time <- Sys.time() print(end.time - start.time) #> Time difference of 0.349581 secs"},{"path":"http://jef.works/scatterbar/articles/using-scatterbar-with-visium.html","id":"using-scatterbar-with-visium-data","dir":"Articles","previous_headings":"","what":"Using scatterbar with Visium data","title":"Using scatterbar with Visium data","text":"use scatterbar provided Visium dataset FFPE preserved adult mouse brain partial coronal section 10X Genomics.   Just like mOB data, can change order bar laid changing order cell-type proportion matrix combine scatterbar ggplot geoms customization.","code":"library(scatterbar) library(ggplot2) data(\"adult_mouse_brain_ffpe\")  plot(adult_mouse_brain_ffpe$pos) head(adult_mouse_brain_ffpe$prop) #>                            1          2         3         4         5         6 #> AAACAGAGCGACTCCT-1 0.1264103 0.00000000 0.0000000 0.2183626 0.0000000 0.0000000 #> AAACCCGAACGAAATC-1 0.0000000 0.00000000 0.0000000 0.0000000 0.1612265 0.7494948 #> AAACCGGGTAGGTACC-1 0.2881994 0.32242398 0.0000000 0.3893766 0.0000000 0.0000000 #> AAACCGTTCGTCCAGG-1 0.3040547 0.27785934 0.2535515 0.0000000 0.0000000 0.0000000 #> AAACGAAGAACATACC-1 0.1585737 0.09403518 0.0000000 0.3510139 0.0000000 0.0000000 #> AAACGAGACGGTTGAT-1 0.0000000 0.00000000 0.2962469 0.0000000 0.0000000 0.0000000 #>                            7 8          9 10         11         12 #> AAACAGAGCGACTCCT-1 0.1865617 0 0.07496736  0 0.39369799 0.00000000 #> AAACCCGAACGAAATC-1 0.0000000 0 0.00000000  0 0.00000000 0.08927876 #> AAACCGGGTAGGTACC-1 0.0000000 0 0.00000000  0 0.00000000 0.00000000 #> AAACCGTTCGTCCAGG-1 0.0768548 0 0.00000000  0 0.08767969 0.00000000 #> AAACGAAGAACATACC-1 0.2808292 0 0.00000000  0 0.11554800 0.00000000 #> AAACGAGACGGTTGAT-1 0.0000000 0 0.00000000  0 0.00000000 0.70375311  start.time <- Sys.time() scatterbar(   adult_mouse_brain_ffpe$prop,   adult_mouse_brain_ffpe$pos,   size_x = 220,   size_y = 220,   legend_title = \"Cell Types\" ) + coord_fixed() end.time <- Sys.time() print(end.time - start.time) #> Time difference of 0.5269275 secs start.time <- Sys.time() custom_colors <- c('1'= '#5d6f99',     '2' = '#985a39',     '3' =  '#d6589a',     '4' = '#4d1395',     '5' = '#b5ef27',     '6' = '#77d5bc',     '7' = '#7830d2',     '8' ='#b43b59',     '9' = '#1c40b1',     '10' = \"#FF5733\",     '11' = '#FFFF00',     '12' = '#f4a6f1') scatterbar::scatterbar(adult_mouse_brain_ffpe$prop[, c(2,3,4,11,5,6,10,7,8,1,9, 12)], adult_mouse_brain_ffpe$pos, size_x = 220, size_y = 220, padding_x = 0.1, padding_y = 0.1, legend_title = 'Cell Type', colors = custom_colors) +   geom_point(data=adult_mouse_brain_ffpe$pos, mapping=aes(x=x, y=y), size = 0.1) +   theme_bw() + ylab('y') + ggplot2::coord_fixed() end.time <- Sys.time() print(end.time - start.time) #> Time difference of 0.4268332 secs"},{"path":"http://jef.works/scatterbar/articles/visualizing-multiple-datasets.html","id":"visualizing-multiple-datasets-with-scatterbar","dir":"Articles","previous_headings":"","what":"Visualizing multiple datasets with scatterbar","title":"Visualizing multiple datasets with scatterbar","text":"tutorial demonstrates visualize multiple datasets together, utilizing package patchwork. can load datasets provided scatterbar create respective scatterbars using datasets save variable. can load patchwork visualize scatterbars one plot.","code":"library(scatterbar) library(ggplot2)  data(\"mOB\") data(\"adult_mouse_brain_ffpe\")  # Basic scatterbar plot with default settings p1 <- scatterbar(mOB$data, mOB$xy) + coord_fixed() p2 <- scatterbar(adult_mouse_brain_ffpe$prop, adult_mouse_brain_ffpe$pos) + coord_fixed() library(patchwork) p1 + p2"},{"path":"http://jef.works/scatterbar/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Dee Velazquez. Author, maintainer. Jean Fan. Author, reviewer.","code":""},{"path":"http://jef.works/scatterbar/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Velazquez D, Fan J (2024). scatterbar: Scattered Stacked Bar Chart Plots. R package version 0.1.0, http://jef.works/scatterbar/, https://github.com/JEFworks-Lab/scatterbar.","code":"@Manual{,   title = {scatterbar: Scattered Stacked Bar Chart Plots},   author = {Dee Velazquez and Jean Fan},   year = {2024},   note = {R package version 0.1.0, http://jef.works/scatterbar/},   url = {https://github.com/JEFworks-Lab/scatterbar}, }"},{"path":"http://jef.works/scatterbar/index.html","id":"scatterbar","dir":"","previous_headings":"","what":"Scattered Stacked Bar Chart Plots","title":"Scattered Stacked Bar Chart Plots","text":"scatterbar open-source R package displaying proportional data across spatially resolved contexts. scatterbar R documentation website. Questions, suggestions, problems submitted GitHub issues.","code":""},{"path":"http://jef.works/scatterbar/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Scattered Stacked Bar Chart Plots","text":"combining concepts scatter plots stacked bar charts, scatterbar allows users visualize variations proportional data data compare across different spatial locations.","code":""},{"path":"http://jef.works/scatterbar/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Scattered Stacked Bar Chart Plots","text":"install scatterbarfrom GitHub, recommend using remotes:","code":"require(remotes) remotes::install_github('JEFworks-Lab/scatterbar')"},{"path":"http://jef.works/scatterbar/index.html","id":"tutorials","dir":"","previous_headings":"","what":"Tutorials","title":"Scattered Stacked Bar Chart Plots","text":"Customizing Scatterbar Getting Started Scatterbar Using Scatterbar SpatialExperiment Using Scatterbar Visium Files Visualizing Multiple Datasets","code":""},{"path":"http://jef.works/scatterbar/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Scattered Stacked Bar Chart Plots","text":"preprint describing scatterbar available bioRxiv: Velazquez D. et al. (2024), “scatterbar: R package visualizing proportional data across spatially resolved coordinates”, bioRxiv","code":""},{"path":"http://jef.works/scatterbar/reference/adult_mouse_brain_ffpe.html","id":null,"dir":"Reference","previous_headings":"","what":"Deconvolved cell-type proportions from STdeconvolve for a Visium data from the adult mouse brain along with the positions of their respective spots — adult_mouse_brain_ffpe","title":"Deconvolved cell-type proportions from STdeconvolve for a Visium data from the adult mouse brain along with the positions of their respective spots — adult_mouse_brain_ffpe","text":"Deconvolved cell-type proportions STdeconvolve Visium data adult mouse brain along positions respective spots","code":""},{"path":"http://jef.works/scatterbar/reference/adult_mouse_brain_ffpe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deconvolved cell-type proportions from STdeconvolve for a Visium data from the adult mouse brain along with the positions of their respective spots — adult_mouse_brain_ffpe","text":"","code":"data(adult_mouse_brain_ffpe)"},{"path":"http://jef.works/scatterbar/reference/adult_mouse_brain_ffpe.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deconvolved cell-type proportions from STdeconvolve for a Visium data from the adult mouse brain along with the positions of their respective spots — adult_mouse_brain_ffpe","text":"list 2 objects, 2264 rows 2 columns: prop, contains 12 deconvolved cell-types proportions 2264 spots/pixels spatial transcriptomics experiment performed adult mouse brain tissue tissue pos, contains x y-coordinates 2264 spots/pixels adult mouse brain tissue slide.","code":""},{"path":"http://jef.works/scatterbar/reference/adult_mouse_brain_ffpe.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Deconvolved cell-type proportions from STdeconvolve for a Visium data from the adult mouse brain along with the positions of their respective spots — adult_mouse_brain_ffpe","text":"https://www.10xgenomics.com/datasets/adult-mouse-brain-ffpe-1-standard-1-3-0","code":""},{"path":"http://jef.works/scatterbar/reference/mOB.html","id":null,"dir":"Reference","previous_headings":"","what":"Deconvolved cell-type proportions from STdeconvolve for a Spatial Transcriptomic dataset of the mouse olfactory bulb along with the positions of their respective spots — mOB","title":"Deconvolved cell-type proportions from STdeconvolve for a Spatial Transcriptomic dataset of the mouse olfactory bulb along with the positions of their respective spots — mOB","text":"Deconvolved cell-type proportions STdeconvolve Spatial Transcriptomic dataset mouse olfactory bulb along positions respective spots","code":""},{"path":"http://jef.works/scatterbar/reference/mOB.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deconvolved cell-type proportions from STdeconvolve for a Spatial Transcriptomic dataset of the mouse olfactory bulb along with the positions of their respective spots — mOB","text":"","code":"data(mOB)"},{"path":"http://jef.works/scatterbar/reference/mOB.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deconvolved cell-type proportions from STdeconvolve for a Spatial Transcriptomic dataset of the mouse olfactory bulb along with the positions of their respective spots — mOB","text":"list 2 objects, 260 rows 2 columns: data, contains 8 deconvolved cell-types proportions 260 spots/pixels spatial transcriptomics experiment performed mouse olfactory bulb tissue xy, contains x y-coordinates 260 spots/pixels mouse olfactory bulb tissue slide.","code":""},{"path":"http://jef.works/scatterbar/reference/mOB.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Deconvolved cell-type proportions from STdeconvolve for a Spatial Transcriptomic dataset of the mouse olfactory bulb along with the positions of their respective spots — mOB","text":"https://science.sciencemag.org/content/353/6294/78","code":""},{"path":"http://jef.works/scatterbar/reference/scatterbar.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a scattered stacked bar chart plot — scatterbar","title":"Create a scattered stacked bar chart plot — scatterbar","text":"function creates scatterbar plot using ggplot2, bars stacked based different proportions groups 2-D location/spot. scatterbar plot combination scatter plot stacked bar chart, allowing visualization proportional data across spatial coordinates. function allows customized scaling factors padding creating plot. scaling factors specified, function automatically determines optimal scaling factors based data.","code":""},{"path":"http://jef.works/scatterbar/reference/scatterbar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a scattered stacked bar chart plot — scatterbar","text":"","code":"scatterbar(   data,   xy,   size_x = NULL,   size_y = NULL,   padding_x = 0,   padding_y = 0,   show_legend = TRUE,   legend_title = \"Group\",   colors = NULL )"},{"path":"http://jef.works/scatterbar/reference/scatterbar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a scattered stacked bar chart plot — scatterbar","text":"data data frame containing proportions different categories location. row represents location, column (except row names) represents category. xy data frame containing positional information location. data frame includes x y coordinates location/spot (respective row names). size_x X-axis scaling factor (default NULL). provided, automatically calculated based data. size_y Y-axis scaling factor (default NULL). provided, automatically calculated based data. padding_x Padding x-axis (default 0). padding_y Padding y-axis (default 0). show_legend Boolean indicating whether display plot legend (default TRUE). legend_title Custom title legend (default \"Group\"). colors Optional vector colors use category (default NULL). provided, default palette used.","code":""},{"path":"http://jef.works/scatterbar/reference/scatterbar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a scattered stacked bar chart plot — scatterbar","text":"ggplot object representing scattered stacked bar chart plot.","code":""},{"path":"http://jef.works/scatterbar/reference/scatterbar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a scattered stacked bar chart plot — scatterbar","text":"","code":"data(mOB) scatterbar(mOB$data, mOB$xy, padding_x = 0.3, padding_y = 0.3, legend_title = \"Cell Types\")   data(adult_mouse_brain_ffpe) scatterbar( adult_mouse_brain_ffpe$prop, adult_mouse_brain_ffpe$pos, size_x = 220, size_y = 220, legend_title = \"Cell Types\")"},{"path":"http://jef.works/scatterbar/news/index.html","id":"scatterbar-010","dir":"Changelog","previous_headings":"","what":"scatterbar 0.1.0","title":"scatterbar 0.1.0","text":"Initial CRAN submission.","code":""}]
diff --git a/sitemap.xml b/sitemap.xml
index 423f47d..0d16208 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -4,6 +4,9 @@
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 <url><loc>http://jef.works/scatterbar/articles/index.html</loc></url>
+<url><loc>http://jef.works/scatterbar/articles/using-scatterbar-with-spatial-experiment.html</loc></url>
+<url><loc>http://jef.works/scatterbar/articles/using-scatterbar-with-visium.html</loc></url>
+<url><loc>http://jef.works/scatterbar/articles/visualizing-multiple-datasets.html</loc></url>
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