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    <title>Jesper Maag PhD</title>
    <description>Data analysis and visualisations</description>
    <link>http://jespermaag.github.io/</link>
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    <pubDate>Sun, 13 Dec 2020 21:05:40 -0500</pubDate>
    <lastBuildDate>Sun, 13 Dec 2020 21:05:40 -0500</lastBuildDate>
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      <item>
        <title>gganatogram</title>
        <description>&lt;h1 id=&quot;gganatogram&quot;&gt;gganatogram&lt;/h1&gt;
&lt;p&gt;&lt;a href=&quot;https://github.com/jespermaag/gganatogram&quot;&gt;https://github.com/jespermaag/gganatogram&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;Create anatogram images for different organisms.  &lt;br /&gt;
For now only human male is available.  &lt;br /&gt;. 
The idea for this package came to me after seeing a twitter post for &lt;a href=&quot;https://github.com/LCBC-UiO/ggseg&quot;&gt;ggseg&lt;/a&gt;.
I thougt something similar would be good for whole organisms. 
Since I could not find anything similar, I deided to give creating my first R package a go.&lt;/p&gt;

&lt;p&gt;This package uses the tissue coordinates from the figure in ArrayExpress Expression Atlas.  &lt;br /&gt;
&lt;a href=&quot;https://www.ebi.ac.uk/gxa/home&quot;&gt;https://www.ebi.ac.uk/gxa/home&lt;/a&gt;  &lt;br /&gt;
&lt;a href=&quot;https://github.com/ebi-gene-expression-group/anatomogram&quot;&gt;https://github.com/ebi-gene-expression-group/anatomogram&lt;/a&gt;  &lt;br /&gt;&lt;/p&gt;

&lt;h2 id=&quot;generation-of-package&quot;&gt;Generation of package&lt;/h2&gt;

&lt;h3 id=&quot;download-all-svg&quot;&gt;Download all svg&lt;/h3&gt;
&lt;p&gt;To create the package, I first had to retrive the coordinates of all tissues from the Expression Atlas. 
The anatogram package was downloaded using the following command.&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;npm install --save anatomogram
&lt;/code&gt;&lt;/pre&gt;

&lt;h3 id=&quot;extract-coordinates-from-svg&quot;&gt;Extract coordinates from svg&lt;/h3&gt;
&lt;p&gt;I used python to extract the coordinates, names, and transformations for each tissue in the homo_sapiens.mal.svg file.
This code takes the svg and writes the name, coordinates, and transformation to a file, which is then processed in R.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-python&quot; data-lang=&quot;python&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kn&quot;&gt;from&lt;/span&gt; &lt;span class=&quot;nn&quot;&gt;xml.dom&lt;/span&gt; &lt;span class=&quot;kn&quot;&gt;import&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;minidom&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;import&lt;/span&gt; &lt;span class=&quot;nn&quot;&gt;os&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;import&lt;/span&gt; &lt;span class=&quot;nn&quot;&gt;csv&lt;/span&gt;
&lt;span class=&quot;n&quot;&gt;organism&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s2&quot;&gt;&amp;quot;homo_sapiens.male&amp;quot;&lt;/span&gt;
&lt;span class=&quot;n&quot;&gt;doc&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;minidom&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;parse&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;organism&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; &lt;span class=&quot;s2&quot;&gt;&amp;quot;.svg&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;n&quot;&gt;your_csv_file&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;nb&quot;&gt;open&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;organism&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; &lt;span class=&quot;s1&quot;&gt;&amp;#39;_coords.tsv&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s1&quot;&gt;&amp;#39;w&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;n&quot;&gt;wr&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;csv&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;writer&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;your_csv_file&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;delimiter&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;&lt;/span&gt;&lt;span class=&quot;se&quot;&gt;\t&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;k&quot;&gt;for&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;path&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;in&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;doc&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;getElementsByTagName&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;path&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;):&lt;/span&gt;
    &lt;span class=&quot;k&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;s2&quot;&gt;&amp;quot;outline&amp;quot;&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;in&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;getAttribute&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;id&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;or&lt;/span&gt; &lt;span class=&quot;s2&quot;&gt;&amp;quot;LAYER_OUTLINE&amp;quot;&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;in&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;getAttribute&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;id&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;:&lt;/span&gt;
        &lt;span class=&quot;n&quot;&gt;wr&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;writerow&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;([&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;getAttribute&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;id&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;getAttribute&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;d&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; &lt;span class=&quot;nb&quot;&gt;str&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;matrix(1,0,0,1,0,0)&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)])&lt;/span&gt; 
    &lt;span class=&quot;k&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;getAttribute&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;id&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;startswith&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;UB&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;):&lt;/span&gt;
        &lt;span class=&quot;n&quot;&gt;wr&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;writerow&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;([&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;getElementsByTagName&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;title&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;&lt;span class=&quot;mi&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;firstChild&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;nodeValue&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;getAttribute&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;d&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; &lt;span class=&quot;nb&quot;&gt;str&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;matrix(1,0,0,1,0,0)&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)])&lt;/span&gt;
    &lt;span class=&quot;k&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;parentNode&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;attributes&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;id&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;value&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;startswith&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;UB&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;):&lt;/span&gt;
        &lt;span class=&quot;k&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;s2&quot;&gt;&amp;quot;transform&amp;quot;&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;not&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;in&lt;/span&gt; &lt;span class=&quot;nb&quot;&gt;list&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;parentNode&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;attributes&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;keys&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;()):&lt;/span&gt; 
            &lt;span class=&quot;n&quot;&gt;wr&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;writerow&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;([&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;parentNode&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;attributes&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;id&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;value&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;getAttribute&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;d&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; &lt;span class=&quot;nb&quot;&gt;str&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;matrix(1,0,0,1,0,0)&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)])&lt;/span&gt;
&lt;span class=&quot;k&quot;&gt;for&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;path&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;in&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;doc&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;getElementsByTagName&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;g&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;&lt;span class=&quot;mi&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;:]:&lt;/span&gt;
    &lt;span class=&quot;k&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;nb&quot;&gt;len&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;childNodes&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;gt;&lt;/span&gt;&lt;span class=&quot;mi&quot;&gt;0&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;:&lt;/span&gt;
        &lt;span class=&quot;k&quot;&gt;for&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;node&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;in&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;childNodes&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;:&lt;/span&gt;
            &lt;span class=&quot;k&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;s2&quot;&gt;&amp;quot;text&amp;quot;&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;not&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;in&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;node&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;nodeName&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;:&lt;/span&gt;
                &lt;span class=&quot;k&quot;&gt;print&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;node&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;nodeName&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
                &lt;span class=&quot;k&quot;&gt;print&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;node&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;attributes&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;keys&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;())&lt;/span&gt;
                &lt;span class=&quot;k&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;s1&quot;&gt;&amp;#39;d&amp;#39;&lt;/span&gt; &lt;span class=&quot;ow&quot;&gt;in&lt;/span&gt; &lt;span class=&quot;nb&quot;&gt;list&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;node&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;attributes&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;keys&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;()):&lt;/span&gt; 
                    &lt;span class=&quot;n&quot;&gt;nodeVal&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;node&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;attributes&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;d&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;value&lt;/span&gt;
                    &lt;span class=&quot;n&quot;&gt;wr&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;writerow&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;([&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;childNodes&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;mi&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;attributes&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;id&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;value&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;n&quot;&gt;nodeVal&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;  &lt;span class=&quot;n&quot;&gt;path&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;attributes&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;s1&quot;&gt;&amp;#39;transform&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;value&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;])&lt;/span&gt;
&lt;span class=&quot;n&quot;&gt;your_csv_file&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;n&quot;&gt;close&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h3 id=&quot;process-the-coordinates-in-r-and-create-a-package&quot;&gt;Process the coordinates in R, and create a package&lt;/h3&gt;
&lt;p&gt;I created a function to extract the coordinates into a data frame and transformed the data. 
Some manual editing was required to get the right coordinates, and remove some tissues that did not work&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;extractCoords &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kr&quot;&gt;function&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;coords&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; name&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; transMatrix&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;
    &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;strsplit&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;coords&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot; &amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
    &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]]&lt;/span&gt;

    &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]][&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;grep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;M&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]]&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;+1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;grep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;M&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]]&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;+2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;NA&lt;/span&gt;

    &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]][&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;grep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;[[:alpha:]]&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]],&lt;/span&gt; invert&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)]&lt;/span&gt;

    anatCoord &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;as.data.frame&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;lapply&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kr&quot;&gt;function&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;u&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; 
        &lt;span class=&quot;kt&quot;&gt;matrix&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;as.numeric&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;unlist&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;strsplit&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;u&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;,&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))),&lt;/span&gt;ncol&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;byrow&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;
    anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;X2&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;is.na&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;X1&lt;span class=&quot;p&quot;&gt;)]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;NA&lt;/span&gt;
    anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;X1&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;is.na&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;X2&lt;span class=&quot;p&quot;&gt;)]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;NA&lt;/span&gt;
    anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;id &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; name

    &lt;span class=&quot;kr&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;length&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;transMatrix&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;grep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;matrix&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; transMatrix&lt;span class=&quot;p&quot;&gt;)])&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;&amp;gt;&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;
        transForm &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;gsub&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;matrix\\(|\\)&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; transMatrix&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
        transForm &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;as.numeric&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;strsplit&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;transForm&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;,&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]])&lt;/span&gt;
       
        anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;x &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;  &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;X1&lt;span class=&quot;o&quot;&gt;*&lt;/span&gt; transForm&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;])&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;X1&lt;span class=&quot;o&quot;&gt;*&lt;/span&gt; transForm&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;])&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; transForm&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;
        anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;y &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;  &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;X2&lt;span class=&quot;o&quot;&gt;*&lt;/span&gt; transForm&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;])&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;X2&lt;span class=&quot;o&quot;&gt;*&lt;/span&gt; transForm&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;4&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;])&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; transForm&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;6&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;
    &lt;span class=&quot;p&quot;&gt;}&lt;/span&gt; &lt;span class=&quot;kr&quot;&gt;else&lt;/span&gt; &lt;span class=&quot;kr&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;grep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;translate&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; transMatrix&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;
        transForm &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;gsub&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;translate\\(|\\)&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; transMatrix&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
        transForm &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;as.numeric&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;strsplit&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;transForm&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;,&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]])&lt;/span&gt;
         &lt;span class=&quot;kr&quot;&gt;if&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;name &lt;span class=&quot;o&quot;&gt;==&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;leukocyte&amp;#39;&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;amp;&lt;/span&gt; transForm&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;==&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;4.5230265&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;
            transForm &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;103.63591+4.5230265&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;-47.577078+11.586659&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
        &lt;span class=&quot;p&quot;&gt;}&lt;/span&gt;
        anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;x &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;  anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;X1 &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; transForm&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;
        anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;y &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;  anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;X2 &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; transForm&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;
    &lt;span class=&quot;p&quot;&gt;}&lt;/span&gt;
    &lt;span class=&quot;c1&quot;&gt;#anatCoord &amp;lt;- anatCoord[complete.cases(anatCoord),]&lt;/span&gt;
    &lt;span class=&quot;kr&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;name &lt;span class=&quot;o&quot;&gt;==&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;bronchus&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;
        &lt;span class=&quot;kr&quot;&gt;if&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;max&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;x&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; na.rm&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;T&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;gt;&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;100&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;
            anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;x &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;NA&lt;/span&gt;
            anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;y &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;NA&lt;/span&gt;
        &lt;span class=&quot;p&quot;&gt;}&lt;/span&gt;
    &lt;span class=&quot;p&quot;&gt;}&lt;/span&gt;
    &lt;span class=&quot;kr&quot;&gt;if&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;any&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;complete.cases&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;p&quot;&gt;),]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;x &lt;span class=&quot;o&quot;&gt;&amp;lt;&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;-5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;
            anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;x &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;NA&lt;/span&gt;
            anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;y &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;NA&lt;/span&gt;
    &lt;span class=&quot;p&quot;&gt;}&lt;/span&gt;

    &lt;span class=&quot;kr&quot;&gt;if&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;any&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;complete.cases&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;p&quot;&gt;),]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;x &lt;span class=&quot;o&quot;&gt;&amp;gt;&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;150&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;
            anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;x &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;NA&lt;/span&gt;
            anatCoord&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;y &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;NA&lt;/span&gt;
    &lt;span class=&quot;p&quot;&gt;}&lt;/span&gt;
    &lt;span class=&quot;kr&quot;&gt;return&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;anatCoord&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;p&quot;&gt;}&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;Finally, I processed the python output using the extractCoords function.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;hsMale &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; read.table&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;homo_sapiens.male_coords.tsv&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; sep&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;\t&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; stringsAsFactors&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;F&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

hgMale_list &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;list&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;
&lt;span class=&quot;kr&quot;&gt;for&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;i &lt;span class=&quot;kr&quot;&gt;in&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;nrow&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;hsMale&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;
    df &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; extractCoords&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;hsMale&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;V2&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; hsMale&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;V1&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt;  hsMale&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;V3&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;])&lt;/span&gt;

    hgMale_list&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;]]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; extractCoords&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;hsMale&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;V2&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; hsMale&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;V1&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt;  hsMale&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;V3&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;])&lt;/span&gt;
    &lt;span class=&quot;kp&quot;&gt;names&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;hgMale_list&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;  &lt;span class=&quot;kp&quot;&gt;paste0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;hsMale&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;V1&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;-&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; i&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;p&quot;&gt;}&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;names&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;hgMale_list&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;gsub&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;-.*&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;names&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;hgMale_list&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;The resulting list was then used as the base for the gganatogram package. 
The package can be installed from github using the instructions below.&lt;/p&gt;

&lt;h2 id=&quot;install&quot;&gt;Install&lt;/h2&gt;

&lt;p&gt;Install from github using devtools.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;c1&quot;&gt;## install from Github&lt;/span&gt;
devtools&lt;span class=&quot;o&quot;&gt;::&lt;/span&gt;install_github&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;jespermaag/gganatogram&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h2 id=&quot;usage&quot;&gt;Usage&lt;/h2&gt;

&lt;p&gt;This package requires &lt;code&gt;ggplot2&lt;/code&gt; and &lt;code&gt;ggpolypath&lt;/code&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ggplot2&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ggpolypath&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;gganatogram&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;dplyr&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;In order to use the function gganatogram, you need to have a data frame with
organ, colour, and value if you want to.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;organPlot &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;data.frame&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;organ &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;heart&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;leukocyte&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;nerve&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;brain&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;liver&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;stomach&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;colon&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 type &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;circulation&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;circulation&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;  &lt;span class=&quot;s&quot;&gt;&amp;quot;nervous system&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;nervous system&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;digestion&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;digestion&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;digestion&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 colour &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;red&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;red&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;purple&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;purple&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;orange&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;orange&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;orange&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 value &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;10&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;8&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 stringsAsFactors&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;F&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

&lt;span class=&quot;kp&quot;&gt;head&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;organPlot&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##       organ           type colour value
## 1     heart    circulation    red    10
## 2 leukocyte    circulation    red     5
## 3     nerve nervous system purple     1
## 4     brain nervous system purple     8
## 5     liver      digestion orange     2
## 6   stomach      digestion orange     5&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;Using the function gganatogram with the filling the organs based on colour.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;gganatogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;organPlot&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fillOutline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#a6bddb&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; organism&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;human&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; sex&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;male&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;colour&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/organPlot-1.svg&quot; alt=&quot;plot of chunk organPlot&quot; /&gt;&lt;/p&gt;

&lt;p&gt;We can use the ggplot themes and functions to adjust the plots&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;gganatogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;organPlot&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fillOutline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#a6bddb&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; organism&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;human&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; sex&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;male&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;colour&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
theme_void&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/organPlotvoid-1.svg&quot; alt=&quot;plot of chunk organPlotvoid&quot; /&gt;&lt;/p&gt;

&lt;p&gt;We can also plot all tissues available using hgMale_key, which is an available object&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;hgMale_key&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;organ&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##  [1] &amp;quot;bone marrow&amp;quot;               &amp;quot;frontal cortex&amp;quot;           
##  [3] &amp;quot;prefrontal cortex&amp;quot;         &amp;quot;gastroesophageal junction&amp;quot;
##  [5] &amp;quot;caecum&amp;quot;                    &amp;quot;ileum&amp;quot;                    
##  [7] &amp;quot;rectum&amp;quot;                    &amp;quot;nose&amp;quot;                     
##  [9] &amp;quot;tongue&amp;quot;                    &amp;quot;penis&amp;quot;                    
## [11] &amp;quot;nasal pharynx&amp;quot;             &amp;quot;spinal cord&amp;quot;              
## [13] &amp;quot;throat&amp;quot;                    &amp;quot;diaphragm&amp;quot;                
## [15] &amp;quot;liver&amp;quot;                     &amp;quot;stomach&amp;quot;                  
## [17] &amp;quot;spleen&amp;quot;                    &amp;quot;duodenum&amp;quot;                 
## [19] &amp;quot;gall bladder&amp;quot;              &amp;quot;pancreas&amp;quot;                 
## [21] &amp;quot;colon&amp;quot;                     &amp;quot;small intestine&amp;quot;          
## [23] &amp;quot;appendix&amp;quot;                  &amp;quot;urinary bladder&amp;quot;          
## [25] &amp;quot;bone&amp;quot;                      &amp;quot;cartilage&amp;quot;                
## [27] &amp;quot;esophagus&amp;quot;                 &amp;quot;skin&amp;quot;                     
## [29] &amp;quot;brain&amp;quot;                     &amp;quot;heart&amp;quot;                    
## [31] &amp;quot;lymph_node&amp;quot;                &amp;quot;skeletal_muscle&amp;quot;          
## [33] &amp;quot;leukocyte&amp;quot;                 &amp;quot;temporal_lobe&amp;quot;            
## [35] &amp;quot;atrial_appendage&amp;quot;          &amp;quot;coronary_artery&amp;quot;          
## [37] &amp;quot;hippocampus&amp;quot;               &amp;quot;vas_deferens&amp;quot;             
## [39] &amp;quot;seminal_vesicle&amp;quot;           &amp;quot;epididymis&amp;quot;               
## [41] &amp;quot;tonsil&amp;quot;                    &amp;quot;lung&amp;quot;                     
## [43] &amp;quot;trachea&amp;quot;                   &amp;quot;bronchus&amp;quot;                 
## [45] &amp;quot;nerve&amp;quot;                     &amp;quot;kidney&amp;quot;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;gganatogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;hgMale_key&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fillOutline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#a6bddb&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; organism&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;human&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; sex&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;male&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;colour&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;theme_void&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/organPlotAll-1.svg&quot; alt=&quot;plot of chunk organPlotAll&quot; /&gt;&lt;/p&gt;

&lt;p&gt;To skip the outline of the graph, use outline=F&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;organPlot &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    dplyr&lt;span class=&quot;o&quot;&gt;::&lt;/span&gt;filter&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;type &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;circulation&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;nervous system&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
gganatogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;outline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;F&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fillOutline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#a6bddb&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; organism&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;human&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; sex&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;male&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;colour&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
theme_void&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/organPlotSubset-1.svg&quot; alt=&quot;plot of chunk organPlotSubset&quot; /&gt;&lt;/p&gt;

&lt;p&gt;We can fill the tissues based on the values given to each organ&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;gganatogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;organPlot&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fillOutline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#a6bddb&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; organism&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;human&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; sex&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;male&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;value&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
theme_void&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
scale_fill_gradient&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;low &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;white&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; high &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;red&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/organPlotValue-1.svg&quot; alt=&quot;plot of chunk organPlotValue&quot; /&gt;&lt;/p&gt;

&lt;p&gt;We can also use facet_wrap to compare groups.&lt;br /&gt;
 First create add two data frames together with different values and the conditions in the type column&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;compareGroups &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;rbind&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;data.frame&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;organ &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;heart&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;leukocyte&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;nerve&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;brain&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;liver&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;stomach&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;colon&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
  colour &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;red&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;red&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;purple&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;purple&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;orange&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;orange&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;orange&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 value &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;10&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;8&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 type &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;rep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Normal&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;7&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 stringsAsFactors&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;F&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;
 &lt;span class=&quot;kt&quot;&gt;data.frame&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;organ &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;heart&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;leukocyte&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;nerve&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;brain&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;liver&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;stomach&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;colon&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
  colour &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;red&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;red&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;purple&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;purple&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;orange&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;orange&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;orange&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 value &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;10&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;8&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 type &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;rep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Cancer&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;7&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 stringsAsFactors&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;F&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;gganatogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;compareGroups&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fillOutline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#a6bddb&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; organism&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;human&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; sex&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;male&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;value&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
    theme_void&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
    facet_wrap&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;~&lt;/span&gt;type&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
    scale_fill_gradient&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;low &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;white&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; high &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;red&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/Condition-1.svg&quot; alt=&quot;plot of chunk Condition&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;gganatogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;hgMale_key&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fillOutline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#a6bddb&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; organism&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;human&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; sex&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;male&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;colour&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
    theme_void&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
    facet_wrap&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;~&lt;/span&gt;type&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/organPlotAllWrap-1.svg&quot; alt=&quot;plot of chunk organPlotAllWrap&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;gganatogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;hgMale_key&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; outline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;F&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fillOutline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#a6bddb&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; organism&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;human&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; sex&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;male&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;colour&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
    theme_void&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
    facet_wrap&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;~&lt;/span&gt;type&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; scale&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;free&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/organPlotAllWrapFree-1.svg&quot; alt=&quot;plot of chunk organPlotAllWrapFree&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;organtype &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; organPlot
organtype &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    mutate&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;type&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;organ&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    gganatogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; outline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;F&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fillOutline&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#a6bddb&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; organism&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;human&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; sex&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;male&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;colour&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme_void&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        facet_wrap&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;~&lt;/span&gt;type&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; scale&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;free&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/organPlotWrapFree-1.svg&quot; alt=&quot;plot of chunk organPlotWrapFree&quot; /&gt;&lt;/p&gt;

</description>
        <pubDate>Sun, 09 Sep 2018 00:00:00 -0400</pubDate>
        <link>http://jespermaag.github.io/blog/2018/gganatogram/</link>
        <guid isPermaLink="true">http://jespermaag.github.io/blog/2018/gganatogram/</guid>
        
        
        <category>jekyll</category>
        
        <category>update</category>
        
      </item>
    
      <item>
        <title>Single cell RNA-seq (ES mouse) using Seurat</title>
        <description>&lt;h2 id=&quot;in-this-post-i-will-analyze-mouse-es-cell-single-cell-rna-seq-data-using-seurat&quot;&gt;In this post I will analyze mouse ES-cell single cell RNA-seq data using Seurat.&lt;/h2&gt;
&lt;p&gt;Data was downlaoded from https://github.com/debsin/dropClust&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;RCurl&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;Seurat&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;cellrangerRkit&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data.table&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tidyverse&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;This post also follows examples from https://davetang.org/muse/2017/08/01/getting-started-seurat/
First we remove all genes that are expressed in less than 3 cells.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;esMus &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; Read10X&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;~/github/jespermaag.github.io/es_mouse/&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;

&lt;span class=&quot;kp&quot;&gt;dim&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMus&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## [1] 24175  2717&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;keep &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;apply&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMus&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kr&quot;&gt;function&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;sum&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;o&quot;&gt;&amp;gt;&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;table&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;keep&lt;span class=&quot;o&quot;&gt;&amp;gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## 
## FALSE  TRUE 
##   153 24022&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;keep &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; keep &lt;span class=&quot;o&quot;&gt;&amp;gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;

esMus &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; esMus&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;keep&lt;span class=&quot;p&quot;&gt;,]&lt;/span&gt;

&lt;span class=&quot;kp&quot;&gt;summary&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;colSums&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMus&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    1647    6263   17373   20033   31086   85686&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;genes &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;apply&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMus&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kr&quot;&gt;function&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;sum&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;o&quot;&gt;&amp;gt;&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;genes &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; 
    melt&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        geom_histogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;steelblue&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme_classic&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        xlab&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Number genes (1&amp;gt;= counts)&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        ggtitle&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Number of genes detected per cell&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
	    theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; axis.title.x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;14&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; axis.text.x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;  
        axis.text.y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; axis.title.y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;14&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/explorePlots-1.svg&quot; alt=&quot;plot of chunk explorePlots&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;colSums&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMus&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    melt&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        geom_histogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;steelblue&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme_classic&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        xlab&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Counts per cell)&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        ggtitle&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Total counts per cell&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; axis.title.x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;14&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; axis.text.x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;  
        axis.text.y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; axis.title.y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;14&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/explorePlots-2.svg&quot; alt=&quot;plot of chunk explorePlots&quot; /&gt;&lt;/p&gt;

&lt;p&gt;As seen in the number of gene plots, there is a binomial distribution of number of genes per cell.
I will keep this in mind for further analysis. 
The binomial distribtion is missing from the total counts per cell.&lt;/p&gt;

&lt;p&gt;To use Seurat, I first have to create a Seurat object&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;esMusSeur &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; CreateSeuratObject&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;raw.data &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMus&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                           min.cells &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                           min.genes &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;100&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                           project &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;ES_mouse&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

esMusSeur&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## An object of class seurat in project ES_mouse 
##  24022 genes across 2717 samples.&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;slotNames&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMusSeur&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##  [1] &amp;quot;raw.data&amp;quot;     &amp;quot;data&amp;quot;         &amp;quot;scale.data&amp;quot;   &amp;quot;var.genes&amp;quot;   
##  [5] &amp;quot;is.expr&amp;quot;      &amp;quot;ident&amp;quot;        &amp;quot;meta.data&amp;quot;    &amp;quot;project.name&amp;quot;
##  [9] &amp;quot;dr&amp;quot;           &amp;quot;assay&amp;quot;        &amp;quot;hvg.info&amp;quot;     &amp;quot;imputed&amp;quot;     
## [13] &amp;quot;cell.names&amp;quot;   &amp;quot;cluster.tree&amp;quot; &amp;quot;snn&amp;quot;          &amp;quot;calc.params&amp;quot; 
## [17] &amp;quot;kmeans&amp;quot;       &amp;quot;spatial&amp;quot;      &amp;quot;misc&amp;quot;         &amp;quot;version&amp;quot;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;esMusSeur &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; NormalizeData&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                      normalization.method &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;LogNormalize&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                      scale.factor &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1e4&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;



 

&lt;span class=&quot;kp&quot;&gt;colSums&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMusSeur&lt;span class=&quot;o&quot;&gt;@&lt;/span&gt;data&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    melt&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        geom_histogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;steelblue&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme_classic&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        xlab&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Normalised counts per cell&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        ggtitle&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Total counts per cell&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; axis.title.x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;14&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; axis.text.x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;  
        axis.text.y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; axis.title.y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;14&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/createSeurat-1.svg&quot; alt=&quot;plot of chunk createSeurat&quot; /&gt;
As seen in the previous figure, after normalised the binomial distribution appears for the total counts.&lt;/p&gt;

&lt;p&gt;Below I want to find the variable genes between the cells and plot the PCA.
Since this is my first single cell analysis, I will use the parameters from https://davetang.org/muse/2017/08/01/getting-started-seurat/&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;esMusSeur &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; FindVariableGenes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                          mean.function &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; ExpMean&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                          dispersion.function &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; LogVMR&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                          x.low.cutoff &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0.0125&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                          x.high.cutoff &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                          y.cutoff &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0.5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/variability-1.svg&quot; alt=&quot;plot of chunk variability&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;length&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMusSeur&lt;span class=&quot;o&quot;&gt;@&lt;/span&gt;var.genes&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## [1] 5707&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;head&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMusSeur&lt;span class=&quot;o&quot;&gt;@&lt;/span&gt;hvg.info&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##        gene.mean gene.dispersion gene.dispersion.scaled
## Gm7102 0.5832131        5.417292              16.151102
## Dcdc2c 0.4870505        5.006380              18.885776
## Rn28s1 2.9695050        4.793843               2.929660
## Rn4.5s 2.7443443        4.607135               3.618150
## Rn45s  3.6240987        4.024695               2.001075
## Ccdc36 3.3616208        3.766651               1.659102&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;esMusSeur&lt;span class=&quot;o&quot;&gt;@&lt;/span&gt;hvg.info &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; x&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; gene.mean&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; gene.dispersion.scaled&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        geom_point&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;pch&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;21&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;steelblue&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme_classic&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        xlab&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Mean gene expression&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        ylab&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;scaled dispersion&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        ggtitle&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Mean expression vs dispersion&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; axis.title.x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;14&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; axis.text.x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;  
        axis.text.y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; axis.title.y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;14&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        geom_smooth&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/variability-2.svg&quot; alt=&quot;plot of chunk variability&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## Regressing out: nUMI&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## Scaling data matrix&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;esMusSeur &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; RunPCA&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
               pc.genes &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;o&quot;&gt;@&lt;/span&gt;var.genes&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
               do.print &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
               pcs.print &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
               genes.print &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## [1] &amp;quot;PC1&amp;quot;
## [1] &amp;quot;Krt8&amp;quot;   &amp;quot;Krt18&amp;quot;  &amp;quot;S100a6&amp;quot; &amp;quot;Gsn&amp;quot;    &amp;quot;Lgals1&amp;quot;
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;Npm1&amp;quot;   &amp;quot;Dppa5a&amp;quot; &amp;quot;Ptma&amp;quot;   &amp;quot;Nlrp1a&amp;quot; &amp;quot;Rpl21&amp;quot; 
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;PC2&amp;quot;
## [1] &amp;quot;Lrrc58&amp;quot; &amp;quot;Tpm1&amp;quot;   &amp;quot;Tagln&amp;quot;  &amp;quot;Eno1b&amp;quot;  &amp;quot;Eno1&amp;quot;  
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;Tdh&amp;quot;     &amp;quot;Mir690&amp;quot;  &amp;quot;Esrrb&amp;quot;   &amp;quot;Zfp42&amp;quot;   &amp;quot;Slc29a1&amp;quot;
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;PC3&amp;quot;
## [1] &amp;quot;Gm15772&amp;quot; &amp;quot;Mt2&amp;quot;     &amp;quot;Esrrb&amp;quot;   &amp;quot;Tdh&amp;quot;     &amp;quot;Hmces&amp;quot;  
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;Acsf2&amp;quot;   &amp;quot;Ppm1k&amp;quot;   &amp;quot;Gm10941&amp;quot; &amp;quot;Agl&amp;quot;     &amp;quot;Mtfmt&amp;quot;  
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;PC4&amp;quot;
## [1] &amp;quot;Klf5&amp;quot;   &amp;quot;Malat1&amp;quot; &amp;quot;Klf6&amp;quot;   &amp;quot;Slc2a3&amp;quot; &amp;quot;Sparc&amp;quot; 
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;Il12a&amp;quot;    &amp;quot;Gm20740&amp;quot;  &amp;quot;Olfr954&amp;quot;  &amp;quot;Fam229b&amp;quot;  &amp;quot;Tmem126b&amp;quot;
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;PC5&amp;quot;
## [1] &amp;quot;Gapdh&amp;quot;  &amp;quot;Gpx4&amp;quot;   &amp;quot;Gm8709&amp;quot; &amp;quot;Dusp9&amp;quot;  &amp;quot;Gsn&amp;quot;   
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;Erdr1&amp;quot;     &amp;quot;Hist1h2ao&amp;quot; &amp;quot;Apoe&amp;quot;      &amp;quot;Hist1h2ap&amp;quot; &amp;quot;Flnb&amp;quot;     
## [1] &amp;quot;&amp;quot;
## [1] &amp;quot;&amp;quot;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;PrintPCAParams&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMusSeur&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## Parameters used in latest PCA calculation run on: 2018-08-11 14:46:38
## =============================================================================
## PCs computed    Genes used in calculation    PCs Scaled by Variance Explained
##     20                  5707                               TRUE
## -----------------------------------------------------------------------------
## rev.pca 
##  FALSE
## -----------------------------------------------------------------------------
## Full gene list can be accessed using 
##  GetCalcParam(object = object, calculation = &amp;quot;RunPCA&amp;quot;, parameter = &amp;quot;pc.genes&amp;quot;)&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;VizPCA&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; pcs.use &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/PCA-1.svg&quot; alt=&quot;plot of chunk PCA&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;PCAPlot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; dim.1 &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; dim.2 &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/PCA-2.svg&quot; alt=&quot;plot of chunk PCA&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;esMusSeur &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; ProjectPCA&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; do.print &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;FALSE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;By plotting the standard deviation for each principal compartment, I can see that the deviation stop at around the 12th compartment.&lt;/p&gt;

&lt;p&gt;K-nearest neighbour finds the number of groups in the data set, which is used to colour the data in the tSNE-plot&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;PCElbowPlot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;esMusSeur&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/subsetPCA-1.svg&quot; alt=&quot;plot of chunk subsetPCA&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;esMusSeur &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; FindClusters&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                     reduction.type &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;pca&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                     dims.use &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;10&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                     resolution &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0.6&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                     print.output &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                     save.SNN &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
 
esMusSeur &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; FindClusters&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                     reduction.type &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;pca&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                     dims.use &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                     resolution &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0.6&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                     print.output &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                     save.SNN &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;


esMusSeur &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; RunTSNE&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                dims.use &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                do.fast &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

TSNEPlot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; do.label &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/subsetPCA-2.svg&quot; alt=&quot;plot of chunk subsetPCA&quot; /&gt;&lt;/p&gt;

&lt;p&gt;I then want to identify the top genes per cluster.&lt;/p&gt;

&lt;p&gt;The top genes can then be plotted as violin plots, feature plots, which projects the expression on the tSNE-plot, or as heatmaps for the top 5 highest expressed genes per cluster.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;topMarkers &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; esMusSeur.markers &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; 
    group_by&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;cluster&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; 
    top_n&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; avg_logFC&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
    
    
VlnPlot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; features.plot &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; topMarkers&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;gene&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; point.size.use &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/topGenes-1.svg&quot; alt=&quot;plot of chunk topGenes&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;FeaturePlot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
            features.plot &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; topMarkers&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;gene&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
            cols.use &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;grey&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;blue&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;
            reduction.use &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;tsne&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/topGenes-2.svg&quot; alt=&quot;plot of chunk topGenes&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;topMarkers5 &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; esMusSeur.markers &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; 
    group_by&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;cluster&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; 
    top_n&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; avg_logFC&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
    
DoHeatmap&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;object &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; esMusSeur&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
          genes.use &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; topMarkers5&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;gene&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
          remove.key &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
          slim.col.label &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/topGenes-3.svg&quot; alt=&quot;plot of chunk topGenes&quot; /&gt;&lt;/p&gt;

&lt;h3 id=&quot;there-you-go-my-first-single-cell-analysis-using-seurat-and-following-the-examples-from-dave-tang&quot;&gt;There you go. My first single cell analysis using Seurat, and following the examples from Dave Tang&lt;/h3&gt;

</description>
        <pubDate>Sun, 25 Mar 2018 00:00:00 -0400</pubDate>
        <link>http://jespermaag.github.io/blog/2018/SingleCellESmouse/</link>
        <guid isPermaLink="true">http://jespermaag.github.io/blog/2018/SingleCellESmouse/</guid>
        
        
        <category>jekyll</category>
        
        <category>update</category>
        
      </item>
    
      <item>
        <title>World bank health data</title>
        <description>
&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data.table&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tidyverse&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;Data has been downloaded and is called data.csv.
https://www.kaggle.com/theworldbank/health-nutrition-and-population-statistics/data&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;data &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; fread&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;~/Downloads/data.csv&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;T&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; stringsAsFactors&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;F&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;dim&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## [1] 89010    61&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;head&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##    Country Name Country Code
## 1:   Arab World          ARB
## 2:   Arab World          ARB
## 3:   Arab World          ARB
## 4:   Arab World          ARB
## 5:   Arab World          ARB
## 6:   Arab World          ARB
##                                                                                                           Indicator Name
## 1: % of females ages 15-49 having comprehensive correct knowledge about HIV (2 prevent ways and reject 3 misconceptions)
## 2:   % of males ages 15-49 having comprehensive correct knowledge about HIV (2 prevent ways and reject 3 misconceptions)
## 3:                                                         Adolescent fertility rate (births per 1,000 women ages 15-19)
## 4:                                                           Adults (ages 15+) and children (0-14 years) living with HIV
## 5:                                                    Adults (ages 15+) and children (ages 0-14) newly infected with HIV
## 6:                                                                                     Adults (ages 15+) living with HIV
##       Indicator Code            1960             1961             1962
## 1: SH.HIV.KNOW.FE.ZS                                                  
## 2: SH.HIV.KNOW.MA.ZS                                                  
## 3:       SP.ADO.TFRT 133.55501327769 134.159118941963 134.857912280869
## 4:       SH.HIV.TOTL                                                  
## 5:    SH.HIV.INCD.TL                                                  
## 6:       SH.DYN.AIDS                                                  
##                1963             1964            1965             1966
## 1:                                                                   
## 2:                                                                   
## 3: 134.504575565342 134.105211273476 133.56962589645 132.675635192775
## 4:                                                                   
## 5:                                                                   
## 6:                                                                   
##                1967             1968             1969             1970
## 1:                                                                    
## 2:                                                                    
## 3: 131.665502129354 129.190980115918 126.736756382819 124.382808900193
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                1971             1972             1973             1974
## 1:                                                                    
## 2:                                                                    
## 3: 122.133431342027 120.020185557559 118.087531093609 116.132988067096
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                1975             1976             1977             1978
## 1:                                                                    
## 2:                                                                    
## 3: 114.100918174437 111.980005447216 109.783821762662 106.033489239906
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                1979             1980             1981             1982
## 1:                                                                    
## 2:                                                                    
## 3: 102.341720681455 98.7390023274647 95.2412508672802 91.7911923993221
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                1983             1984             1985             1986
## 1:                                                                    
## 2:                                                                    
## 3: 88.0011769487606 84.2072557839419 80.3593225600132 76.4415956498419
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                1987             1988             1989             1990
## 1:                                                                    
## 2:                                                                    
## 3: 72.5145803648751 71.1706639452677 69.8887679924858 69.0044133814268
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                1991             1992             1993             1994
## 1:                                                                    
## 2:                                                                    
## 3: 67.7559924352118 66.9284506867798 64.9489678572737 62.9227777228154
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                1995             1996             1997             1998
## 1:                                                                    
## 2:                                                                    
## 3: 60.7070695260477 58.5966308804751 56.4401276304142 55.5315395528949
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                1999             2000             2001             2002
## 1:                                                                    
## 2:                                                                    
## 3: 54.6587808352011 53.8314102398679 52.9015276443892 51.9907926813042
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                2003             2004             2005             2006
## 1:                                                                    
## 2:                                                                    
## 3: 51.5228563035101 51.1032496482833 50.7325902239383 50.3291352282938
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                2007             2008             2009             2010
## 1:                                                                    
## 2:                                                                    
## 3: 49.9998514069402 49.8870459355469 49.7812066054555 49.6729747116906
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##                2011             2012             2013             2014
## 1:                                                                    
## 2:                                                                    
## 3: 49.5360469363113 49.3837446924523 48.7965576984378 48.1964180547578
## 4:                                                                    
## 5:                                                                    
## 6:                                                                    
##    2015 V61
## 1:       NA
## 2:       NA
## 3:       NA
## 4:       NA
## 5:       NA
## 6:       NA&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;gsub&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot; &amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;_&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;Dataset consists of countries and larger regions. 
First I want to investigate the differences in life expectancy per region.&lt;/p&gt;

&lt;p&gt;We see that different regions have different life expectancy for both female and male.
The survival of men is always lower comapred to females.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;regions &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; data&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;Country_Name &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;unique&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;Country_Name&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;41&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],]&lt;/span&gt;
regions2014 &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; regions&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;4&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;59&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)]&lt;/span&gt;
regions2014 &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    filter&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;Indicator_Name &lt;span class=&quot;o&quot;&gt;==&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;Life expectancy at birth, female (years)&amp;quot;&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;|&lt;/span&gt; 
        Indicator_Name &lt;span class=&quot;o&quot;&gt;==&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;Life expectancy at birth, male (years)&amp;quot;&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    melt&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;4&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; 
    mutate&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;Sex &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;gsub&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;Life expectancy at birth, |\\(years\\)&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; Indicator_Name&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    arrange&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    filter&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;!&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;grepl&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;income|&amp;amp;|dividend|small|Small|area|UN|conflict|poor&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; Country_Name&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    mutate&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;Country_Name &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;factor&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;Country_Name&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; levels&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;unique&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;Country_Name&lt;span class=&quot;p&quot;&gt;)))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; Country_Name&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;as.numeric&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;Sex&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; group&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;Country_Name&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        coord_flip&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        ylim&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;90&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        &lt;span class=&quot;c1&quot;&gt;#geom_segment(aes(x = 0, x = Country_Name, xend = value), color = &amp;quot;grey50&amp;quot;) +&lt;/span&gt;
        geom_line&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
    	geom_point&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;pch&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;21&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        scale_fill_brewer&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;palette&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;Set1&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
    	&lt;span class=&quot;c1&quot;&gt;#scale_fill_manual(values=c(&amp;#39;deepskyblue&amp;#39;,&amp;#39;darkorange2&amp;#39;)) +&lt;/span&gt;
    	theme_classic&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
    	theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; axis.title.x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;14&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; axis.text.x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;  
            axis.text.y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;12&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; axis.title.y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;14&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
    	ggtitle&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Life expetancy per region&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
    	xlab&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Region&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
        ylab&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Life expectancy from birth (years)&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/Female_lifeExpectancy-1.png&quot; alt=&quot;plot of chunk Female_lifeExpectancy&quot; /&gt;&lt;/p&gt;

&lt;h2 id=&quot;further-analysis-will-investigate-these-differneces&quot;&gt;Further analysis will investigate these differneces&lt;/h2&gt;
</description>
        <pubDate>Sun, 18 Mar 2018 00:00:00 -0400</pubDate>
        <link>http://jespermaag.github.io/blog/2018/WorldBankHealth/</link>
        <guid isPermaLink="true">http://jespermaag.github.io/blog/2018/WorldBankHealth/</guid>
        
        
        <category>jekyll</category>
        
        <category>update</category>
        
      </item>
    
      <item>
        <title>Bayesian regression of heart data</title>
        <description>&lt;p&gt;This post tries to use Bayesian linear regression to explore
causes of heart disease.&lt;/p&gt;
&lt;h2 id=&quot;bayesian-linear-regression&quot;&gt;Bayesian linear regression&lt;/h2&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;corrplot&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ncvreg&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ipred&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;dplyr&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ggplot2&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;RColorBrewer&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;c1&quot;&gt;#data(dystrophy)&lt;/span&gt;
data&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;heart&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;dim&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;heart&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## [1] 462  10&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;str&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;heart&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## &amp;#39;data.frame&amp;#39;:	462 obs. of  10 variables:
##  $ sbp      : int  160 144 118 170 134 132 142 114 114 132 ...
##  $ tobacco  : num  12 0.01 0.08 7.5 13.6 6.2 4.05 4.08 0 0 ...
##  $ ldl      : num  5.73 4.41 3.48 6.41 3.5 6.47 3.38 4.59 3.83 5.8 ...
##  $ adiposity: num  23.1 28.6 32.3 38 27.8 ...
##  $ famhist  : num  1 0 1 1 1 1 0 1 1 1 ...
##  $ typea    : int  49 55 52 51 60 62 59 62 49 69 ...
##  $ obesity  : num  25.3 28.9 29.1 32 26 ...
##  $ alcohol  : num  97.2 2.06 3.81 24.26 57.34 ...
##  $ age      : int  52 63 46 58 49 45 38 58 29 53 ...
##  $ chd      : int  1 1 0 1 1 0 0 1 0 1 ...&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;##Omit NA’s and plot variables to see if there’s correlations&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;dat &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; heart
Cor &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; cor&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;dat&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
corrplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;Cor&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; type&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;upper&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; method&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;ellipse&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; tl.pos&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;d&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
corrplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;Cor&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; type&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;lower&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; method&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;number&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; col&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;black&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
         add&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; diag&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kc&quot;&gt;FALSE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; tl.pos&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;n&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; cl.pos&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;n&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/corrplot-1.svg&quot; alt=&quot;plot of chunk corrplot&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;dat &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; 
    &lt;span class=&quot;kp&quot;&gt;as.data.frame&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    select&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;-&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;famhist&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    melt&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;variable&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        geom_histogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;black&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        facet_wrap&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;~&lt;/span&gt;variable&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; ncol&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; scale&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;free&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme_classic&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        scale_fill_brewer&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;palette&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;Set1&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;legend.position&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;none&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/corrplot-2.svg&quot; alt=&quot;plot of chunk corrplot&quot; /&gt;&lt;/p&gt;

&lt;p&gt;#Divide the data into training and test set&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;chdYes &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; heart&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;heart&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;chd&lt;span class=&quot;o&quot;&gt;==&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,]&lt;/span&gt;
chdNo &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; heart&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;heart&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;chd&lt;span class=&quot;o&quot;&gt;==&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,]&lt;/span&gt;

sampleYes &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;sample&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;rownames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;chdYes&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;nrow&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;chdYes&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;*&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.8&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
sampleNo &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;sample&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;rownames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;chdNo&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;nrow&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;chdNo&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;*&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.8&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

trainYes &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; chdYes&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;sampleYes&lt;span class=&quot;p&quot;&gt;,]&lt;/span&gt;
trainNo &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; chdNo&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;sampleNo&lt;span class=&quot;p&quot;&gt;,]&lt;/span&gt;

testYes &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; chdYes&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;!&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;rownames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;chdYes&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; sampleYes&lt;span class=&quot;p&quot;&gt;,]&lt;/span&gt;
testNo &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; chdNo&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;!&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;rownames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;chdNo&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; sampleNo&lt;span class=&quot;p&quot;&gt;,]&lt;/span&gt;

dat &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;rbind&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;trainYes&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; trainNo&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
test &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;rbind&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;testYes&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; testNo&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;###Model the data with JAGS
As we have centered the data around 0, the distribution of Beta will follow a double exponential distriubtion.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;X &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;scale&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;dat&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;-10&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt;  center&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; scale&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

X &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; 
    &lt;span class=&quot;kp&quot;&gt;as.data.frame&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    select&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;-&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;famhist&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    melt&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;variable&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        geom_histogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;black&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        facet_wrap&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;~&lt;/span&gt;variable&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; ncol&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; scale&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;free&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme_classic&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        scale_fill_brewer&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;palette&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;Set1&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;legend.position&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;none&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/Model_data-1.svg&quot; alt=&quot;plot of chunk Model_data&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;mod_glm &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;summary&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;glm&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;chd &lt;span class=&quot;o&quot;&gt;~&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;.&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;dat&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;#JAGS model&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;rjags&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
mod1_string &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot; model {&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;    for (i in 1:length(y)) {&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;        y[i] ~ dbern(p[i])&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;        #logit(p[i]) = int + b[1]*AGE[i] + b[2]*CK[i] + b[3]*H[i] + b[4]*PK[i] + b[5]*LD[i]&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;        logit(p[i]) = int + b[1]*sbp[i] + b[2]+tobacco[i] + b[3]*ldl[i] + &lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;            b[4]*adiposity[i] + b[5]*famhist[i] +b[6]*typea[i] +b[7]*obesity[i] + b[8]*alcohol[i] + b[9]*age[i]&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;    }&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;    int ~ dnorm(0.0, 1.0/25.0)&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;    for (j in 1:9) {&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;        b[j] ~ ddexp(0.0, sqrt(2.0)) # has variance 1.0&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;        #b[j] ~ dnorm(0.0, 2) # noninformative for logistic regression&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;        #b[j] ~ dnorm(0.0, 1.0/4.0^2)&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;    }&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;} &amp;quot;&lt;/span&gt;


data_jags &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;list&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;y&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;dat&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;10&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; sbp&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;sbp&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; tobacco&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;tobacco&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; ldl&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;ldl&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; 
        adiposity&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;adiposity&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; famhist&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;famhist&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; 
        typea&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;typea&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; obesity&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;obesity&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; alcohol&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;alcohol&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt; age&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;age&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;])&lt;/span&gt;


params &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;int&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;b&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;##Run JAGS&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## Error: &amp;lt;text&amp;gt;:3:1: unexpected &amp;#39;,&amp;#39;
## 2: suppressMessages(update(mod1, 5e3))
## 3: ,
##    ^&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h2 id=&quot;convergence-diagnostics&quot;&gt;convergence diagnostics&lt;/h2&gt;
&lt;p&gt;1) No pattern in traceplot
2) After 5e3 updates (e.g. burn ins I still observe autocorrelation in b[2] and in int)
    Increasing it to 5e4 
3) DIC 
Mean deviance:  503.9 
penalty 8.646 
Penalized deviance: 512.5&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;plot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;mod1_sim&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/Plotting diagnostics-1.svg&quot; alt=&quot;plot of chunk Plotting diagnostics&quot; /&gt;&lt;img src=&quot;/assets/Rfig/Plotting diagnostics-2.svg&quot; alt=&quot;plot of chunk Plotting diagnostics&quot; /&gt;&lt;img src=&quot;/assets/Rfig/Plotting diagnostics-3.svg&quot; alt=&quot;plot of chunk Plotting diagnostics&quot; /&gt;&lt;img src=&quot;/assets/Rfig/Plotting diagnostics-4.svg&quot; alt=&quot;plot of chunk Plotting diagnostics&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;gelman.diag&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;mod1_sim&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## Potential scale reduction factors:
## 
##      Point est. Upper C.I.
## b[1]       1.00       1.00
## b[2]       1.05       1.11
## b[3]       1.00       1.00
## b[4]       1.00       1.01
## b[5]       1.00       1.00
## b[6]       1.00       1.00
## b[7]       1.00       1.00
## b[8]       1.00       1.00
## b[9]       1.00       1.00
## int        1.04       1.10
## 
## Multivariate psrf
## 
## 1.02&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;autocorr.diag&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;mod1_sim&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##               b[1]      b[2]          b[3]        b[4]          b[5]
## Lag 0  1.000000000 1.0000000  1.0000000000 1.000000000  1.0000000000
## Lag 1  0.287920926 0.9851922  0.3462278072 0.722909298  0.2658015636
## Lag 5  0.010262570 0.9378278  0.0008810413 0.205100190  0.0024193182
## Lag 10 0.007303032 0.8806068  0.0132742196 0.030675749 -0.0005156971
## Lag 50 0.005479209 0.5317571 -0.0033351594 0.005065785 -0.0052446834
##                b[6]        b[7]         b[8]         b[9]       int
## Lag 0   1.000000000 1.000000000  1.000000000  1.000000000 1.0000000
## Lag 1   0.301678048 0.630132049  0.239460718  0.534791017 0.9852943
## Lag 5   0.004675731 0.172722918 -0.006375527  0.092841859 0.9369034
## Lag 10  0.004933605 0.036995541 -0.002855998  0.005109218 0.8799680
## Lag 50 -0.002915316 0.007974022  0.004067879 -0.006795221 0.5316811&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;autocorr.plot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;mod1_sim&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/Plotting diagnostics-5.svg&quot; alt=&quot;plot of chunk Plotting diagnostics&quot; /&gt;&lt;img src=&quot;/assets/Rfig/Plotting diagnostics-6.svg&quot; alt=&quot;plot of chunk Plotting diagnostics&quot; /&gt;&lt;img src=&quot;/assets/Rfig/Plotting diagnostics-7.svg&quot; alt=&quot;plot of chunk Plotting diagnostics&quot; /&gt;&lt;img src=&quot;/assets/Rfig/Plotting diagnostics-8.svg&quot; alt=&quot;plot of chunk Plotting diagnostics&quot; /&gt;&lt;img src=&quot;/assets/Rfig/Plotting diagnostics-9.svg&quot; alt=&quot;plot of chunk Plotting diagnostics&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;effectiveSize&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;mod1_sim&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##       b[1]       b[2]       b[3]       b[4]       b[5]       b[6] 
## 8172.85337   96.52570 6961.24000 2350.24891 8535.10192 7542.87353 
##       b[7]       b[8]       b[9]        int 
## 2810.94261 8762.84597 3950.24210   98.74925&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;##Summary statistics
I observe that tobacco, adiposity and alcohol have
posterior probabilities centered around 0.
This means that they do not contribute much to heart disease
I remove these and compare between models&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;dic1&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## Mean deviance:  394.9 
## penalty 8.171 
## Penalized deviance: 403.1&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;posterior &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; mod1_csim&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;9&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;posterior&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

posterior&lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; 
    &lt;span class=&quot;kp&quot;&gt;as.data.frame&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    select&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;-&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;famhist&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    melt&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;variable&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        geom_histogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;black&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; binwidth&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        facet_wrap&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;~&lt;/span&gt;variable&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; ncol&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme_classic&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        scale_fill_brewer&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;palette&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;Set1&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;legend.position&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;none&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        xlim&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;-3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/unnamed-chunk-1-1.svg&quot; alt=&quot;plot of chunk unnamed-chunk-1&quot; /&gt;&lt;/p&gt;

&lt;p&gt;##Ajust model to remove terms centered around 0
Here the autocorrelation disappers and the effective smaple size is larger for all variables&lt;/p&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/unnamed-chunk-2-1.svg&quot; alt=&quot;plot of chunk unnamed-chunk-2&quot; /&gt;&lt;img src=&quot;/assets/Rfig/unnamed-chunk-2-2.svg&quot; alt=&quot;plot of chunk unnamed-chunk-2&quot; /&gt;&lt;img src=&quot;/assets/Rfig/unnamed-chunk-2-3.svg&quot; alt=&quot;plot of chunk unnamed-chunk-2&quot; /&gt;&lt;img src=&quot;/assets/Rfig/unnamed-chunk-2-4.svg&quot; alt=&quot;plot of chunk unnamed-chunk-2&quot; /&gt;&lt;img src=&quot;/assets/Rfig/unnamed-chunk-2-5.svg&quot; alt=&quot;plot of chunk unnamed-chunk-2&quot; /&gt;&lt;/p&gt;

&lt;h1 id=&quot;comparing-the-models&quot;&gt;Comparing the models&lt;/h1&gt;
&lt;p&gt;DIC for model 1 is larger than for model 2. Therefore, model2 is better and I will use this&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;dic1&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## Mean deviance:  394.9 
## penalty 8.171 
## Penalized deviance: 403.1&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;dic2&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## Mean deviance:  388.3 
## penalty 6.957 
## Penalized deviance: 395.2&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;dic1 &lt;span class=&quot;o&quot;&gt;-&lt;/span&gt; dic2&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## Difference: 7.843772
## Sample standard error: 26.6649&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;summary&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;mod2_sim&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## 
## Iterations = 6001:11000
## Thinning interval = 1 
## Number of chains = 3 
## Sample size per chain = 5000 
## 
## 1. Empirical mean and standard deviation for each variable,
##    plus standard error of the mean:
## 
##          Mean     SD Naive SE Time-series SE
## b[1]  0.14946 0.1264 0.001032       0.001493
## b[2]  0.47494 0.1349 0.001101       0.001532
## b[3]  0.40884 0.1226 0.001001       0.001293
## b[4]  0.34692 0.1351 0.001103       0.001542
## b[5] -0.06677 0.1289 0.001052       0.001496
## b[6]  0.80272 0.1645 0.001343       0.002163
## int  -0.87060 0.1362 0.001112       0.001631
## 
## 2. Quantiles for each variable:
## 
##          2.5%     25%     50%     75%   97.5%
## b[1] -0.08968  0.0631  0.1470  0.2336  0.4073
## b[2]  0.21582  0.3816  0.4739  0.5666  0.7386
## b[3]  0.16948  0.3266  0.4088  0.4910  0.6501
## b[4]  0.08586  0.2571  0.3455  0.4353  0.6193
## b[5] -0.32615 -0.1513 -0.0634  0.0181  0.1826
## b[6]  0.48890  0.6896  0.8020  0.9113  1.1381
## int  -1.14168 -0.9611 -0.8686 -0.7798 -0.6092&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;posterior &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; mod2_csim&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;6&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;posterior&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;X&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;-&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;4&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;8&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)]&lt;/span&gt;

posterior&lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; 
    &lt;span class=&quot;kp&quot;&gt;as.data.frame&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    select&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;-&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;famhist&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    melt&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
    ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;variable&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        geom_histogram&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;black&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; binwidth&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        facet_wrap&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;~&lt;/span&gt;variable&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; ncol&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme_classic&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        scale_fill_brewer&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;palette&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;Set1&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;legend.position&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;none&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
        xlim&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;-2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/Posterior-1.svg&quot; alt=&quot;plot of chunk Posterior&quot; /&gt;&lt;/p&gt;

&lt;p&gt;```
#Predict
Using our trained model we have a 0.72 accuracy&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;pm_coef &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;colMeans&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;mod2_csim&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##        b[1]        b[2]        b[3]        b[4]        b[5]        b[6] 
##  0.14946415  0.47494319  0.40884479  0.34692490 -0.06676623  0.80272040 
##         int 
## -0.87059519&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;pm_Xb &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; pm_coef&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;int&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; X&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;6&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;7&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;9&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%*%&lt;/span&gt; pm_coef&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;6&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;
phat &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1.0&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;/&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1.0&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;exp&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;-&lt;/span&gt;pm_Xb&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;head&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;phat&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##          [,1]
## 217 0.3155766
## 353 0.7529948
## 413 0.8381924
## 20  0.6011533
## 4   0.7105916
## 335 0.5084351&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;plot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;phat&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;jitter&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;dat&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;10&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/unnamed-chunk-3-1.svg&quot; alt=&quot;plot of chunk unnamed-chunk-3&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tab0.5 &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;table&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;phat &lt;span class=&quot;o&quot;&gt;&amp;gt;&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0.5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_jags2&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;y&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##        
##           0   1
##   FALSE 202  63
##   TRUE   39  65&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;sum&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;diag&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tab0.5&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;/&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;sum&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tab0.5&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## [1] 0.7235772&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;c1&quot;&gt;#0.72&lt;/span&gt;

X.test &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;scale&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;test&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;-10&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;],&lt;/span&gt;  center&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; scale&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kc&quot;&gt;TRUE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

pm_Xb &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; pm_coef&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;int&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; X.test&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;6&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;7&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;9&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%*%&lt;/span&gt; pm_coef&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;6&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt;
phat &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1.0&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;/&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1.0&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;exp&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;-&lt;/span&gt;pm_Xb&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;head&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;phat&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##         [,1]
## 8  0.6404793
## 19 0.8607690
## 30 0.6674311
## 31 0.1959541
## 36 0.1227429
## 54 0.1375159&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;plot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;phat&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;jitter&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;test&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;10&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/unnamed-chunk-3-2.svg&quot; alt=&quot;plot of chunk unnamed-chunk-3&quot; /&gt;&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tab0.5 &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;table&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;phat &lt;span class=&quot;o&quot;&gt;&amp;gt;&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0.5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; test&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;10&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;##        
##          0  1
##   FALSE 49 16
##   TRUE  12 16&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;sum&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;diag&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tab0.5&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;/&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;sum&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tab0.5&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## [1] 0.6989247&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;c1&quot;&gt;#0.73&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

</description>
        <pubDate>Sat, 17 Mar 2018 00:00:00 -0400</pubDate>
        <link>http://jespermaag.github.io/blog/2018/BayesianHeart/</link>
        <guid isPermaLink="true">http://jespermaag.github.io/blog/2018/BayesianHeart/</guid>
        
        
        <category>jekyll</category>
        
        <category>update</category>
        
      </item>
    
      <item>
        <title>New york census data</title>
        <description>&lt;h1 id=&quot;plotting-new-york-city-neighbourhoods&quot;&gt;Plotting New York city neighbourhoods&lt;/h1&gt;
&lt;p&gt;This blog plots the percentage of low-income housholds in 
each census are of NYC. 
Low-income households are defined as households with an 
income of less than $25,000&lt;/p&gt;

&lt;p&gt;Inspiration form: http://zevross.com/blog/2015/10/14/&lt;/p&gt;

&lt;p&gt;For census tables: https://censusreporter.org/topics/table-codes/&lt;/p&gt;

&lt;p&gt;Loading libraries&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tigris&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;acs&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;stringr&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; 
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;dplyr&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ggmap&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;maptools&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ggplot2&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;maps&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;RColorBrewer&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;htmlwidgets&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;rvg&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ggiraph&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;gganimate&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;gridExtra&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;grid&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;sp&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;rgdal&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;rgeos&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;proj4&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data.table&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tidyverse&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;broom&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h2 id=&quot;retrive-census-data-and-nyc-map&quot;&gt;Retrive census data and NYC map&lt;/h2&gt;
&lt;p&gt;Here we download all the census information for NYC regarding income&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;counties &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;47&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;61&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;81&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;85&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
tracts &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; tracts&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;state &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;NY&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; county &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;47&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;61&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;81&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;85&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; cb&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;T&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

&lt;span class=&quot;c1&quot;&gt;#tract &amp;lt;- readOGR(dsn=&amp;quot;2010 Census Blocks&amp;quot;, layer = &amp;quot;geo_export_0d5391be-e106-4007-ba4b-8b9ca965d298&amp;quot;)&lt;/span&gt;

api.key.install&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;key&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;e39e18eef6390892f0e0f1a1273b9ddd09cfbc7f&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;c1&quot;&gt;# create a geographic set to grab tabular data (acs)&lt;/span&gt;
geo&lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;geo.make&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;state&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;NY&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;
              county&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;47&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;61&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;81&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;85&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; tract&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;*&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
              

income&lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;acs.fetch&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;endyear &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;2012&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; span &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; geography &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; geo&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                              table.number &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;B19001&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; col.names &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;pretty&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;


edu&lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;acs.fetch&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;endyear &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;2012&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; span &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; geography &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; geo&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
table.number &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;B15001&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; col.names &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;pretty&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

income_df &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;data.frame&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;paste0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;str_pad&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;income&lt;span class=&quot;o&quot;&gt;@&lt;/span&gt;geography&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;state&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;left&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; pad&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;0&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
                             str_pad&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;income&lt;span class=&quot;o&quot;&gt;@&lt;/span&gt;geography&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;county&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;left&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; pad&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;0&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
                             str_pad&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;income&lt;span class=&quot;o&quot;&gt;@&lt;/span&gt;geography&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;tract&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;6&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;left&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; pad&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;0&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)),&lt;/span&gt; 
                        income&lt;span class=&quot;o&quot;&gt;@&lt;/span&gt;estimate&lt;span class=&quot;p&quot;&gt;[,&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;Household Income: Total:&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;  
                        &lt;span class=&quot;s&quot;&gt;&amp;quot;Household Income: $200,000 or more&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
                        &lt;span class=&quot;s&quot;&gt;&amp;quot;Household Income: $20,000 to $24,999&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
                        &lt;span class=&quot;s&quot;&gt;&amp;quot;Household Income: $15,000 to $19,999&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                        &lt;span class=&quot;s&quot;&gt;&amp;quot;Household Income: $10,000 to $14,999&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
                        &lt;span class=&quot;s&quot;&gt;&amp;quot;Household Income: Less than $10,000&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)],&lt;/span&gt; 
                        stringsAsFactors &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kc&quot;&gt;FALSE&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

&lt;span class=&quot;kp&quot;&gt;rownames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;income_df&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;nrow&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;income_df&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;names&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;income_df&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;GEOID&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;total&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
                &lt;span class=&quot;s&quot;&gt;&amp;quot;over_200&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
                &lt;span class=&quot;s&quot;&gt;&amp;#39;between20_24&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
                &lt;span class=&quot;s&quot;&gt;&amp;#39;between15_20&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
                &lt;span class=&quot;s&quot;&gt;&amp;#39;betwee10_14&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
                &lt;span class=&quot;s&quot;&gt;&amp;#39;under10&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
income_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;percent &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;100&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;*&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;((&lt;/span&gt;income_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;between20_24 &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
                        income_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;between15_20 &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
                        income_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;betwee10_14 &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
                        income_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;under10&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;/&lt;/span&gt;income_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;total&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;


ggtract&lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;fortify&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;tracts&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; region &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;GEOID&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; 
ggtract&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;region &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; ggtract&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;id
ggtract &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;subset&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ggtract&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; select&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;long&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; lat&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h2 id=&quot;get-the-water-coordinates&quot;&gt;Get the water coordinates&lt;/h2&gt;
&lt;p&gt;For some reason the census tracks downloaded extends into the water.
To remove this, I downloaded the water coordinates for all boroughs in NYC
and plotted them.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;NYC_water &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; area_water&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;NY&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;NEW YORK&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
NYC_water &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;tidy&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;NYC_water&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;NYC_water&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;long&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;lat&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;region&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

bronkxWater &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; area_water&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;NY&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;BRONX&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;
bronkxWater &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;tidy&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;bronkxWater&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;bronkxWater&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;long&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;lat&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;region&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

quansWater &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; area_water&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;NY&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;QUEENS&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
quansWater &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;tidy&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;quansWater&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;quansWater&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;long&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;lat&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;region&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

brookWater &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; area_water&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;NY&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;KINGS&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
brookWater &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;tidy&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;brookWater&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;brookWater&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;long&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;lat&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;region&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

statWater &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; area_water&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;NY&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;RICHMOND&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
statWater &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt;tidy&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;statWater&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;statWater&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;long&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;lat&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;region&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h2 id=&quot;get-nyc-neighborhoods-from-httpsrpubscomjhofmannycmaps&quot;&gt;Get NYC neighborhoods (From https://rpubs.com/jhofman/nycmaps)&lt;/h2&gt;
&lt;p&gt;I also wanted to split the map into different NYC neighbourhoods to get 
a sense of how the split of low-income households are per neighbourhood&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;r &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; GET&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;paste0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;http://data.beta.nyc//dataset/0ff93d2d-90ba-457c-9f7e-39e47bf2ac5f/&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;&amp;#39;resource/35dd04fb-81b3-479b-a074-a27a37888ce7/&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;&amp;#39;download/d085e2f8d0b54d4590b1e7d1f35594c1pediacitiesnycneighborhoods.geojson&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;
nyc_neighborhoods &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; readOGR&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;content&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;r&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;text&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;OGRGeoJSON&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; verbose &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;bp&quot;&gt;F&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

nyc_df &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; tidy&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;nyc_neighborhoods&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
nyc_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;region &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; nyc_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;id
nyc_df &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;subset&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;nyc_df&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; select&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;long&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; lat&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; region&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h2 id=&quot;annotate-neighbourhoods&quot;&gt;Annotate neighbourhoods&lt;/h2&gt;
&lt;p&gt;Make sure to separate the parks for the data&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;neighbourhood_names &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;data.frame&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;nyc_neighborhoods&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
neighbourhood_names&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;id &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;rownames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;neighbourhood_names&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;


nycParks &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; neighbourhood_names&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;grep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Park&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; neighbourhood_names&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;neighborhood&lt;span class=&quot;p&quot;&gt;),]&lt;/span&gt;

nycParks &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; nycParks&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;grep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Park Slope|Sunset Park|Borough Park|Park Hill|&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;            Parkchester|Morris Park|Rego Park|Floral Park&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
            nycParks&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;neighborhood&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; invert&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;T&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),]&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h2 id=&quot;add-info-for-interactive-plot&quot;&gt;Add info for interactive plot&lt;/h2&gt;
&lt;p&gt;Interactive map is not used here.&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;income_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;tip &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;paste0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;&amp;quot;&amp;lt;br&amp;gt;&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;paste0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;round&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;income_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;percent&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;%&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h2 id=&quot;plot-nyc&quot;&gt;Plot NYC&lt;/h2&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;p &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;income_df&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;GEOID&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
 geom_map_interactive&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;income_df&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; map&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;ggtract&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
         aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;GEOID&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;GEOID&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; tooltip&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;tip&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;percent&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kc&quot;&gt;NA&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 geom_map_interactive&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;neighbourhood_names&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; map&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;nyc_df&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
         aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;id&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;id&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;black&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; alpha&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.25&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 geom_map_interactive&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;income_df&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;income_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;total&lt;span class=&quot;o&quot;&gt;&amp;lt;&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;100&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,],&lt;/span&gt; 
         map&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;ggtract&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;GEOID&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;GEOID&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#969696&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 geom_map_interactive&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;nycParks&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; map&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;nyc_df&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
         aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;id&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;id&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;#c7e9c0&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 geom_map_interactive&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;NYC_water&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; map&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;NYC_water&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
         aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 geom_map_interactive&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;bronkxWater&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; map&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;bronkxWater&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
         aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 geom_map_interactive&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;quansWater&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; map&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;quansWater&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
         aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 geom_map_interactive&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;brookWater&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; map&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;brookWater&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
         aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 geom_map_interactive&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;statWater&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; map&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;statWater&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
         aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 expand_limits&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; nyc_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;long&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; nyc_df&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;lat&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 theme_void&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;plot.background &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_rect&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;fill &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;white&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
 scale_fill_gradientn&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;colours &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;#99000d&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;#fcbba1&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;white&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;
                        values &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;.3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;.2&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;.1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
&lt;span class=&quot;c1&quot;&gt;# scale_fill_brewer(palette=&amp;#39;Blues&amp;#39;)+&lt;/span&gt;
 ggtitle&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Percentage of households earning less than &amp;lt; $25,000&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
 
 ggiraph&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;code &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;print&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;p&lt;span class=&quot;p&quot;&gt;)},&lt;/span&gt;  hover_css &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;fill:red;r:3pt;&amp;quot;&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;height_svg&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;6&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/NewYorkMap-1.png&quot; alt=&quot;plot of chunk NewYorkMap&quot; /&gt;&lt;/p&gt;
</description>
        <pubDate>Sat, 17 Mar 2018 00:00:00 -0400</pubDate>
        <link>http://jespermaag.github.io/blog/2018/NewYorkCensus/</link>
        <guid isPermaLink="true">http://jespermaag.github.io/blog/2018/NewYorkCensus/</guid>
        
        
        <category>jekyll</category>
        
        <category>update</category>
        
      </item>
    
      <item>
        <title>Sweden election 2014</title>
        <description>&lt;h1 id=&quot;plotting-the-swedish-election-2014&quot;&gt;Plotting the Swedish Election 2014&lt;/h1&gt;
&lt;p&gt;This post plots the results from the 2014 Swedish general election
for each political party per county.
The values plotted are votes as z-value for each county compared to the whole country.&lt;/p&gt;

&lt;p&gt;Loading libraries&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;httr&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;lubridate&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;jsonlite&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ggplot2&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;swemaps&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;rkolada&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;maps&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;dplyr&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;RColorBrewer&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;htmlwidgets&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;rvg&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;ggiraph&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;gganimate&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;gridExtra&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;grid&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
&lt;span class=&quot;kn&quot;&gt;library&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;gtable&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h4 id=&quot;getting-data&quot;&gt;Getting data&lt;/h4&gt;
&lt;p&gt;Get all the election data per county and per election.
This involves trying to figure out where on the Swedish Statistical Bureau you can find information (http://api.scb.se/OV0104/v1/doris/sv/ssd/) .
For english go to http://api.scb.se/OV0104/v1/doris/en/ssd&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;url &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;http://api.scb.se/OV0104/v1/doris/sv/ssd/ME/ME0104/ME0104C/ME0104T3&amp;quot;&lt;/span&gt;

SCB &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; jsonlite&lt;span class=&quot;o&quot;&gt;::&lt;/span&gt;fromJSON&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;url&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

SCB&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;variables&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;code&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## [1] &amp;quot;Region&amp;quot;       &amp;quot;Partimm&amp;quot;      &amp;quot;ContentsCode&amp;quot; &amp;quot;Tid&amp;quot;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;query &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;paste0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39; { &amp;quot;query&amp;quot;: [  {&amp;quot;code&amp;quot;: &amp;quot;ContentsCode&amp;quot;,&amp;quot;selection&amp;quot;: {&amp;quot;filter&amp;quot;: &amp;quot;item&amp;quot;, &amp;quot;values&amp;quot;: [ &amp;quot;ME0104B7&amp;quot;] } }, {&amp;quot;code&amp;quot;: &amp;quot;Tid&amp;quot;,&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt; &amp;quot;selection&amp;quot;: {&amp;quot;filter&amp;quot;: &amp;quot;item&amp;quot;,&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt; &amp;quot;values&amp;quot;: [&amp;quot;&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;paste&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;SCB&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;variables&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;values&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;4&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]],&lt;/span&gt;collapse&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;&amp;quot; &amp;quot;&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;&amp;quot;]}},   &lt;/span&gt;
&lt;span class=&quot;s&quot;&gt; {&amp;quot;code&amp;quot;: &amp;quot;Region&amp;quot;,&amp;quot;selection&amp;quot;: {&amp;quot;filter&amp;quot;: &amp;quot;item&amp;quot;, &amp;quot;values&amp;quot;: [&amp;quot;&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;paste&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;SCB&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;variables&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;values&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]],&lt;/span&gt;collapse&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;&amp;quot; &amp;quot;&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
 &lt;span class=&quot;s&quot;&gt;&amp;#39;&amp;quot;] } } ],&amp;quot;response&amp;quot;: {&amp;quot;format&amp;quot;: &amp;quot;csv&amp;quot;}  }&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

results &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; POST&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;url&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; body&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;query&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;
SCBdata &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; content&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;results&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

SCBdata&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## # A tibble: 3,553 x 15
##    region  `parti mm`  `Andel röster (a… `Andel röster (… `Andel röster (…
##    &amp;lt;chr&amp;gt;   &amp;lt;chr&amp;gt;       &amp;lt;chr&amp;gt;             &amp;lt;chr&amp;gt;            &amp;lt;chr&amp;gt;           
##  1 0114 U… Moderaterna 15.5              17.1             23.5            
##  2 0114 U… Centerpart… 23.6              20.1             12.8            
##  3 0114 U… Folkpartiet 9.7               13.8             12.1            
##  4 0114 U… Kristdemok… 1.0               0.6              0.8             
##  5 0114 U… Miljöparti… ..                ..               ..              
##  6 0114 U… Socialdemo… 42.9              41.4             41.9            
##  7 0114 U… Vänsterpar… 6.5               6.5              7.8             
##  8 0114 U… Sverigedem… ..                ..               ..              
##  9 0114 U… övriga par… 0.6               0.5              1.0             
## 10 0114 U… ogiltiga v… ..                ..               ..              
## # ... with 3,543 more rows, and 10 more variables: `Andel röster (av
## #   giltiga röster) 1982` &amp;lt;chr&amp;gt;, `Andel röster (av giltiga röster)
## #   1985` &amp;lt;chr&amp;gt;, `Andel röster (av giltiga röster) 1988` &amp;lt;chr&amp;gt;, `Andel
## #   röster (av giltiga röster) 1991` &amp;lt;chr&amp;gt;, `Andel röster (av giltiga
## #   röster) 1994` &amp;lt;chr&amp;gt;, `Andel röster (av giltiga röster) 1998` &amp;lt;chr&amp;gt;,
## #   `Andel röster (av giltiga röster) 2002` &amp;lt;chr&amp;gt;, `Andel röster (av
## #   giltiga röster) 2006` &amp;lt;chr&amp;gt;, `Andel röster (av giltiga röster)
## #   2010` &amp;lt;chr&amp;gt;, `Andel röster (av giltiga röster) 2014` &amp;lt;chr&amp;gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h4 id=&quot;extract-county-code-and-remove-lan&quot;&gt;Extract county code and remove lan&lt;/h4&gt;
&lt;p&gt;As we only want to plot the county data, we remove the larger Lan&lt;/p&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;SCBdata&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;kod &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;unlist&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;lapply&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;strsplit&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;SCBdata&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;split&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39; &amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; &lt;span class=&quot;kr&quot;&gt;function&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;p&quot;&gt;{&lt;/span&gt;x&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]}))&lt;/span&gt;
SCBdata &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; SCBdata&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;grep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;VR&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; SCBdata&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;kod&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; invert&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;T&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),]&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h4 id=&quot;clean-data-and-make-interactive&quot;&gt;Clean data and make interactive&lt;/h4&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;sweden_map &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; map_kn &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
	select&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;leaflet_long&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; leaflet_lat&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; knkod&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; knnamn&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; lnnamn&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
	rename&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;long &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; leaflet_long&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; lat&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; leaflet_lat&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; region&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;knkod&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; subregion&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;knnamn&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
	fortify&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
        &lt;span class=&quot;kp&quot;&gt;unique&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt;

SCBdata &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; SCBdata&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBdata&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;kod&lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt;sweden_map&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;,]&lt;/span&gt;

SCBmelt &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; melt&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;SCBdata&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;region&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;parti mm&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;kod&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;
SCBmelt&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;value&lt;span class=&quot;o&quot;&gt;==&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;..&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,]&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;value &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;value &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;as.numeric&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;


SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;tip &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;paste0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;&amp;quot;&amp;lt;b&amp;gt;&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;sub&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;.*? (.+)&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;\\1&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;region&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;&amp;lt;/b&amp;gt; &amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;
&lt;span class=&quot;s&quot;&gt;&amp;quot;&amp;lt;br&amp;gt;&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;paste0&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;round&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;value&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;%&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;variable&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;gsub&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;Andel röster \\(av giltiga röster\\) &amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;variable &lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

&lt;span class=&quot;kp&quot;&gt;colnames&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;SCBmelt&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;region&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;parti&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;kod&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;year&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;percent&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;tip&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;

SCBmelt &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; SCBmelt&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;grep&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;ogiltiga valsedlar|ej röstande&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; invert&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;bp&quot;&gt;T&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;),]&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h4 id=&quot;create-colour-for-each-party&quot;&gt;Create colour for each party&lt;/h4&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;unique&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-text&quot; data-lang=&quot;text&quot;&gt;&lt;span&gt;&lt;/span&gt;## [1] &amp;quot;Moderaterna&amp;quot;         &amp;quot;Centerpartiet&amp;quot;       &amp;quot;Folkpartiet&amp;quot;        
## [4] &amp;quot;Kristdemokraterna&amp;quot;   &amp;quot;Miljöpartiet&amp;quot;        &amp;quot;Socialdemokraterna&amp;quot; 
## [7] &amp;quot;Vänsterpartiet&amp;quot;      &amp;quot;Sverigedemokraterna&amp;quot; &amp;quot;övriga partier&amp;quot;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;#129B93&amp;quot;&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;Socialdemokraterna&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;firebrick2&amp;quot;&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;Moderaterna&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;deepskyblue4&amp;quot;&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;Centerpartiet&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;darkgreen&amp;quot;&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;Folkpartiet&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;dodgerblue3&amp;quot;&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;Kristdemokraterna&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;navy&amp;quot;&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;Miljöpartiet&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;green3&amp;quot;&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;Vänsterpartiet&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;red3&amp;quot;&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;Sverigedemokraterna&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;goldenrod3&amp;quot;&lt;/span&gt;
SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;övriga partier&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;quot;gray52&amp;quot;&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;h4 id=&quot;plot-data&quot;&gt;Plot data&lt;/h4&gt;

&lt;figure class=&quot;highlight&quot;&gt;&lt;pre&gt;&lt;code class=&quot;language-r&quot; data-lang=&quot;r&quot;&gt;&lt;span&gt;&lt;/span&gt;partiPlot &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; SCBmelt&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;SCBmelt&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;year&lt;span class=&quot;o&quot;&gt;==&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;2014&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,]&lt;/span&gt;
plotlist &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;list&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;c1&quot;&gt;# create empty list to fill with plots&lt;/span&gt;
&lt;span class=&quot;kr&quot;&gt;for&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;i &lt;span class=&quot;kr&quot;&gt;in&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;1&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;:&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;length&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;unique&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;partiPlot&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti&lt;span class=&quot;p&quot;&gt;)))&lt;/span&gt;
  &lt;span class=&quot;kp&quot;&gt;local&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;({&lt;/span&gt;
    i &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; i
    &lt;span class=&quot;c1&quot;&gt;# filter data to only contain current party&lt;/span&gt;
    plotdata &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; partiPlot &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt; filter&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;parti &lt;span class=&quot;o&quot;&gt;%in%&lt;/span&gt; &lt;span class=&quot;kp&quot;&gt;unique&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;partiPlot&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;])&lt;/span&gt;
    plotdata&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;Long &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;all&amp;#39;&lt;/span&gt;
    plotdata&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;Long&lt;span class=&quot;p&quot;&gt;[&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;as.numeric&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;plotdata&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;kod&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;&amp;lt;&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0563&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;-&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;south&amp;#39;&lt;/span&gt;
    &lt;span class=&quot;c1&quot;&gt;# save plot as list element  &lt;/span&gt;
    plotlist&lt;span class=&quot;p&quot;&gt;[[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;]]&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;&amp;lt;&amp;lt;-&lt;/span&gt;    plotdata &lt;span class=&quot;o&quot;&gt;%&amp;gt;%&lt;/span&gt;
                                ggplot&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt; aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;kod&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;percent&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; frame &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; year&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt; 
                                geom_map_interactive&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;data&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;plotdata&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; map&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;sweden_map&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; aes&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;fill&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;percent&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; 
                                tooltip&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;tip&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; map_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;kod&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; data_id&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;kod&lt;span class=&quot;p&quot;&gt;),&lt;/span&gt; 
                                colour&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;white&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; size&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;0.05&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
                                expand_limits&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;x &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; sweden_map&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;long&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; y &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; sweden_map&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;lat&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
                                theme_void&lt;span class=&quot;p&quot;&gt;()&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
                                scale_fill_gradient2&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;low&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;#F4F4F4&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; high&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;unique&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;plotdata&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;cols&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt; &lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
                                theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;legend.position&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;#39;none&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;)&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
                                ggtitle&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;kp&quot;&gt;unique&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;partiPlot&lt;span class=&quot;o&quot;&gt;$&lt;/span&gt;parti&lt;span class=&quot;p&quot;&gt;)[&lt;/span&gt;i&lt;span class=&quot;p&quot;&gt;])&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
                                theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;plot.background &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_rect&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;fill &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;s&quot;&gt;&amp;#39;#999999&amp;#39;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;o&quot;&gt;+&lt;/span&gt;
                                theme&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;line &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_blank&lt;span class=&quot;p&quot;&gt;(),&lt;/span&gt;plot.title &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; element_text&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;hjust &lt;span class=&quot;o&quot;&gt;=&lt;/span&gt; &lt;span class=&quot;m&quot;&gt;0.5&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;span class=&quot;c1&quot;&gt;#+&lt;/span&gt;
                                &lt;span class=&quot;c1&quot;&gt;#facet_zoom(xlim = c(10, 18), ylim = c(55, 60), zoom.size = 2)&lt;/span&gt;
&lt;span class=&quot;p&quot;&gt;})&lt;/span&gt;
&lt;span class=&quot;kp&quot;&gt;do.call&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;&lt;span class=&quot;s&quot;&gt;&amp;quot;grid.arrange&amp;quot;&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; &lt;span class=&quot;kt&quot;&gt;c&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;(&lt;/span&gt;plotlist&lt;span class=&quot;p&quot;&gt;,&lt;/span&gt; ncol&lt;span class=&quot;o&quot;&gt;=&lt;/span&gt;&lt;span class=&quot;m&quot;&gt;3&lt;/span&gt;&lt;span class=&quot;p&quot;&gt;))&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/figure&gt;

&lt;p&gt;&lt;img src=&quot;/assets/Rfig/unnamed-chunk-6-1.svg&quot; alt=&quot;plot of chunk unnamed-chunk-6&quot; /&gt;&lt;/p&gt;

</description>
        <pubDate>Sat, 17 Mar 2018 00:00:00 -0400</pubDate>
        <link>http://jespermaag.github.io/blog/2018/SwedenElection/</link>
        <guid isPermaLink="true">http://jespermaag.github.io/blog/2018/SwedenElection/</guid>
        
        
        <category>jekyll</category>
        
        <category>update</category>
        
      </item>
    
  </channel>
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