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(This article was first published on <strong><a href="http://moderndata.plot.ly/manhattanly-r-package-for-interactive-manhattan-plots/"> R – Modern Data</a></strong>, and kindly contributed to <a rel="nofollow" href="http://www.r-bloggers.com/">R-bloggers)</a> </div>
<h3>Introduction</h3>
<p>The new R package, <a target="_blank" href="https://cran.r-project.org/web/packages/manhattanly/">manhattanly</a>, creates interactive manhattan plots using the <a target="_blank" href="https://plot.ly/">plotly.js</a> engine. The plots are usable from the R console, the RStudio viewer pane, <code>R Markdown</code> documents, in Shiny apps, embeddable in websites and can be exported as <code>.png</code> files. By hovering the mouse over a point, you can see annotation information such as the SNP identifier and GENE name. You can also drag a rectangle to zoom in on a region of interest and then export the image as a <code>.png</code> file.</p>
<p>Visit the <a target="_blank" href="https://github.com/sahirbhatnagar/manhattanly">package website</a> for full details and example usage. </p>
<h3>Quick Start</h3>
<p>The following three lines of code will produce the plot below</p>

<pre>install.packages(&quot;manhattanly&quot;)
library(manhattanly)
manhattanly(HapMap, 
            snp = &quot;SNP&quot;, gene = &quot;GENE&quot;, 
            annotation1 = &quot;ZSCORE&quot;, annotation2 = &quot;EFFECTSIZE&quot;, 
            highlight = significantSNP)</pre>

<p><iframe height="800" width="900" src="https://plot.ly/~sahirbhatnagar/52.embed"></iframe></p>
<h3>Related Work</h3>
<p>This work is based on the <a target="_blank" href="https://github.com/stephenturner/qqman">qqman</a> package by <a target="_blank" href="http://stephenturner.us/">Stephen Turner</a>. It produces similar manhattan plots as the <code>qqman::manhattan</code> function; the main difference here is being able to interact with the plot, including extra annotation information and seamless integration with HTML.</p>
<p>The splitting of the tasks into data pre-processing and plot rendering is inspired by the <a target="_blank" href="https://cran.r-project.org/web/packages/heatmaply/vignettes/heatmaply.html">heatmaply</a> package by <a target="_blank" href="http://www.r-statistics.com/">Tal Galili</a>.</p>
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<div>To <strong>leave a comment</strong> for the author, please follow the link and comment on their blog: <strong><a href="http://moderndata.plot.ly/manhattanly-r-package-for-interactive-manhattan-plots/"> R – Modern Data</a></strong>.</div>
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