A Mitochondrial Manhattan Plot

November 6, 2013

(This article was first published on Getting Genetics Done, and kindly contributed to R-bloggers)

Manhattan plots have become the standard way to visualize results for genetic association studies, allowing the viewer to instantly see significant results in the rough context of their genomic position.  Manhattan plots are typically shown on a linear X-axis (although the circos package can be used for radial plots), and this is consistent with the linear representation of the genome in online genome browsers.  Many genetic studies often overlook the other genome within all our cells, the mitochondrial genome. This circular molecule has been shown to be associated (albeit inconsistently) with many disease traits, and functional variants from this genome are now included in most genotyping platforms.

Thanks to the clever work of several graduate students in the Vanderbilt Center for Human Genetics Research (most notably Ben Grady), mitochondrial genetic associations can be visualized in the context of key regions of the mitochondrial genome using a radial plot in the R package ggplot2.

To make this plot, download the code and run the script (alternatively open the script in R and run interactively):

On the command line:

git clone [email protected]:stephenturner/solarplot.git
cd solarplot
R CMD BATCH solarplot.R

GitHub: Mitochondrial solar plot code and data

To leave a comment for the author, please follow the link and comment on their blog: Getting Genetics Done.

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