This is a simple use case of using the D3ManhattanPlots HTMLWidget for R to generate interactive manhattan plots for genome wide association studies (GWAS). The package/widget are on github where you are encuraged to submit issues for desired features (or pull requests for the more adventurous).

What is this plot?

Each balloon and string represents a single snp, or base pair on the genome. The height of the bar represents its significance of correlation with a trait or phenotype. These data are a subsection (100 most significant snps when stratified by the male gender) of the data from Complement factor H polymorphism in age-related macular degeneration. Klein et al. 2005.

How to use:

First we load the library and data:

d = sampleVals

Take a quick peak at the data:

##   X        SNP        PVal
## 1 1   rs848208 0.009142308
## 2 2 rs10492990 0.011585225
## 3 3   rs725389 0.019716484
## 4 4 rs10489155 0.007363745
## 5 5 rs10493028 0.014088796
## 6 6 rs10493029 0.014088796

…and plot:


Some more examples:

If we want to see it with slightly less homogeneous data we can use an included randomly generated dataset.


We can also play around with some of the options.

manhattanPlot(random, sigLine = FALSE, animationSpeed = 0)