Manhattanly: R package for Interactive Manhattan Plots

June 13, 2016
By

(This article was first published on R – Modern Data, and kindly contributed to R-bloggers)

Introduction

The new R package, manhattanly, creates interactive manhattan plots using the plotly.js engine. The plots are usable from the R console, the RStudio viewer pane, R Markdown documents, in Shiny apps, embeddable in websites and can be exported as .png 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 .png file.

Visit the package website for full details and example usage.

Quick Start

The following three lines of code will produce the plot below

install.packages("manhattanly")
library(manhattanly)
manhattanly(HapMap, 
            snp = "SNP", gene = "GENE", 
            annotation1 = "ZSCORE", annotation2 = "EFFECTSIZE", 
            highlight = significantSNP)

Related Work

This work is based on the qqman package by Stephen Turner. It produces similar manhattan plots as the qqman::manhattan function; the main difference here is being able to interact with the plot, including extra annotation information and seamless integration with HTML.

The splitting of the tasks into data pre-processing and plot rendering is inspired by the heatmaply package by Tal Galili.

To leave a comment for the author, please follow the link and comment on their blog: R – Modern Data.

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