Interactive Q-Q and Manhattan Plots Using 'plotly.js'

Create interactive manhattan, Q-Q and volcano plots that are usable from the R console, in 'Dash' apps, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a point to show details or drag a rectangle to zoom. A manhattan plot is a popular graphical method for visualizing results from high-dimensional data analysis such as a (epi)genome wide association study (GWAS or EWAS), in which p-values, Z-scores, test statistics are plotted on a scatter plot against their genomic position. Manhattan plots are used for visualizing potential regions of interest in the genome that are associated with a phenotype. Interactive manhattan plots allow the inspection of specific value (e.g. rs number or gene name) by hovering the mouse over a cell, as well as zooming into a region of the genome (e.g. a chromosome) by dragging a rectangle around the relevant area. This work is based on the 'qqman' package and the 'plotly.js' engine. It produces similar manhattan and Q-Q plots as the 'manhattan' and 'qq' functions in the 'qqman' package, with the advantage of including extra annotation information and interactive web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.

The goal of manhattanly is to create interactive manhattan, Q-Q and volcano plots

Installation

You can install manhattanly from CRAN:

install.packages("manhattanly")

Alternatively, you can install the development version of manhattanly from GitHub with:

install.packages("devtools")
devtools::install_github("sahirbhatnagar/manhattanly", build_vignettes = TRUE)

Vignette

See the online vignette for example usage of the functions.

Credit

This package is inspired by the qqman package by Stephen Turner. The pre-processing of the data in the manhattanly package is based on the qqman::manhattan and qqman::qq functions.

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

Related Work

• qqman
• D3ManhattanPlots

Contact

• Issues: https://github.com/sahirbhatnagar/manhattanly/issues
• Pull Requests: https://github.com/sahirbhatnagar/manhattanly/
• e-mail: [email protected]

Latest news

You can see the most recent changes to the package in the NEWS.md file

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.