Create interactive Q-Q, manhattan and volcano plots that are usable from the R console, 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 by Stephen Turner 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
You can install
manhattanly from CRAN:
Alternatively, you can install the development version of
manhattanly from GitHub with:
install.packages("devtools")devtools::install_github("sahirbhatnagar/manhattanly", build_vignettes = TRUE)
See the online vignette for example usage of the functions.
You can see the most recent changes to the package in the NEWS.md file
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.
volcanolyfunction creates interactive volcano plots with automatic highlighting of points
evaluateargument deprecated (@thebioengineer, #4)
Introduction to manhattanlyvignette by using
html_document) which by default uses smaller plot sizes. See sahirbhatnagar.com/manhattanly for full vignette.
NEWS.mdfile to track changes to the package.