Interactive Q-Q and Manhattan Plots Using 'plotly.js'
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.
- Issues: https://github.com/sahirbhatnagar/manhattanly/issues
- Pull Requests: https://github.com/sahirbhatnagar/manhattanly/
- e-mail: firstname.lastname@example.org
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.
Functions in manhattanly
|volcanoly||Creates a plotly volcano plot|
|HapMap||Subset of HapMap data with simulated GWAS results|
|manhattanly||Creates a plotly manhattan plot|
|qqly||Creates a plotly Q-Q plot|
|significantSNP||Character vector of SNPs to highlight|
Vignettes of manhattanly
Last month downloads
|License||MIT + file LICENSE|
|Packaged||2016-11-15 23:55:25 UTC; sahir|
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