manhattanly v0.2.0

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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.

Readme

Travis-CI Build Status CRAN_Status_Badge

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manhattanly

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

Contact

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.

Functions in manhattanly

Name Description
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
No Results!

Vignettes of manhattanly

Name
manhattanly.Rmd
No Results!

Last month downloads

Details

Type Package
Date 2016-11-17
LazyData true
VignetteBuilder knitr
License MIT + file LICENSE
URL https://github.com/sahirbhatnagar/manhattanly/, http://sahirbhatnagar.com/manhattanly/
BugReports https://github.com/sahirbhatnagar/manhattanly/issues
RoxygenNote 5.0.1
NeedsCompilation no
Packaged 2016-11-15 23:55:25 UTC; sahir
Repository CRAN
Date/Publication 2016-11-16 01:56:53

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