IntAssoPlot: Visualize Genome-Wide Association Study with Gene Annotation and Linkage Disequiblism

Availability

Installation

install compiler

The install_github(), in the R package remotes, requires that you build from source, thus make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.

For Windows system, rtools, a compiler, is required and can be found at https://cran.r-project.org/bin/windows/Rtools/.
For Ubuntu/Linux system, compilers could be installed by the command: sudo apt-get install libcurl4-openssl-dev libssl-dev. For more information, please see https://stackoverflow.com/questions/20923209/problems-installing-the-devtools-package.

install R package devtools and remotes

install.packages(c("devtools","remotes"))

install depended packages, including ggplot2, SNPRelate, ggrepel, gdsfmt and reshape2

#ggplot2, ggrepel, and reshape2 are installed from CRAN
install.packages(c("ggplot2","ggrepel","reshape2"))
#SNPRelate and gdsfmt are installed from Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("SNPRelate","gdsfmt"))

install IntAssoPlot from GitHub:

library(remotes) # version 2.1.0
#download, build, and install IntAssoPlot without creating vignette
install_github("whweve/IntAssoPlot")
#download, build, and install IntAssoPlot with creating vignette
install_github("whweve/IntAssoPlot",build=TRUE,build_vignettes = TRUE)

example

#load IntAssoPlot
library(IntAssoPlot)
# an example of association plot at a gene level
example("IntGenicPlot")
# an example of association plot at a region level
example("IntRegionalPlot")

Citation

*If IntAssoPlot is used in your work, considering cite IntAssoPlot.

#get the citation in R enviroment
citation("IntAssoPlot")

Fengyu He, Shuangcheng Ding, Hongwei Wang and Feng Qin. IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix. Frontiers in Genetics, 2020, 11, 260. doi: 10.3389/fgene.2020.00260.

whweve / IntAssoPlot

readme