The PCAviz R package provides a simple interface for quickly creating visually compelling plots from Principal Components Analysis (PCA) and accompanying data.
Install the most recent version of the PCAviz package using devtools:
install.packages("devtools")
devtools::install_github("NovembreLab/PCAviz",build_vignettes = TRUE)Alternatively, to install and test PCAviz, run the following commands in the shell:
R CMD build PCAviz
R CMD check --as-cran PCAviz_0.3-37.tar.gz
R CMD INSTALL PCAviz_0.3-37.tar.gzNote that these commands require that the dependencies have already been installed. See the DESCRIPTION file for details.
Load PCAviz into the R environment, and get an overview of the package:
library(PCAviz)
help(package = PCAviz)Explore the vignettes:
vignette("iris")
vignette("popres")
vignette("regmap")These are the R commands to build the website (make sure you are connected to Internet while running these commands):
library(pkgdown)
build_site(mathjax = FALSE)Version 1.1.0 of pkgdown was used.
This is the current structure of the R package:
├── DESCRIPTION
├── LICENSE
├── NAMESPACE
├── _pkgdown.yaml
├── README.md
├── R
│ └── pcaviz.R
├── data
│ ├── popres.RData
│ └── regmap.RData
├── inst
│ └── CITATION
├── man
├── tests
│ ├── testthat
│ │ └── test_pcaviz.R
│ └── testthat.R
└── vignettes
├── iris.Rmd
├── popres.Rmd
└── regmap.Rmd
These are the additional files used in development of the package:
├── NOTES.md
├── inst
│ ├── curate
│ ├── original-demos
│ │ ├── R-2.5
│ │ ├── R-3.2
│ │ ├── README.md
│ │ ├── SETUP.md
│ │ └── functions.R
│ └── original-files