PCAviz

The PCAviz R package provides a simple interface for quickly creating visually compelling plots from Principal Components Analysis (PCA) and accompanying data.

Quick start

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.gz

Note 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")

How to build static HTML documentation

These are the R commands to build the website (make sure you are connected to Internet while running these commands):

pkgdown::build_site(mathjax = FALSE)

Version 1.1.0 of pkgdown was used.

What’s included

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