Installing Packages

The most common place to get packages from is CRAN. To install packages from CRAN you use install.packages(“packagename”). For instance, if you want to install the ggplot2 package, which is a very popular visualization package you would type the following in the console:

# install package from CRAN
install.packages("ggplot2") 

As previously stated, packages are also available through Bioconductor and GitHub. Bioconductor provides R packages primarily for genomic data analyses and packages on GitHub are usually under development but have not gone through all the checks and balances to be loaded onto CRAN (aka download and use these packages at your discretion). You can learn how to install Bioconductor packages here and GitHub packages here.

Loading Packages

Once the package is downloaded to your computer you can access the functions and resources provided by the package in two different ways:

# load the package to use in the current R session
library(packagename)

# use a particular function within a package without loading the package
packagename::functionname 

For instance, if you want to have full access to the tidyr package you would use library(tidyr); however, if you just wanted to use the gather() function which is provided by the tidyr package without fully loading tidyr you can use tidyr::gather(…) (here … just represents the arguments that you would include in this function)

Getting Help on Packages

For more direct help on packages that are installed on your computer you can use the help and vignette functions. Here we can get help on the ggplot2 package with the following:

help(package = "ggplot2")     # provides details regarding contents of a package
vignette(package = "ggplot2") # list vignettes available for a specific package
vignette("ggplot2-specs")     # view specific vignette 
vignette()                    # view all vignettes on your computer 

Note that some packages will have multiple vignettes. For instance vignette(package = “grid”) will list the 13 vignettes available for the grid package. To access one of the specific vignettes you simply use vignette(“vignettename”).