Packages¶
We’ve so far used a lot of fundamental functions in R, the sort without which you couldn’t execute simple scripts at all. When performing data analysis however, there may well be better or more specific functions available for what you are trying to do. R is very flexible because it allows the loading of additional packages created by the user community to enhance and add functionality.
Loading a Package¶
To load a package, we use the library function. Once loaded, all of the functions inside the package become available to R. If a function should have the identical name to an existing function, it will mask the current version and refer instead to the version in the package, and give you a warning.
# For instance if we want to work with phylogenetic trees
# If you look at the example.tree file itself you can see the format is non-intuitive
library(ape)
tree <- read.tree("/science/teaching/example.tree")
# Packages can load other packages and mask functions
library(Hmisc)
Installing a Package¶
For native R packages, the install.packages function allows installation of new packages into a personal user library.
# Install a new package
install.packages("beeswarm")
# Load the package and demonstrate
library(beeswarm)
random_numbers <- rnorm(100)
beeswarm(random_numbers)
beeswarm(random_numbers,method="hex")
If the package has not been submitted to the standard R repositories, but exists for instance on github, the package devtools allows you to install it directly - you may have to install it yourself using the method above.
# Load devtools
library(devtools)
# Install a package from github
install_github(https://github.com/Gibbsdavidl/CatterPlots)
# Load the package and demonstrate
library(catterplots)
x <- rnorm(10)
y <- rnorm(10)
multicat(x,y)
Bioconductor¶
Bioconductor is a popular set of specific bioinformatics tools, such as DESeq2 and Biostrings, that need to be installed via the BiocManager package.
# First of all install the manager
install.packages("BiocManager")
# Use it directly without loading
BiocManager::install("Biostrings")
# Load the package and demonstrate
library(Biostrings)
cdss <- read.DNAStringSet("ecoli/EC_K12_MG1655_genomic.fna")
subseq(cdss,1,10)