rsaccharis

A rendering package for creating phylogenetic trees from SACCHARIS 2 .json and .tree files, in the R statistical computing language.

Installation

Option 1:

• The rsaccharis package is packaged for conda and distributed on the bioconda channel. To install r-saccharis on it's own, simply use conda install r-saccharis after setting up the bioconda channel.

Option 2:

• You can install the latest version of the repository by using the devtools package in r and the following command:

  devtools::install_github("saccharis/rsaccharis")

  This will automatically download and build the package using the latest version of the main branch of the git repo. BEWARE that this is not guaranteed to be stable and functional, as beta release code may be pushed to the repo before being fully tested.

Option 3:

• You can install the latest R package by going to the releases section on the GitHub sidebar, downloading the latest rsaccharis_x.x.x.tar.gz archive and then using install.packages(file_name_and_path, repos = NULL, type="source") in R or RStudio to install using the downloaded archive.

Usage

1. Change your working directory to where your SACCHARIS output files are located.

2. library(rsaccharis) This initializes the R package.

3. A_load_data() This first function will load in all the data, and it will prompt you to enter the file name for the .json and .tree output files from SACCHARIS.

4. B_plots_all() This will then just go through all the plotting to make our default plots.

All plots are produced as PDFs, and can be further edited in vector graphics software (e.g. Inkscape). The .csv file producted by the R package includes all the metadata from CAZy as well as the assigned Tree IDs produced during plotting.

Note to maintainers

Check MAINTENANCE.md for instructions on updating the packaging and uploading new versions to package repositories.