oeu

Requirements

You'll need the R packages:

• ggplot2
• dplyr
• optparse
• reshape2

You can install a package by running install.packages("foo") in R.

Installation

These are standalone scripts and shouldn't require installation. You can run them as if they were shell scripts using Rscript.

Usage

The two R executables oeu.R and make-plots.R can call OTUs and make plots of OTUs in each OEU.

Both scripts use optparse, so you can call, say, oeu.R --help to get reminders about the order of arguments.

oeu.R

This script takes an OTU table that:

• is normalized (i.e., it shows relative abundance in sample),
• is preprocessed (i.e., replicated have been pooled, bad OTUs/samples have been removed),
• has OTU names in the first column (preferably under "OTU_ID"), and
• is tab-separated.

This script produces a "groups file", which is a tab-separated file with two columns: OTU ID and group number.

make-plots.R

This script takes

• an OTU table, the same kind that fed to oeu.R, and
• a groups file, the same kind produced by oeu.R.

The script will produce a one plot per OEU in a directory you choose.