You'll need the R packages:
- ggplot2
- dplyr
- optparse
- reshape2
You can install a package by running install.packages("foo") in R.
These are standalone scripts and shouldn't require installation. You can
run them as if they were shell scripts using Rscript.
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.
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.
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.