bilateria

Code for generating figures and statistics for bilaterian animal microbiome project. The bulk of the code for this project can be found in bilateria.R with additional code in the speciesArea directory.

R libraries

You will need to have the following R libraries installed for various code chunks:

pander ape phytools phylobase vegan ggplot2 dplyr reshape2 pheatmap dnar Rtsne lattice grid gridExtra ggimage phyloseq eclectic ade4

Set work_dir

Replace "/home/kevin/projects/bilateria" with your working directory on line 24 of bilateria.R

Define functions

Running the code under sections "Libraries", "Setup", and "Functions" is necessary before running any analysis code.

Running analysis code

The code from each analysis code chunk (e.g. "Figure 1") can be run independently from each other. Data is reset (re-loaded from OTU table and sample sheet) within each code chunk.

The speciesArea code can be run by calling make within that directory.