Custom Scripts from Lundberg et. al 2012 "Defining the core Arabidopsis thaliana root microbiome"

These R scripts were designed for specific analysis of samples in Lundberg et al. 2012.  We have documented these to be clear to us and to experienced R users, but the custom nature of these scripts makes their general utility limited. If the scripts are unclear, or for any specific tasks related to analysis not supported by these scripts, or for help in getting these scripts to work on your machine, please contact Jeff Dangl (

The "scripts" folder holds the scripts that perform analysis tasks. The scripts by D. Lundberg require access to the "functions" folder. The location of this folder is specified at the top of the scripts. You should check that the scripts point to the correct location of the "functions" folder before running them.

The "functions" folder holds the functions that are dependencies of some of the scripts in the "scripts" folder.  IMPORTANT: The function called "new_model_manipulator" interprets the generalized linear mixed modle (GLMM) results.  To work, this function must point to the correct directory of GLMM output. It is by default set up to point to the GLMM folder in the "workspace" folder.

The "workspace" folder is the default input and output directory for files in the scripts by D. Lundberg. The 'heatmap' and 'taxonomy_histograms' scripts require results from the generalized linear mixed model (GLMM) and the required GLMM results are already inside the workspace folder for convenience.

Zip Package of Scripts