Linking microbial communities to ecosystem functions: what we can learn from genotype-phenotype mapping in organisms

This is the project directory for the Royal Society paper cited below. All intermediate data files (in output/) and all figures (in figures/) have been created so the final script 7_analysis.R can be run immediately to recreate figures and results. Otherwise, run scripts in order of numbering to recreate the output.

How to cite this manuscript:

Morris, Andrew, Meyer, Kyle, and Bohannan, Brendan 2020. Linking microbial communities to ecosystem functions: what we can learn from genotype–phenotype mapping in organisms. Phil. Trans. R. Soc. B 375:20190244. https://doi.org/10.1098/rstb.2019.0244

Data are from:

Meyer, KM, Hopple, AM, Klein, AM, Morris, AH, Bridgham, SD, Bohannan, BJM. Community structure – Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function. Mol Ecol. 2020; 29: 1806– 1819. https://doi.org/10.1111/mec.15442

Data

raw_data/ contains raw data as received from colleagues. This is never modified.

output/ is where modified data files are saved.

talapas-output/ is where model output from the talapas HPC cluster are saved.

figures/ contains figures output from scripts

R/ contains scripts that run plus helper functions

Scripts

R/

0_setup.R has code to install all required packages. May need to modify to address your local dependencies.

1_clean_sample_data.R takes in the raw sample date file and munges it for analysis.

2_clean_asvs.R takes in the raw ASV table and munges it for analysis.

3_geodist_processing.R takes in the raw GPS data and converts it to meters using UTM.

4_var_stab_transform.R performs the varianceStabilizingTransformation from DESeq2.

5_combine_data.R pulls in the asvs, sample data, and GPS data and combines them into a single data structure.

6_var_comp.R is the script that fits variance component models from the raw data. This is typically submitted to the cluster and the output from the cluster is scped into talapas-output/.

7_analysis.R is the primary file that presents the results and creates the figures and tables.

functions.R contains the user-made functions specific to this project.

License

Software and code licensed under the MIT license. Does not include datasets under raw_data/.