R code that reproduces all analyses, results and figures in the manuscript Møller, TE, et al. (2022) Mapping microbial abundance and prevalence to changing oxygen concentration in deep-sea sediments using machine learning and differential abundance. In Frontiers in Microbiology. DOI:to come.
All code was run and tested using R version 3.6.3 on a computer with the ubuntu linux 18.04 OS.
The files in the script must be run in the order specified within the README_FIRST_processing_script.R file in order to properly work.
Additionally, the data required to run the scripts may be found as supplements to the referenced article.
These must be stored within the R working directory in a separate folder named data in order to run as intended.
Furthermore, the files cmultRepl_inhouse.R, differential_expression_helpers.R, get_unique_taxa.R, ggbarplot_gen.R,
multiplot.R, o2_concentration_helpers.R, pca2ggplot.R, process_tax_file.R, remove_empty_columns.R and svm_output_helpers.R
should be stored in a subdirectory named auxillary_functions.
Files used for sequence processing do not have to be part of the folder structure described above.