Code and Data to reproduce figures in -> Relationship of bacterial phylotype with specialized metabolite production in the culturable microbiome of two freshwater sponges

To reproduce the figures/analyses from this work, download the entire Zenodo code/data release (warning- this is a few GB large)

Due to a requirement of the mass spectrometry conversion software, data was first converted on a Windows machine to an IDBac database using the script `R/convert_from_bruker.R`. ProteoWizard must be installed before running this script.

The resulting SQLite database is available within the Zenodo code/data release

To reproduce the figures/analyses you will need to download the Zenodo code/data release and have Docker installed

To build the Docker image from scratch open a terminal at `sponge_analysis` and run the following command (warning: this is not fast):

docker build -f dockerfile --tag chasemc2/sponge_manuscript .

The image has also been archived within the Zenodo code/data release as "docker_image.tar.gz"

To build the notebooks/create the figures open a terminal at the top directory of the downloaded Zenodo code/data release and run the following three commands :

docker run --user `id -u` --rm -ti -v${PWD}:/top -w/top/analyses chasemc2/sponge_manuscript Rscript -e 'rmarkdown::render("analysis.Rmd", params = list(conditions = "all") , output_file = "all_isolates.html")'

docker run --user `id -u` --rm -ti -v${PWD}:/top -w/top/analyses chasemc2/sponge_manuscript Rscript -e 'rmarkdown::render("analysis.Rmd", params = list(conditions = "matched"), output_file = "matched_isolates.html")'

docker run --user `id -u` --rm -ti -v${PWD}:/top -w/top/analyses chasemc2/sponge_manuscript Rscript -e 'rmarkdown::render("16s_analysis.Rmd")'