Published July 22, 2021 | Version v1
Dataset Open

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

Authors/Creators

Contributors

Project leader:

  • 1. Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL
  • 2. Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Genova, Italy
  • 3. Dipartimento Medicina Veterinaria, Università di Sassari, Sassari, Italy

Description

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The image has also been archived within the Zenodo code/data release as "docker_image.tar.gz"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

 

Files

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