This github repository is the data analysis portion associated with the preprint and subsequent manuscript by Heal et. al "Marine community metabolomes carry fingerprints of phytoplankton community composition". Published in mSystems, DOI: 10.1128/mSystems.01334-20.
Note that these scripts, figures, and tables have been corrected according to the author correction for Heal et. al "Marine community metabolomes carry fingerprints of phytoplankton community composition". Published in mSystems. Correction DOI: 10.1128/msystems.01086-22.
The Control.Rmd file is the data analysis notebook, which performs quality control, B-MIS normalization, identification, k-means clustering and bootstrapping.
- Sources scripts from 'SourceCode' folder
- Sources files from 'MetaData' and 'RawOutput' folders
- Writes products into the 'Intermediates' folder
The Figures.Rmd file is the figure creation notebook. Main text and supplemental figures are both created (not separated in the output).
- Sources scripts from 'Figures/Code' folder
- Sources files from 'Intermediates', 'Figures/Annotations', and 'Figures/Molecules' folders
- Writes products figures into the 'Manuscript_figures' and 'Presentation_figures' folders
The Tables.Rmd is the table creation notebook. Tables are made into Latex formulated tables except the ones provided as xcel document, which are made as separate .csv and then combined.
- Sources scripts from 'Tables/Code' folder
- Sources files from 'Intermediates' folder
- Writes products figures into the 'Manuscript_tables' and 'Manuscript_tables/SuppTables' folders