This folder contains scripts and notebooks for the analysis of a dataset of publications where a microbial community was used to produce a target compound. Python functions to make all plots included in the thesis are found in plotting.py and network_visualisations.py.
| Folder | Description |
|---|---|
| data_exploration/ | Notebooks that were used in the initial data exploration |
| plots/ | A folder of graphs and plots |
| File | Description |
|---|---|
| all_articles.csv | Annotated dataset of publications |
| co-occurence_metrics.ipynb | Notebook for network analysis |
| defined_articles.csv | Subset of litearture dataset for defined consortia |
| maps.py | Dictionaries mapping from compounds to compound groups |
| network_visualisations.py | Functions to create co-occurrence networks |
| plot_generator.ipynb | Notebook used to generate plots for thesis |
| plotting.py | Python functions for plotting |