mtag-Spatial_Abx_Manuscript

Code for the spatial analysis of the gut microbiota of mice before and after antibiotics exposure.

To regenerate the neighborhood analysis:

Run the python scripts in bin/. Run them by first setting up bug_config.py according to the instructions within. Then run each python script in order: count_bugs_1.py, search_nhoods_2corrected.py, plot_study_heatmap_3.py. Or alternatively to run them all together use run_all_files.py

To regenerate the figures in the spatial antibiotics manuscript:

Run the R scripts first to pre-process the data. Then run the corresponding Rmd file to regenerate the figures.