Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation

This is the repo of the code containing the necessary functions to reproduce the analyses and figure panels presented in our paper.

Installation and Setup

1. Clone the repository.
2. Download the data from https://zenodo.org/records/17956270?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6IjczOWNlZDI0LTFlM2EtNGJjNy1iOTQwLTVlNDRjYTMzMjRlZCIsImRhdGEiOnt9LCJyYW5kb20iOiJkMGY2YjE2MjA4MDk0OWE2NTFiZjYxNzM4ZTI1YTgzZSJ9.Krydne1ABLYQe4DYJi13XDA6LZZ5mSfEpAeeTy32doKHx45VSEQEj8LUXBhq4CtHB1-Yfpmuih_lPA_jW-iaxg
3. Download from 'Moor, A. E., Harnik, Y., Ben-Moshe, S., Massasa, E. E., Rozenberg, M., Eilam, R., ... & Itzkovitz, S. (2018). Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis. Cell, 175(4), 1156-1167.' (a) table_A_LCM_TPM_values.tsv (b) table_D_zonation_reconstruction.tsv and save them in an additional director 'in_vivo_villus_data' b. at this point the directories should be in the following structure: in a directory path of your choosing which will be defined in the variable HOME_DIR: ---in_vivo_villus_data --table_A_LCM_TPM_values.tsv --table_D_zonation_reconstruction.tsv ---- sprinkled -- 12hr --roi1 --roi2 --roi3 -- 72hr --roi1 --roi2 --roi3 --roi4 ---- unperturbed --- monolayer_erosion
4. change the directory path for HOME_DIR in utils/constants.py to where you have saved these directories in the format explained above
5. download packages using the requirements.txt file found in utils subdirectory
6. under paper/plotScripts exists the python file plotALL.py includes a function plot_all_figures() , call and run it in main.py
7. the plots shown in the figures will be saved to paper/graphs/ to four different directions a. autonomous_zonation_figure_plots b. zonation_plasticity_plots c. neighborhood_zone_adoption_plots d. continuous_regenerative_figure_plots

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