main module

main.py module is the main code that runs all analyses. It generates aggregated data based on the preprocessed and shuffled data.

To successfully tun the code, you need to have python version of 3.9 or higher installed on your machine. To install the required packages, run the following command in the terminal:

pip install -r requirements.txt

This will install all required packages.

generate_cross_experiment_spatial_significance_data

This function generates the data for the spatial significance analysis, as in Figures 1-3.

generate_per_sample_community_statistics

This function generates the data for the community statistics analysis, as in Figures 1-3.

Other executables

The following modules are preprocessing steps that are not executed by the main code.

arcos_shuffle_analysis

arcos_shuffle_analysis.py module is responsible for creating the data for the ARCOS shuffle analysis, as in Figure1. The main code doesn't run it directly, as this function is randomized and may result in different outputs from one execution to another.

arcos_hotspots_shuffle_analysis

arcos_hotspots_shuffle_analysis.py module is responsible for creating the data for the ARCOS hotspots shuffle analysis, as in Figure2. The main code doesn't run it directly, as this function is randomized and may result in different outputs from one execution to another.

preprocess_data

preprocess_data.py module is responsible for preprocessing the raw data received from the imaging. The main code doesn't run it directly, as we are using the preprocessed data. Tha module is included in the repository for reference.