# Cell Signalling Information

This code was used to generate part of the data for the paper "[The ability to sense the environment is heterogeneously distributed in cell populations](https://www.biorxiv.org/content/10.1101/2023.03.07.531554v2.abstract)" by Andrew Goetz*, Hoda Akl*, Purushottam D Dixit *contributed equally

doi: [https://doi.org/10.1101/2023.03.07.531554](https://doi.org/10.1101/2023.03.07.531554)

# Project Organization

This project is structured around the generation of figures for the paper. As a result, programs which are directly used for making a specific figure in the paper are stored in a directory reflects the figure and subfigure they are used to generate. "[Figure_Generating_Programs](Mutual_Information_Main/Figure_Generating_Programs)" is the main directory which contains all figure generating programs. Each figure generating program is stored in a directory along with a readme file which provides instructions for generating the data used to obtain the figure. All generated figure images are stored in "[Figures](Mutual_Information_Main/Figures)".

The "[functions](Mutual_Information_Main/functions/)" directory contains custom function libraries and encompasses the bulk of the machinery of the project.

The "[General_Data_Generation](Mutual_Information_Main/General_Data_Generation/)" directory contains programs used to generate essential data for plots but do not directly generate plots themselves.

The "[Initialization_File](Mutual_Information_Main/Initialization_File/)" directory contains the ".pth" file which may be used to add the project to sys.path.

The "[Mathematica_Moment_Code](Mutual_Information_Main/Mathematica_Moment_Code/)" directory contains mathematica code used to generate and process the moment closure equations.

# Setup

The raw data used in this code is stored [here](https://zenodo.org/record/7743531). To run any of the programs used in this project, download the raw data and place it in the [Mutual_Information_Main](Mutual_Information_Main) directory.

## Troubleshooting

Errors with custom function imports:
The Cell_signalling_information directory should be a sources root directory. This can be done by replacing the contents of [signaling_paths.pth](Mutual_Information_Main/Initialization_File/signaling_paths.pth) with the path to your "Cell_signaling_information" folder then adding it into your python's site-packages directory.

Errors with setting working directory:
The program automatically searches for the "Cell_signaling_information" directory, but in rare cases this will fail
There are two possible fixes:
1. Replace the contents of [signaling_paths.pth](Mutual_Information_Main/Initialization_File/signaling_paths.pth) with the path to your "Cell_signaling_information" folder then adding it into your python's site-packages directory.
2. Add the path to your "Cell_signaling_information" folder directly into the .py file just under the "# Cell_signaling_information path here" comment