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Commit 4501b627 authored by Argyris Z's avatar Argyris Z
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Added some instructions on how to run the code

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## Introduction
This directory contains all the code and data needed to recreate the analysis of the Gene Regulatory Network (GRN) in Figure 1 using
spatial genetic information in the Atlas.
## Scripts and Methods
## Main Contacts
Setup (manual) assuming you have Python 3 (and pip) installed:
```
pip install -r ../requirements.txt
pip install notebook
pip install ../common/
```
or use the Docker image (see main directory) and cd to this directory.
To run the code that analyses the GRN and produces new hypotheses using spatial genetic information as well
as creating and testing random networks used as a baseline do the following:
```
python mk_fs.py
jupyter nbconvert --to notebook --execute random_net.ipynb
jupyter nbconvert --to notebook --execute fig6.ipynb
```
If you just want the subsequent analysis code that generates the figures in the paper,
```
jupyter nbconvert --to notebook --execute fig6.ipynb
```
in which case the precomputed results available in this directory (.pkl files) will be used instead.
## Main Contacts
Argyris Zardilis argyris.zardilis@slcu.cam.ac.uk
## Introduction
This directory contains code and data needed to recreate all the
growth and growth anisotropy analysis figures in the article.
## Scripts and Methods
Setup (manual) assuming you have Python 3 (and pip) installed:
```
pip install -r ../requirements.txt
pip install notebook
pip install ../common/
apt-get install parallel
```
or use the Docker image (see main directory) and cd to this directory.
To run things:
```
# run specific for flower 1
python -c 'import growth_control; growth_control.go()'
jupyter nbconvert --to notebook --execute grates.ipynb
jupyter nbconvert --to notebook --execute anisos.ipynb
# run for all flowers
parallel ./run-grate-distrs.sh {} ::: 1 2 3 4 5
parallel ./run-aniso-distrs.sh {} ::: 1 2 3 4 5
```
or use the `run.sh` script that contains all the above instructions.
## Main Contacts
Argyris Zardilis argyris.zardilis@slcu.cam.ac.uk
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