Overview

This repository contains the code necessary to collect the data, run the analysis and render the figures/text for the paper at (TODO: add biorxiv link).

Highlights:

• All of the analysis is in a single notebook at analysis.ipynb.
• Logic for collecting and preparing Open Targets data is in the module analysis.py (more specifically here).
• The most recently rendered version of the paper is at paper/paper.pdf.
• The xrml.py module is a frozen, near-replica of https://github.com/related-sciences/xrml

Reproduction

Here are commands necessary to reproduce this analysis:

mamba env create --file environment.yml
conda activate paper

echo 'GOOGLE_CLOUD_PROJECT="<YOUR_PROJECT_NAME>"' > .env
export DATA_DIR="<YOUR_DATA_DIR>"
export CLI="analysis.py"
export OT_VERSION="23.12"

# This will download and extract all necessary datasets from a particular OT release
./bin/run_py --output_mode=dev -- $CLI \
export_features --version="$OT_VERSION" --output-path=$DATA_DIR

# This will run the analysis.ipynb notebook, which will generate all figures and tables
./bin/run_py --output_mode=dev -- $CLI \
run_analysis --version="$OT_VERSION" --output-path=$DATA_DIR

# This will run the same notebook with multiple configurations as a part of the sensitivity analysis (takes an hour or two)
./bin/run_py --output_mode=dev -- $CLI \
run_analysis_configs --output-path=$DATA_DIR 2>&1 | tee /tmp/log.txt

To build the paper.tex file:

• Install Latex Workshop for VS Code
• Follow the instructions for installing TeX Live, which is used by that extension
• Open paper.text and press the green play arrow at the top to build the tex project at the top, or make a change of some kind and save the file
  • Conveniently, the project will also rebuild if any of the figures/tables are changed on disk (i.e. if you run cells that do this in analysis.ipynb)