GENBAIT Reproducibility

This repository contains the GENBAIT project for bait selection in BioID experiments. This project is designed to be reproducible using Snakemake. Below are the instructions on how to reproduce the results of each step in the workflow using the provided configuration files.

Requirements

Before running the workflow, ensure you have the following installed:

• Python 3.10+
• Snakemake
• Git LFS (for handling large files)

Setup

Create a Virtual Environment

It is recommended to create a virtual environment to manage dependencies:

python -m venv genbait_env
source genbait_env/bin/activate  # On Windows use `genbait_env\Scripts\activate`

Install the Package

Navigate to the root directory of the project and run:

git clone https://github.com/camlab-bioml/genbait_reproducibility.git
cd genbait_reproducibility
pip install .

This will install the package along with all required dependencies.

Running the Workflow

You can reproduce the results for each dataset by running the Snakemake workflow. The configuration files for dataset1 and dataset2 are provided in the config directory.

Load data

snakemake --cores 1 data/dataset1/df_norm.csv --configfile config/config_dataset1.yaml
snakemake --cores 1 data/dataset2/df_norm.csv --configfile config/config_dataset2.yaml

Run genetic algorithm

snakemake --cores 1 results/dataset1/GA_results/popfile.pkl --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/GA_results/popfile.pkl --configfile config/config_dataset2.yaml

Get genetic algorithm results

snakemake --cores 1 results/dataset1/plots/GA_vs_Random_plot.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/GA_vs_Random_plot.png --configfile config/config_dataset2.yaml

Run genetic algorithm with different number of baits and seeds

snakemake --cores 1 results/dataset1/GA_number_of_baits_seeds/popfile_features_{num_features}_seed_{seed}.pkl --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/GA_number_of_baits_seeds/popfile_features_{num_features}_seed_{seed}.pkl --configfile config/config_dataset2.yaml

Visualize results for different number of baits and seeds

snakemake --cores 1 results/dataset1/plots/nbaits_vs_max_value_seeds_boxplot_GA.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/nbaits_vs_max_value_seeds_boxplot_GA.png --configfile config/config_dataset2.yaml

Run machine learning methods

snakemake --cores 1 results/dataset1/plots/ml_correlation_plot_averaged.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/ml_correlation_plot_averaged.png --configfile config/config_dataset2.yaml

Plot NMF scores

snakemake --cores 1 results/dataset1/plots/nmf_scores_vs_each_method.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/nmf_scores_vs_each_method.png --configfile config/config_dataset2.yaml

Plot NMF Cosine similarity scores

snakemake --cores 1 results/dataset1/plots/nmf_cos_scores_vs_each_method.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/nmf_cos_scores_vs_each_method.png --configfile config/config_dataset2.yaml

Plot NMF KL Divergence scores

snakemake --cores 1 results/dataset1/plots/nmf_kl_scores_vs_each_method.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/nmf_kl_scores_vs_each_method.png --configfile config/config_dataset2.yaml

Plot NMF ARI

snakemake --cores 1 results/dataset1/plots/nmf_ari_values_vs_each_method.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/nmf_ari_values_vs_each_method.png --configfile config/config_dataset2.yaml

Plot NMF GO Jaccard index

snakemake --cores 1 results/dataset1/plots/nmf_go_components_scores_values_vs_each_method.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/nmf_go_components_scores_values_vs_each_method.png --configfile config/config_dataset2.yaml

Plot remaining preys percentage

snakemake --cores 1 results/dataset1/plots/remaining_preys_vs_each_method_sorted.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/remaining_preys_vs_each_method_sorted.png --configfile config/config_dataset2.yaml

Plot GO retrieval percentage

snakemake --cores 1 results/dataset1/plots/GO_terms_retrieval_percentage_vs_each_method.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/GO_terms_retrieval_percentage_vs_each_method.png --configfile config/config_dataset2.yaml

Plot Leiden ARI

snakemake --cores 1 results/dataset1/plots/Leiden_ARI_values_vs_each_method.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/Leiden_ARI_values_vs_each_method.png --configfile config/config_dataset2.yaml

Plot GMM ARI

snakemake --cores 1 results/dataset1/plots/GMM_ARI_values_vs_each_method.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/GMM_ARI_values_vs_each_method.png --configfile config/config_dataset2.yaml

Plot GMM mean correlation

snakemake --cores 1 results/dataset1/plots/GMM_mean_correlation_values_vs_each_method.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/GMM_mean_correlation_values_vs_each_method.png --configfile config/config_dataset2.yaml

Plot combined metrics

snakemake --cores 1 results/dataset1/plots/combined_metrics_comparison_plot.png --configfile config/config_dataset1.yaml
snakemake --cores 1 results/dataset2/plots/combined_metrics_comparison_plot.png --configfile config/config_dataset2.yaml