Metagenome analysis output visualizer (MetA-OV)

A collection of Jupyter notebooks for visualizing outputs from AMR++ (resistome profiling), MetaPhlAn (taxonomic profiling), and HUMAnN (functional profiling) on human gut metagenome datasets. These scripts generate PCA plots, bar charts, heatmaps, bubble plots, and clustered visualizations for resistome and taxonomic abundance analysis.

Features

• Visualizations Include:
  • PCA plots for HUMAnN pathway abundance by country.
  • Bar plots and stacked contributions for AMR classes, mechanisms, and genes.
  • Heatmaps (scaled and clustered) for taxonomic and AMR profiles.
  • Bubble plots for non-zero abundances.
• Supports country-wise metadata merging for grouped analysis.
• Easy customization: Update file paths in notebooks to your data.

Example output plots

Other visualisation plot examples provided in 'images/'.

Installation

1. Clone the repo: git clone https://github.com/dxsillydzeko/AMR-Metagenome-Visualizer.git cd AMR-Metagenome-Visualizer

2. Install dependencies (use a virtual environment like venv or conda): pip install -r requirements.txt

3. Install Jupyter: pip install jupyter

4. Launch Jupyter: jupyter notebook

Usage

1. Place your data files (e.g., merged_pathabundance-cpm.tsv, metadata.csv) in the data/ folder or update paths in the notebooks.
2. Open a notebook in Jupyter (e.g., notebooks/humann_pca_plot.ipynb).
3. Run the cells – outputs will generate plots inline or as saved files (e.g., PNGs).
4. Customize: Edit country/sample metadata columns as needed.

Example

For HUMAnN PCA:

• Input: Pathway abundance TSV and country metadata CSV.
• Output: Scatter plot with country-wise colour coding.

See notebooks for detailed comments.

Data Requirements

• AMR++ outputs: AMR++ will provide you with gene,class,type,mechanism outputs for all samples seperately, you shall merge them into combined gene/class/mechanism CSV files.
• MetaPhlAn: Species abundance TSV file for all samples.
• HUMAnN: Pathway abundance TSV (CPM normalized) file.
• Metadata: CSV file with SAMPLE and COUNTRY columns.

Sample input file formats provided in 'data/'.

Contributing

Pull requests welcome! See CONTRIBUTING.md for guidelines.

License

MIT License – see LICENSE for details.

Acknowledgments

Built for visualisation aid in resistome analyses on human gut metagenomes. Inspired by tools like AMR++, MetaPhlAn, and HUMAnN.