ComutPlotLib - Genomic Comutation Plots

Welcome to ComutPlotLib, a Python tool for generating genomic comutation plots. These plots visualize co-occurrence patterns of genomic alterations—mutations, copy number variations (CNVs), and other genetic events—across multiple patients or samples.

Example Output

This comutation plot (central panel) visualizes the mutation landscape across a patient cohort. Rows represent genes, and columns correspond to patients. Each cell indicates a gene’s mutation status in a patient: rectangles denote copy-number variations (CNVs), and ellipses indicate short nucleotide variations (SNVs), with multiple SNVs shown as subdivided wedges. Colors encode mutation types and functional effects.

The top panel displays tumor mutation burden (TMB) per patient, with high TMB (≥10/Mb) highlighted in red. The mutational signature panel shows the relative fraction of exposures to different mutational signatures for each patient or sample. The left panel summarizes mutation recurrence, showing SNV and CNV frequencies per gene, annotated with recurrent protein alterations. It also reports the percentage of patients with high-level CNVs, supplemented by low-level CNVs in brackets, along with the total percentage of patients carrying either an SNV or a high-level CNV in the gene.

The bottom panel presents patient- and sample-level metadata. For patients with multiple samples, metadata cells are subdivided accordingly.

Features

✔ Visualizes SNVs and CNVs in a single plot
✔ Summarizes mutational burden, recurrence, and metadata
✔ Customizable layout and annotation
✔ Compatible with MAF, GISTIC, and SIF files
✔ Integrates with GATK Funcotator, GISTIC 2.0, and other genomic tools

---

Installation

To install ComutPlotLib, run:

pip install -r requirements.txt

Alternatively, use the provided installation script:

bash install.sh

Usage

Run ComutPlotLib with:

python comut_argparse.py --output output_plot.png --maf input.maf

For a full list of options, use:

python comut_argparse.py --help

📌 For detailed examples, refer to the .

Input Files:

ComutPlotLib requires at least one of the following input files:

1. Mutation Annotation Format (MAF):
   • Output of GATK Funcotator
   • Contains mutation calls and annotations
2. GISTIC output:
   • From GISTIC 2.0
   • Provides copy number alteration calls (file: all_thresholded.by_gene.txt)

Sample information can be provided via

• Sample Information File (SIF):
  • Tab-separated metadata file
  • Contains sample attributes (e.g., tumor purity, platform, histology)
  • See for required columns

Demo & Examples:

🔬 Try the demo:

• Generate your own synthetic data:

python make_data.py

• Generate a plot

bash call_comut.sh

This will generate an example comutation plot using the synthetic test datasets.

Dependencies:

Required dependencies are listed in requirements.txt. Install them via:

pip install -r requirements.txt

Author:

Developed by Philipp Hähnel. For questions, send an email.

License

This project is licensed under the MIT License. See the LICENSE file for details.