GenomeTornadoPlot Wrapper

This is a Python wrapper for the GenomeTornadoPlot R script. It streamlines the process of running the GenomeTornadoPlot visualization on a batch of genes based on a provided CSV file.

Clone with Submodules

Make sure to clone this repository with the --recurse-submodules flag to include the necessary submodules:

git clone --recurse-submodules https://github.com/nicholas-abad/genome-tornado-plot-wrapper.git

If you’ve already cloned without submodules, run:

git submodule update --init --recursive

This will ensure that both GenomeTornadoPlot/ and GenomeTornadoPlot-files/ are available.

Using Conda

To ensure reproducibility and install all necessary dependencies (Python, R, and Bioconductor packages), you can use the provided environment.yml file.

Create and activate the environment:

If you’re on Apple Silicon (M1/M2), run:

CONDA_SUBDIR=osx-64 conda env create -f environment.yml

Otherwise:

conda env create -f environment.yml

Then activate it:

conda activate gtp

This sets up the environment with all required packages for both Python and R scripts.

Repository Structure

genome-tornado-plot-wrapper/
├── main.py                     # Main wrapper script
├── _singular_tornado_plot.R   # R script wrapper
├── GenomeTornadoPlot/         # Git submodule
├── GenomeTornadoPlot-files/   # Git submodule
└── README.md

Requirements

  • Python 3.x

  • pandas

  • R with required packages for GenomeTornadoPlot

Usage

To run the wrapper script:

python main.py \
  --path-to-csv examples/sample_file.tsv \
  --output-folder examples/output/ \
  --delimiter "\t" \
  --starting-index 0 \
  --ending-index 3

Arguments

  • --path-to-csv: Path to the input CSV file.

  • --output-folder: Folder where output plots will be saved.

  • --delimiter: Delimiter used in the CSV file (e.g., ,, \t).

  • --starting-index: Start index of the CSV rows to process.

  • --ending-index: End index of the CSV rows to process.

Ensure the input CSV has at least #CHROM and GENE columns.

Examples

Running this main.py generates two PNG files: a chromosome-level plot and a zoomed-in version of that plot. An example of each of these can be seen below:

Chromosome-level Plot

Zoomed-in Plot

License

This wrapper script is based on the original GenomeTornadoPlot by chenhong-dkfz. Refer to their repository for licensing details.