plot-plasmids 0.1.0

A tool to generate PCoA or NMDS plots for plasmids.

plot_plasmids

A tool to generate PCoA or NMDS plots for plasmids, colored by carbapenemase genes and rep types.

Installation

You can install plot_plasmids from PyPI:

pip install plot-plasmids

Or, for development, you can install it from this repository:

git clone https://github.com/example/plot_plasmids.git
cd plot_plasmids
pip install -e .

Usage

plot_plasmids -d tests/data/dist_matrix.csv -a tests/data/amr.tsv -m tests/data/mob.tsv -o example.png

Arguments

• -d, --dist_matrix: Path to the plasmid distance matrix (CSV or TSV format).
• -a, --amr: Path to the AMRfinderPlus summary results file (TSV format).
• -m, --mob: Path to the MOB-typer mob_recon_results.txt file (TSV format).
• -o, --output: Path for the output plot file (e.g., plot.png, plot.svg).
• -p, --plot_type: Type of ordination plot to generate (pcoa or nmds). Default is pcoa.