plot-plasmids 0.2.1

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 has two subcommands: prep and plot.

prep

The prep command takes the raw output from skani, mob_typer, and amrfinderplus and prepares the files for the plot command.

plot_plasmids prep --skani <skani_matrix> --mob_dir <mob_dir> --amr_dir <amr_dir> --output_dir <out_dir>

Arguments

• --skani: Path to the skani triangle output file.
• --mob_dir: Directory containing the mob_typer output files.
• --amr_dir: Directory containing the amrfinderplus output files.
• --output_dir: Directory to save the processed files.

plot

The plot command generates the PCoA or NMDS plot.

plot_plasmids plot -d <distance_matrix> -a <amr_results> -m <mob_results> -o <plot.png>

Arguments

• -d, --dist_matrix: Path to the plasmid distance matrix (CSV or TSV format), as generated by the prep command.
• -a, --amr: Path to the AMRfinderPlus summary results file (TSV format), as generated by the prep command.
• -m, --mob: Path to the MOB-typer results file (TSV format), as generated by the prep command.
• -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.