sourmash_plugin_betterplot

What is this?

sourmash compare and sourmash plot produce basic distance matrix plots that are useful for comparing and visualizing the relationships between dozens to hundreds of genomes. And this is one of the most popular use cases for sourmash!

But! The visualization could be improved a lot beyond the basic viz that sourmash plot produces, and there are a lot of only slightly more complicated use cases for comparing, clustering, and visualizing many genomes!

This plugin will explore these use cases!

Specific goals:

• provide a variety of plotting and exploration commands that can be used with sourmash tools;
• provide both command-line functionality and functions that can be imported and used in Jupyter notebooks;
• (maybe) explore other backends than matplotlib;

and who knows what else??

Installation

pip install sourmash_plugin_betterplot

Usage

@CTB: info goes here!

Examples

sourmash scripts plot2 3sketches.cmp -o examples/plot2.3sketches.cmp.png

yields:

Support

We suggest filing issues in the main sourmash issue tracker as that receives more attention!

Dev docs

betterplot is developed at https://github.com/sourmash-bio/sourmash_plugin_betterplot.

Testing

Run:

pytest tests

Generating a release

Bump version number in pyproject.toml and push.

Make a new release on github.

Then pull, and:

python -m build

followed by twine upload dist/....

CTB May 2024