mmm4microbiome

mmm4microbiome is the microbiome layer on top of stripesankey (>= 0.4.1). mmm4microbiome reads the output of stripesankey and makes interpretation plots for microbiome data analysis.

Install

pip install mmm4microbiome # with pip
uv add mmm4microbiome # with uv

Input: a stripesankey base folder

Everything takes a base folder written by stripesankey:

import stripesankey as ss

ss.prepare(base, counts, feature_annotation, metadata, level="Genus")
ss.sweep(base, k_range=range(2, 11))

Use

import mmm4microbiome as mmm

# the sweep, with captions like "MC3 · Prevotella"
mmm.stripesankey_mb(base, metadata_df=meta, hover_field="METADATA_COLUMN")
mmm.metasankey_mb(base, metadata_df=meta, hover_field="METADATA_COLUMN")

# one k, sample by sample
mmm.heatmap_sample(base, 5, metadata_df=meta, include=["METADATA_COLUMN"])
mmm.bar_sample(base, 5, metadata_df=meta, sort="METADATA_COLUMN")

# what the MCs are made of
mmm.heatmap_mc(base, 5, feature_level="Family")

# everything in one self-contained HTML page: base/visualization/onestop_app.html
mmm.onestop(base, meta)

Taxonomic levels

The fit level is what prepare(level=) collapsed the counts to. The display level (feature_level=) is what a figure names. By default it is the fit level, except that an ASV (or Species) fit is shown at Genus. A coarser level sums the probabilities of its child taxa; a level finer than the fit cannot be recovered and falls back to the fit level with a warning.

License

MIT