micom.viz.growth

Visualization for growth rates.

Functions

plot_growth(.strftime, groups, tolerance)

Plot the taxa growth rates.

Module Contents

micom.viz.growth.plot_growth(results: micom.workflows.results.GrowthResults, filename: str = 'growth_rates_%s.html' % datetime.now().strftime('%Y%m%d'), groups: pandas.Series = None, tolerance: float = 1e-06) → None[source]

Plot the taxa growth rates.

Parameters:

  • results (micom.workflows.GrowthResults) – The results returned by the grow workflow.

  • filename (str) – The HTML file where the visualization will be saved.

  • groups (pandas.Series) – Additional metadata to color points. The index must correspond to the sample_id in the results and values must be categorical. The .name attribute will be used to name the groups. If not provided will color by taxon.

  • tolerance (float) – Smallest growth rate that will be considered. Everything lower will be considered not growing.

Returns:

A MICOM visualization. Can be served with viz.serve.

Return type:

Visualization