Source code for micom.viz.growth

"""Visualization for growth rates."""

from datetime import datetime
from micom.viz import Visualization

[docs]def plot_growth( results, filename="growth_rates_%s.html" %"%Y%m%d"), tolerance=1e-6, ): """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. tolerance : float Smallest growth rate that will be considered. Everything lower will be considered not growing. Returns ------- Visualization A MICOM visualization. Can be served with `viz.serve`. """ rates = results.growth_rates rates = rates[rates.growth_rate > tolerance][ ["taxon", "sample_id", "abundance", "growth_rate"] ] data = {"growth_rates": rates} viz = Visualization(filename, data, "growth.html") aspect = max(0.05, rates.taxon.nunique() / 50)"records"), width=int(aspect * 400), height=400) return viz