Source code for micom.viz.tradeoff

"""Visualizations for tradeoff analysis."""

from datetime import datetime
from micom.viz import Visualization
import numpy as np
import pandas as pd

[docs]def plot_tradeoff( tradeoff_rates, filename="tradeoff_%s.html" %"%Y%m%d"), tolerance=1e-6 ): """Plot diagnostics for varying tradeoff values. Parameters ---------- tradeoff_rates : pandas.DataFrame The growth rates returned by the `tradeoff` 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 = tradeoff_rates data = {"tradeoff": rates} viz = Visualization(filename, data, "tradeoff.html") growth = rates[ ["taxon", "sample_id", "abundance", "tradeoff", "growth_rate"] ].copy() growth.tradeoff = growth.tradeoff.round(6).astype(str) growth.loc[growth.tradeoff == "nan", "tradeoff"] = "none" growth.loc[growth.growth_rate < tolerance, "growth_rate"] = tolerance growth.loc[:, "log_growth_rate"] = np.log10(growth.growth_rate) tradeoff = ( growth.groupby(["tradeoff", "sample_id"]) .apply( lambda df: pd.Series( { "n_taxa": df.shape[0], "n_growing": df[df.growth_rate > tolerance].shape[0], "fraction_growing": ( df[df.growth_rate > tolerance].shape[0] / df.shape[0] ), } ) ) .reset_index() ) growth=growth.to_json(orient="records"), tradeoff=tradeoff.to_json(orient="records"), extent=[growth.log_growth_rate.min(), growth.log_growth_rate.max()], width=400, height=300, ) return viz