def exchanges_per_taxon(output_dir: str,
results: MicomResultsDirectory,
direction: str = "import") -> None:
"""Plot the exchange fluxes."""
template = env.get_template("umap.html")
data_loc = path.join(output_dir, "umap.csv")
exchanges = results.exchange_fluxes.view(pd.DataFrame)
exchanges = exchanges[(exchanges.taxon != "medium")
& (exchanges.direction == direction)
& (exchanges.flux.abs() > 1e-6)]
exchanges.flux = exchanges.flux.abs()
mat = exchanges.pivot_table(values="flux",
index=["sample_id", "taxon"],
columns="reaction",
fill_value=0)
umapped = UMAP().fit_transform(mat.values)
umapped = pd.DataFrame(umapped,
index=mat.index,
columns=["UMAP 1", "UMAP 2"]).reset_index()
umapped.to_csv(data_loc)
template.stream(data=umapped.to_json(orient="records"),
width=800,
height=600).dump(path.join(output_dir, "index.html"))
