micom.viz.exchanges

Visualization for exchanges.

Module Contents

Functions

plot_exchanges_per_sample(results, filename='sample_exchanges_%s.html' % datetime.now().strftime('%Y%m%d'), direction='import', cluster=True) → None

Plot the per sample exchange fluxes.

plot_exchanges_per_taxon(results, filename='taxon_exchanges_%s.html' % datetime.now().strftime('%Y%m%d'), direction='import', use_total_flux=False, **tsne_args) → None

Plot the exchange fluxes per taxon.

micom.viz.exchanges.plot_exchanges_per_sample(results, filename='sample_exchanges_%s.html' % datetime.now().strftime('%Y%m%d'), direction='import', cluster=True) None[source]

Plot the per sample exchange fluxes.

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

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

  • direction (str either "import" or "export") – The direction of fluxes to plot.

  • cluster (bool) – Whether to reorder samples so that samples with similar exchange fluxes are close to another.

Returns

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

Return type

Visualization

micom.viz.exchanges.plot_exchanges_per_taxon(results, filename='taxon_exchanges_%s.html' % datetime.now().strftime('%Y%m%d'), direction='import', use_total_flux=False, **tsne_args) None[source]

Plot the exchange fluxes per taxon.

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

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

  • direction (str either "import" or "export") – The direction of fluxes to plot.

  • use_total_fluxes (bool) – Whether to use fluxes normalized to 1gDW of bacteria or the total flux.

  • tsne_args (dict) – Additional arguments passed to TSNE.

Returns

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

Return type

Visualization