micom.viz

Init file for MICOM Visualization.

Package Contents

Classes

Visualization

A visualization object.

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.

plot_growth(results, filename='growth_rates_%s.html' % datetime.now().strftime('%Y%m%d'), tolerance=1e-06)

Plot the taxa growth rates.

plot_fit(results, phenotype, variable_type='binary', variable_name='phenotype', filename='fit_%s.html' % datetime.now().strftime('%Y%m%d'), flux_type='production', min_coef=0.001, atol=1e-06)

Test for differential metabolite production.

class micom.viz.Visualization(filename, data, template)[source]

Bases: object

A visualization object.

filename

The filename of trhe saved visualization.

Type

str

data

The data used to create the Visualization.

Type

dict

template

The jinja template used to render the visualization.

Type

jinja2.Template

view(self)

Open the visualization in a browser.

Parameters

None.

Returns

Return type

nothing

save(self, **kwargs)

Render and and save the visualization.

micom.viz.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.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

micom.viz.plot_growth(results, filename='growth_rates_%s.html' % datetime.now().strftime('%Y%m%d'), tolerance=1e-06)[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.

  • 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

micom.viz.plot_fit(results, phenotype, variable_type='binary', variable_name='phenotype', filename='fit_%s.html' % datetime.now().strftime('%Y%m%d'), flux_type='production', min_coef=0.001, atol=1e-06)[source]

Test for differential metabolite production.

This will fit the phenotype response using L1-regularized linear models with log-fluxes as features. Will use LASSO regression for a continuous response and L1-regularized Logistic regression for a binary response.

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

  • phenotype (pandas.Series) – The data to be fitted. Its index must correspond to sample_id in exchanges.

  • variable_type (str of ["binary", "continuous"]) – The type of the variable.

  • variable_name (str) – A short description of the phenotype for instance “disease_status”.

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

  • flux_type (str of ["import", "production"]) – Whether to fit using import or production fluxes.

  • min_coef (float in [0.0, Inf]) – Only report coefficient that are at least that large.

  • atol (float) – Tolerance to consider a flux different from zero. Should be roughly equivalent to the solver tolerance.

Returns

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

Return type

Visualization