micom.viz
#
Init file for MICOM Visualization.
Submodules#
Package Contents#
Classes#
A visualization object. |
Functions#
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Plot the per sample exchange fluxes. |
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Plot the exchange fluxes per taxon. |
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Plot the taxa growth rates. |
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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()#
Open the visualization in a browser.
- Parameters:
None. –
- Return type:
nothing
- save(**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:
- 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:
- 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:
- 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: