skbio.stats.ordination.OrdinationResults¶

class skbio.stats.ordination.OrdinationResults(short_method_name, long_method_name, eigvals, samples, features=None, biplot_scores=None, sample_constraints=None, proportion_explained=None)[source]¶

Store ordination results, providing serialization and plotting support.

Stores various components of ordination results. Provides methods for serializing/deserializing results, as well as generation of basic matplotlib 3-D scatterplots. Will automatically display PNG/SVG representations of itself within the IPython Notebook.

short_method_name¶

Abbreviated ordination method name.

Type: str

long_method_name¶

Ordination method name.

Type: str

eigvals¶

The resulting eigenvalues. The index corresponds to the ordination axis labels

Type: pd.Series

samples¶

The position of the samples in the ordination space, row-indexed by the sample id.

Type: pd.DataFrame

features¶

The position of the features in the ordination space, row-indexed by the feature id.

Type: pd.DataFrame

biplot_scores¶

Correlation coefficients of the samples with respect to the features.

Type: pd.DataFrame

sample_constraints¶

Site constraints (linear combinations of constraining variables): coordinates of the sites in the space of the explanatory variables X. These are the fitted site scores

Type: pd.DataFrame

proportion_explained¶

Proportion explained by each of the dimensions in the ordination space. The index corresponds to the ordination axis labels

Type: pd.Series

See also

ca, cca, pcoa, rda

Attributes

`default_write_format`
`png`	Display basic 3-D scatterplot in IPython Notebook as PNG.
`svg`	Display basic 3-D scatterplot in IPython Notebook as SVG.

Built-ins

`__hash__`	Return hash(self).
`str(or)`	Return a string representation of the ordination results.

Methods

`plot`([df, column, axes, axis_labels, title, …])	Create a 3-D scatterplot of ordination results colored by metadata.
`read`(file[, format])	Create a new `OrdinationResults` instance from a file.
`write`(file[, format])	Write an instance of `OrdinationResults` to a file.