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.