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

__getstate__()

Helper for pickle.

__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.