skbio.stats.ordination.OrdinationResults#

class skbio.stats.ordination.OrdinationResults(short_method_name, long_method_name, eigvals, samples, sample_ids=None, features=None, feature_ids=None, biplot_scores=None, sample_constraints=None, constraint_ids=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.

Attributes:
short_method_namestr

Abbreviated ordination method name.

long_method_namestr

Ordination method name.

eigvalstable_like

The resulting eigenvalues. The index corresponds to the ordination axis labels. See the DataTable type documentation for details.

samplestable_like

The position of the samples in the ordination space, row-indexed by the sample id. See the DataTable type documentation for details.

featurestable_like

The position of the features in the ordination space, row-indexed by the feature id. See the DataTable type documentation for details.

biplot_scorestable_like

Correlation coefficients of the samples with respect to the features. See the DataTable type documentation for details.

sample_constraintstable_like

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. See the DataTable type documentation for details.

proportion_explainedtable_like

Proportion explained by each of the dimensions in the ordination space. The index corresponds to the ordination axis labels. See the DataTable type documentation for details.

sample_ids, feature_ids, constraint_ids, output_formatoptional

Standard DataTable parameters. See the DataTable type documentation for details.

See also

ca
cca
pcoa
rda

Attributes

Methods

plot([df, column, axes, axis_labels, title, ...])

Create a 3-D scatterplot of ordination results colored by metadata.

read([format])

Create a new OrdinationResults instance from a file.

rename(mapper[, matrix, strict])

Rename sample or feature IDs in the data matrix.

write(file[, format])

Write an instance of OrdinationResults to a file.

Special methods

__str__()

Return a string representation of the ordination results.

Special methods (inherited)

__eq__(value, /)

Return self==value.

__ge__(value, /)

Return self>=value.

__getstate__(/)

Helper for pickle.

__gt__(value, /)

Return self>value.

__hash__(/)

Return hash(self).

__le__(value, /)

Return self<=value.

__lt__(value, /)

Return self<value.

__ne__(value, /)

Return self!=value.

Details

default_write_format = 'ordination'#
__str__()[source]#

Return a string representation of the ordination results.

String representation lists ordination results attributes and indicates whether or not they are present. If an attribute is present, its dimensions are listed. A truncated list of features and sample IDs are included (if they are present).

Returns:
str

String representation of the ordination results.