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)

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.

eigvalspd.Series

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

samplespd.DataFrame

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

featurespd.DataFrame

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

biplot_scorespd.DataFrame

Correlation coefficients of the samples with respect to the features.

sample_constraintspd.DataFrame

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

proportion_explainedpd.Series

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

See also

ca

cca

pcoa

rda

Attributes

default_write_format

Attributes (inherited)

png	Get figure data in PNG format.
svg	Get figure data in SVG format.

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__()

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.