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

__init_subclass__ This method is called when a class is subclassed.
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.