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.

See also

ca, cca, pcoa, rda

Attributes

png Display basic 3-D scatterplot in IPython Notebook as PNG.
svg Display basic 3-D scatterplot in IPython Notebook as SVG.
short_method_name (str) Abbreviated ordination method name.
long_method_name (str) Ordination method name.
eigvals (pd.Series) The resulting eigenvalues. The index corresponds to the ordination axis labels
samples (pd.DataFrame) The position of the samples in the ordination space, row-indexed by the sample id.
features (pd.DataFrame) The position of the features in the ordination space, row-indexed by the feature id.
biplot_scores (pd.DataFrame) Correlation coefficients of the samples with respect to the features.
sample_constraints (pd.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_explained (pd.Series) Proportion explained by each of the dimensions in the ordination space. The index corresponds to the ordination axis labels

Methods

str(or) Return a string representation of the ordination results.
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.