skbio.stats.ordination.OrdinationResults

class skbio.stats.ordination.OrdinationResults(eigvals, species=None, site=None, biplot=None, site_constraints=None, proportion_explained=None, species_ids=None, site_ids=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

png Display basic 3-D scatterplot in IPython Notebook as PNG.
svg Display basic 3-D scatterplot in IPython Notebook as SVG.
eigvals (1-D numpy array) The result eigenvalues
species (2-D numpy array) The result coordinates for each species
site (2-D numpy array) The results coordinates for each site
biplot (2-D numpy array) The result biplot coordinates
site_constraints (2-D numpy array) The result coordinates for each site constraint
proportion_explained (1-D numpy array) The proportion explained by each eigenvector
species_ids (list of str) The species identifiers
site_ids (list of str) The site identifiers

Methods

from_file(ord_res_f) Load ordination results from text file.
plot([df, column, axes, axis_labels, title, ...]) Create a 3-D scatterplot of ordination results colored by metadata.
read(fp[, format]) Create a new OrdinationResults instance from a file.
to_file(out_f) Save ordination results to file in text format.
write(fp[, format]) Write an instance of OrdinationResults to a file.