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.
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eigvals
¶ The resulting eigenvalues. The index corresponds to the ordination axis labels
- Type
pd.Series
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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
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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
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
Return hash(self).
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.-