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.
- 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
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
__eq__
(value, /)Return self==value.
__ge__
(value, /)Return self>=value.
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.
__str__
()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.