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
¶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
Attributes
default_write_format |
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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. |