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.
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. |
