emperor.Emperor._process_data

Emperor._process_data(custom_axes, jackknifing_method)

Handle the coordinates data

Parameters:

custom_axes : list of str, optional

Custom axes to embed in the ordination.

jackknifing_method : {‘IQR’, ‘sdef’}, optional

Used only when plotting ellipsoids for jackknifed beta diversity (i.e. using a directory of coord files instead of a single coord file). Valid values are "IQR" (for inter-quartile ranges) and "sdev" (for standard deviation). This argument is ignored if self.jackknifed is None or an empty list.

Returns:

list of str

Sample identifiers in the ordination.

list of lists of floats

Matrix of coordinates in the ordination data with custom_axes if provided.

list of float

either the eigenvalues of the input coordinates or the average eigenvalues of the multiple coords that were passed in

list of lists floats

coordinates representing the span of each ellipse on every axis; None if no jackknifing is applied

list of str

Name of the metadata columns and the index name.

list of lists of str

Data in mf.

list of str

Names of the dimensions in the resulting ordination.

list of list of str

An edge list for procrustes plots

list of list of float

Arrow locations for the biplots.

list of str

Arrow identifiers for biplots.

list of str

Header names for biplot metadata.

list of list of str

Metadata for the biplots.

Notes

This method is exercised by testing the make_emperor method, and is not intended to be used by end-users.