Principal coordinates or principal components

PCoA (classical multidimensional scaling) works from any distance matrix. PCA needs numeric data; missing values are replaced by the column mean, and traits (not markers) are scaled to unit variance.

Usage

ordinate(dist = NULL, d = NULL, method = c("pcoa", "pca"), n_axes = 5)

Arguments

dist

A dist object (for PCoA).

d

A cl_data object (for PCA).

method

"pcoa" or "pca".

n_axes

Number of axes to keep.

Value

A cl_ord list with scores, variance (percent for every axis) and method.