Calculating a PCA and MDS on a character data set

This tutorial illustrates how to calculate a Principal Components Analysis (PCA) and a Multi Dimensional Scaling (MDS) on a character data set and how to change the layout of the obtained plots.


A character is basically a name-value pair of which the value can be binary, multi-state or continuous. Because of this very broad definition, a wide variety of data can be analyzed as character types (= an array of characters). This includes morphological and biochemical features, commercial test panels (API®, Biolog®, Vitek®, etc.), antibiotics resistance profiles, fatty acid profiles, microarrays, SNP arrays, repeat numbers in MLVA, allelic profiles in MLST, etc.