3-d ordination plots & axes selection

As we have seen for the nMDS run on the Exe nematode data, in the first graphic of this Section, a default MDS run produces both 2-d and 3-d configuration plots, and their associated Shepard diagrams, placed into a multi-plot (Multiplot1). A different plot window is created for the 2-d than the 3-d solution because the operations are entirely separate. This is in contrast with PCA (Section 12) or PCO (in the PERMANOVA+ add-on) where the 2-d solution is just the first two axes of the 3-d solution, and a single plot window is sufficient to capture all the possibilities. There, the Graph >Special>Main>Axes section will allow a choice of which two or three of the (many) PCA axes are selected for plotting, in either the specified (Plot type•2D) or (Plot type•3D) configuration. For MDS plots, which can in PRIMER 7 also be produced for many dimensions, each new dimension requires a different iterative process and, for example, the 2-d solution will not be the first two axes of the 3-d solution. Hence the plot windows for different dimensions are listed separately, though the option to select different combinations of axes from each, for a 2- or 3-d plot, remains the same.