12. Analysing environmental variables (Draftsman Plot, PCA)
Environment-type data
PRIMER uses the term environmental variables as a shorthand for a wide variety of data types (inc...
Draftsman plots recap & transform choices
Normalisation (subtracting the mean and dividing by the standard deviation, for each variable), a...
Principal Components Analysis
PCA is an ordination method in which samples, regarded as points in the high-dimensional variable...
PCA eigen-vector plot
Though the vector overlay has a tendency to clutter the plot, the changing contaminant load along...
PC scores
The final table in the results window is headed Principal Component Scores – these can instead be...
PCA plot options
Many of the options for manipulating PCA configurations are exactly the same as for MDS plots, co...
Trajectories on PCA
From the Graph>Special menu, remove the vector overlay by unchecking the (✓Overlay vectors) box o...
Bubble plots on PCA
Of the other options on the Graph>Special menu, overlaying groups from a CLUSTER run (which to be...
Multiple 2-d & 3-d plots
As with MDS, use of Graph>Special>Main>Axes, with (Plot type•2D or •3D), allows any pairs or trip...
Interpreting PCA vs MDS pairwise plots
Another subtle distinction from MDS is that only a single PCA graph window is produced initially,...
PCA of data on biomarkers
An example where a 3-d plot is marginally more necessary is given by the biomarker data last see...