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Overlay trajectories
A trajectory joining points on an ordination is simply added using Graph>Special>Overlays and tak...
Higher-d & scree plots (WA fish diet)
Run nMDS at a wider range of dimensionalities than the default and ask for a scree plot: Analyse>...
(W Australia fish diets)
Re-open the workspace WA fish ws from C:\Examples v7\WA fish diets, which will provide an example...
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, ...
Cluster overlays on MDS plots
The second way in which a cluster analysis can be displayed on a 2-d MDS plot, to aid assessment ...
Linking MDS plots to cluster analysis
The 2-d ordination plot shows a clear separation of the nematode assemblages at these 19 sites in...
Special menu for ordination; Aspect ratio of boundary
We have seen before that, whilst the Graph>Sample Labels & Symbols and General menus are universa...
Zoom & MDS subset plots
It is scarcely necessary here, with only 19 samples, to zoom in on part of the plot in order to s...
Align graphs automatically
A new feature in PRIMER 7 is the ability to automatically reflect in the axes and rotate an MDS c...
Graph menu: rotating and flipping the 2-d ordination
nMDS ordinations (unlike mMDS) have no meaningful axis scales for the configuration, since they u...
Accuracy & fit scheme
For the MDS run above, two of the defaults taken for options in the MDS dialog were (Minimum stre...
Dissimilarity preservation as a matrix correlation
One can also ask how well the (Euclidean) distances among points in the nMDS plot correlate with ...
Running an nMDS (Exe nematodes)
From the directory C:\Examples v7\Exe nematodes, File>Open the workspace Exe ws, last seen in Sec...
Overlaying factors or other data (bubble plot)
The ability to display, on any ordination plot, external structure such as factors (e.g. for site...
Diagnostic tools for MDS plots
In addition to the ability in a previous PRIMER version to Graph>Special>Overlays>(✓Overlay clust...
Rationale for nMDS & mMDS
Chapter 5 of the CiMC methods manual describes the operation and rationale of multi-dimensional s...
Workspace planning
To conclude this section, it is worth remarking that care taken in structuring workspaces will of...
Plots menu
PRIMER 7 has a new Plots main menu, available when the active window is a data matrix. This bring...
User creation/ manipulation of multi-plots
In addition to automatic generation by certain routines, multi-plots can be created and populated...
Automatic creation of multi-plots
The concept of a Multi-plot is a new feature in PRIMER 7. This construction has already been met ...