I know how to perform 2 D principal coordinate analysis in GenAlex. I could not figure out about 3D PCoA. My data type is microsatellite. I am trying to use unbiased Nei's genetic distance.
I know of no way to graph the PCoA result in 3 dimensions using GENALEX.
You can however view the 3rd axis versus axes 1 or 2.
With the sheet containing your PCoA active, click the GENALEX menu, select PCoA, then you can visualize any pairwise combination of the three axes. 1v2, 1v3, 2v3.
Hi Michael, thank you for the information. Can we use Eigen values for three axis (1 = X, 2 =Y and 3 = z) to have 3 D plot. GenAelx estimates Eigen value for each axis per population. Can we plot them using XSTAT to show 3 dimension PCoA plot?
I have never made a 3D PCoA with Genalex data, but I'm told (Rod Peakall) that importing the results to a package such as JMP, one can do this.
So your suggestion sounds sensible. Export the eigen values to any package capable of producing the 3D visual.
Yes Michael I tried it yesterday and it worked. Glad to communicate :))
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