Error in plot.gm.prcomp

[Mariah Schlis-Elias]

Hello!

I am trying to plot the first and second PC axes from a PCA I just ran on the symmetric component of my shape data. When I try to use the function plot.gm.prcomp though, R gives me an error saying it could not find the function even though I have activated geomorph in this R session. I have also double-checked that all my packages are updated and that R and RStudio are updated (so this is geomorph v4.0.1), tried uninstalling and reinstalling geomorph, restarting R, restarting my whole computer, and still no luck.

I am extra confused because I can successfully use the gmShiny app on my local computer and produce PCA plots (which if I understand correctly should rely on plot.gm.prcomp on the back-end), but I cannot use gmShiny for this particular plot since my data has more than ten groups.

Have I missed something, or does this indicate something is wrong with the package?

Any advice would be greatly appreciated!

Mariah

[Emanuel Seculi]

Hello Marhia, Try with the plot function, for example:

plot(PCA, pch= as.numeric(facto),cex=1.5,pch=19)

Maybe the function plot.gm.prcomp has been deleted in the package.

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[Mike Collyer]

The function has not been deleted.  It is an S3 generic function.  One uses

plot(my.PCA)

and not

plot.gm.prcomp(my.PCA)

The “.gm.prcomp” part of the function instructs R when somebody uses plot(), for gm.prcomp class objects.

You can learn more here.

Also look at the gm.prcomp file, and notice that the examples do not use plot.gm.prcomp, but use plot only.

Best,

Mike

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