I can't replicate this with the toy data in geomorph:
library(geomorph)
data("plethodon")
gpa=gpagen(plethodon$land)
Performing GPA
|===============================================================================================================================|
100%
Making projections... Finished!
pca=gm.prcomp(gpa$coords)
cols=c(rep('black', 20), rep('red', 20))
plot(pca, col=cols, pch=20)
seems to give the expected figure with 20 black and red points. So I
suspect it is an issue with your data ordering. Perhaps you do not have 60
points. I noticed that plot is not throwing an error when the length of the
color vector is longer than the number of points to plot.
On Sunday, November 26, 2023 at 1:39:30 PM UTC-8 Mauro Cavalcanti wrote:
> Dear ALL,
>
> In a GM study of 60 specimens of two fish species (with 30 specimens for
> each species), I am using the gm.prcomp() function in the geomorph 4.0.6
> package to perform an ordinary PCA of the Procrustes-aligned coordinates
> (where 'proc' is my GM data frame):
>
> PCA <- gm.prcomp(proc$coords)
> summary(PCA)
>
> I want that the two species appear in different colors in the PCA plot, so
> I used:
>
> plot(PCA, pch = 20, col = c(rep("red", 30), rep("black", 30)))
>
> or:
>
> plot(PCA, pch = 20, col = df$species) (where 'df' is my original data
> frame)
>
> But strangely in neither case the plot is correctly displayed (see the
> attached figures): just a few points appear in either "red" or "black",
> instead of the expected result of 30 points in one color and 30 points in
> another.
>
> Any hints?
>
> Thanks in advance for any assistance you can provide.
>
> With best regards,
>
> --
> Dr. Mauro J. Cavalcanti
> E-mail: [email protected]
> Web: https://github.com/maurobio
> "Life is complex. It consists of real and imaginary parts."
>
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