Hi, Thanks a lot for your so fast replies!
As it happened, it seems that my data in NTSYS format was not being correctly read by the readland.nts() function. I changed the code to read my data in TPS format with the readland.tps() and it worked fine. Now the plot displays as expected (see attached image): Thank you very much! With warmest regards, Em dom., 26 de nov. de 2023 às 18:47, Murat Maga <[email protected]> escreveu: > 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." >> > -- > You received this message because you are subscribed to the Google Groups > "Morphmet" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/morphmet2/a026ad3b-eadc-4047-86f3-cfcb62bd298dn%40googlegroups.com > <https://groups.google.com/d/msgid/morphmet2/a026ad3b-eadc-4047-86f3-cfcb62bd298dn%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- Dr. Mauro J. Cavalcanti E-mail: [email protected] Web: https://github.com/maurobio "Life is complex. It consists of real and imaginary parts." -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/CAC1JhZbS6gUrrN1G5__bRTiR%2BU-VTXu21XzwXk9LMvhGmOQ4jw%40mail.gmail.com.
