Skip, As a work around you can subset your own data. All the values you will need to do your own PCA scatter plot is in the pseudoxy.PCA$pcscores.
That way, you get to do choose the coloring scheme and symbols. From: Phillip Skipwith [mailto:pskipw...@gmail.com] Sent: Friday, January 5, 2018 2:00 PM To: MORPHMET <email@example.com> Subject: [MORPHMET] Issues with subsetting nts array with classifiers and plotTangentSpace visualization Hi, I'm using Geomorph to analyze a 3D landmark dataset. I'm having a number of issues both in subsetting my array and visualizing these data after Procrustes analysis. I'm working with a set of 28 specimens and 61 3D landmarks. Below is a sample of my .dta file from Landmark Editor. #### trial.coords <- readland.nts('pseudoxy_project3.dta') 1 28L 183 0 Dim=3 C_infralineatus_AMNH165799 D_quadralineatus_AMNH153343 D_quadralineatus_AMNH153345 D_quadralineatus_AMNH160061 .......... -9.8451595e+000 -2.8541670e+000 -2.8408973e+000 -1.0106355e+001 -5.0837624e-001 -1.3406076e+000 -8.7275896e+000 -2.4869413e+000 -1.2266474e+000 -7.3323584e+000 -3.3111162e+000 -3.0307722e+000 .......... I then make classifiers for later grouping and subsetting based on species (please see below). I can neither subset the data or properly visualize the resulting PCA plot. I get can error regarding the class of my array dimnames. Instead of a PCA plot of the designated axes organized by species, I get two 3D plots of PC1 (positive and negative loadings) with no labeling or legend. Below is some of my simple code. I'm new to Geomorph, so any help or advice would be greatly appreciated. If need be, I can send a reduced dataset to help with troubleshooting. #### pseudoxy.gpa <- gpagen(trial.coords, ProcD = TRUE, Proj = TRUE, print.progress = TRUE) # PCA categories.qpa <- strsplit(dimnames(pseudoxy.gpa$coords)[], "_") # unlist into matrix format classifiers.qpa <- matrix(unlist(categories.qpa), ncol=3, byrow=T) # add the specimen ID to the first column of the table classifiers.qpa <- cbind(dimnames(pseudoxy.gpa$coords)[], classifiers.qpa) # rename the column headings colnames(classifiers.qpa) <- c("FullID", "Genus", "Species", "ID") # converts to data frame so can index using $ classifiers.qpa <- as.data.frame(classifiers.qpa) gp <- as.factor(paste(classifiers.qpa$Genus, classifiers.qpa$Species)) # create grouping variable sub.gpa <- coords.subset(A = pseudoxy.gpa$coords, group = gp) # I get the following error Error in dimnames(specimens)[] <- names : 'dimnames' must be a list #trying to coerce dimnames to a list does not help pseudoxy.PCA <- plotTangentSpace(pseudoxy.gpa$coords, groups = gp, label = TRUE, legend = TRUE, axis1 = 1, axis2 = 2, warpgrids = TRUE) # See attachment for confusing plot. Thanks in advance, Skip -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- 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 morphmet+unsubscr...@morphometrics.org<mailto:morphmet+unsubscr...@morphometrics.org>. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- 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 morphmet+unsubscr...@morphometrics.org.