I am concerned about some differences I am seeing in my PCA scatterplot in 3DSlicer after having produced GPA and PCA results to slide semi-LMs in the geomorph R package.
As a very coarse way to sanity checking myself, I uploaded my geomorph output to 3DSlicer to better visualize which specimens fall where in the morphospace (a very convenient feature in SlicerMorph). As you can see in the Geomorph R PCA plot, a datapoint with a factor of stage “2” and colored pink is positioned in the lower right quadrant at the intersection of .02 on PC1 and close to -.06 on PC2.
When I uploaded this geomorph output into 3Dslicer to see which specimen this is, I went to search for that specific data point and I can’t seem to locate it in the morphospace where my Geomorph R plotted it along PC1 and PC2.
Now, as I compare the plots, I am concerned about the overall differences in these scatterplots. Of course scaling differences between plots can alter the visualization of the data, but as I compare the plots, I don’t think that’s the case. Am I missing something here?
