Maybe a dumb PCA question: Just to be safe, I want to compare my PCA graphical outputs between different programs. Previously, I would upload my x,y,z spatial points for each landmark into R, run the PCA, and view the plots, scores, etc. But I started getting some odd results in R when I would re-run the same dataset (hench wanting to compare). When I uploaded my x,y,z values in JMP, and select Analyze > Multivariate Methods > Principal Components, it seems like it’s just treating the points as normal values. These landmarks are from highly 3D objects, yet in the JMP PCA, the 3D graphical output has all of the specimens pretty much on a single plane. (and this looks 100% different from the output done in R) So, could I upload the PC scores into JMP and run the analysis from there? (or would that somehow be generating new scores derived from scores already?) If there’s something I’m missing, or a better alternative, I would greatly appreciate any and all advice/assistance.
Thanks Phil. For the 3D plots I want to visualize the x,y,z, coordinates from the principal component scores. If it helps to clarify, I've attached an Excel spreadsheet. You'll see one tab which is just the spacial x,y,z coordinates for each landmark from each specimen. The second tab are the PC scores for each landmark. I want the visualize the 3D spacial relationship dervived from the PC scores, but I want to make sure the steps I'm following to create the graph is the proper sequence.
Hopefully I can clarify things. For each of the specimens there are 36 3D landmarks (X1,Y1,Z1,X2,Y2,Z2, etc.). In the program I used to originally get the spatial coordinates (a program called Landmark), the output was to arrange the entire data set with an X, Y, and Z column, with the rows constituting the landmarks. When I originally tried to upload that form of the data set, JMP was reading each row (i.e. each landmark) as a separate specimen. When I sought help in a previous JMP Community post, it was advised to convert each specimen and all of it's X,Y,Z points to a single row (hench the 108 row low entries). Then I found out the output 3D graph was just creating a scatterplot of the spatial points - for example, it was literally plotting a landmark with 3D coordinate 1,2,3 and another with 3,4,5 in those spacial dimensions, not the PC values.
So from there I took the PC values from my data set that I got in R and "JMP converted" them (a row constituting a specimens and all of it's PC scores). Even though I have the physical specimens in hand, I want to compare their spatial relationships via a PCA. That's why I thought doing the steps to view the 3D PCA in JMP that I mentioned in the previous comment are okay...but I wanted to double check before preceding too far.