Pablo,
Yes this can be done in geomorph. The step you are missing is to first predict
the shapes at say, the min/max of your data for PC1. For instance:
PC <- pca$x[,1]
preds <- shape.predictor(shape, x= PC, Intercept = FALSE,
pred1 = min(PC), pred2 = max(PC))
The object ‘preds’ now contains landmark coordinates for specimens along PC1.
These can then be used in plotRefToTarget along with a mesh. Note that often
times, since there is not a 3D mesh for the reference, one may first ‘unwarp’
an object’s mesh to the reference, and then use that in plotRefToTarget. The
function warpRefMesh is used for this (see help file).
Dean
Dr. Dean C. Adams (he/him)
Distinguished Professor of Evolutionary Biology
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
https://faculty.sites.iastate.edu/dcadams/
phone: 515-294-3834
From: [email protected] <[email protected]> On Behalf Of
Pablo Fisichella
Sent: Thursday, October 19, 2023 12:24 PM
To: Morphmet <[email protected]>
Subject: [MORPHMET2] 3D Warping/morphing methods using PCs
Dear morphogeometricians
Hope you are well. I ran a GM analysis using 3D landmarks obtained in aviso for
mice skulls and I used shapes and Morpho R packages. I’m trying to obtain
deformations (so-called warping or morphing) for the negative and positive PC
shape changes of a 3D model. However, I can’t find a method to do this in R. I
realized Morpho allows to obtain a 3D warp movie but I’m not sure that method
is the one I’m looking for and in Geomorph there is a function (warpRefMesh) to
create warpings but using just the mean shape (ref) and a specific individual
not for PCs. I have used MorphoJ and Landmark IDAV to do this in the past but
since I’m using a lot of semilandmarks it is a bit difficult to digitize my
dataset in Landmark to do the warpings. I uploaded my dataset in Morpho, and by
using the function write.pts I was able to transform the 3D coordinates in a
.PTS file. Despite that the file uploads correctly in the corresponding mesh in
Landmark I don’t know why I can’t run the method explained in the MorphoJ user
guide. It seems the landmarks uploaded in Landmark must be obtained directly in
Landmark IDAV and not using the method described above. In any case, I want to
obtain 3D shape deformations of a 3D mesh according to PC scores in R but I was
not able to use any of the methods mentioned above in Morpho and Geomorph.
Thanks in advance for any help with this issue.
All best,
Pablo
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