Dear Prof Dean, Thanks a lot for the details of the geomorph package. I'll take a look at the help file.
All best, Pablo <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Libre de virus.www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> El jue, 19 oct 2023 a las 14:54, Adams, Dean [EEOB] (<[email protected]>) escribió: > 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 > > > > > > > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > > Libre de virus.www.avg.com > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > > -- > 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/CANPrD1jb7V8FuQSXjGsT-NdnVU%2BAcw5eHf3VcxBQ1GDSKDAteQ%40mail.gmail.com > <https://groups.google.com/d/msgid/morphmet2/CANPrD1jb7V8FuQSXjGsT-NdnVU%2BAcw5eHf3VcxBQ1GDSKDAteQ%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- 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/CANPrD1hwQTFzt20g3v6vizvAnGGBR-y-1S_CWpb4a1DZSh3_0A%40mail.gmail.com.
