Michael, Thanks for your helpful message. Indeed, after posting my question about plot customization, I was able to generate a PCA plot from plotTangentSpace with axes labels, using the "par" function immediately before calling the plotTangentSpace routine, as follows: par(xlab="PC 1", ylab="PC 2"). Obviously, the solution you suggested is even more generic and flexible and it also works fine.
When means are available to customize the display of deformation grids, then geomorph will be near perfection! Thanks again for your help. With best regards, 2015-04-12 11:19 GMT-03:00 Collyer, Michael <michael.coll...@wku.edu>: > Mauro, > > The extractable parts from prcomp() are also extractable from > plotTangentSpace. One can make custom plots, relabel axes, change symbols, > etc. Example: > > myplot = plotTangentSpace(mydata) > attributes(myplot) # shows extractable parts > > PC.scores = myplot$x > > par(…) > plot(PC.scores, …) > > Keep in mind with plotTangentSpace, the product is actually multiple > plots, as the transformation grids are also plots. Therefore, it is not > easy to pass on par() input to the result. But because users can extract > the scores, all base R plotting functions are available. > > Cheers! > -Mike > > Michael Collyer > > Assistant Professor > Department of Biology > Western Kentucky University > 1906 College Heights Blvd. #11080 > Bowling Green, KY 42101-1080 > Phone: 270-745-8765; Fax: 270-745-6856 > Email: michael.coll...@wku.edu > > On Apr 12, 2015, at 8:05 AM, Mauro Cavalcanti <mauro...@gmail.com> wrote: > > Dear Emma & ALL, > > Indeed, when reading my data with readland.nts I get the data in the > format required by the geomorph analytical routines. The problem is that I > was calling by mistake a routine from Ian Dryden's shapes package (procGPA) > to generate the Procrustes-aligned coordinates, instead of the gpagen > routine. Fixed this and now everything works fine. > > I take this opportunity to ask another question, this time relating to > the plots generated by geomorph. Is there a way to customize them, > including for example axis labels in the PCA plots? In fact, the "Quick > Guide" shows these plots with labels, but I could not figure out how to > include them in my plots. Calling the R par function (as one should have > done when using the usual "plot" command) did not work. > > Again, thanks for your help. > > Best regards,. > > 2015-04-12 1:39 GMT-03:00 Emma Sherratt <emma.sherr...@gmail.com>: > >> Mauro, >> >> If you read in your NTS data file using readland.nts, it will >> automatically be in the 3D array format required by plotTangentSpace (after >> you use gpagen to do a Procrustes Superimposition). >> >> If you have your data as a 2D matrix, you simply use arrayspecs to make >> it a 3D array. >> >> Emma >> >> On Sunday, April 12, 2015, Mauro Cavalcanti <mauro...@gmail.com> wrote: >> >>> Dear ALL, >>> >>> I have a number of questions about the geomorph R package, that I will >>> post here in separate messages. >>> >>> First one concerns Principal Components Analysis, using the >>> plotTangentSpace routine. It requires a 3D matrix as argument, however my >>> data (on fishes) are 2D and I could not figure out how to convert my data >>> to the required format; the explanation of the arrayspecs routine in the >>> "Quick Guide to Geomorph" was not clear for me (and it lacks a workin >>> exemple). >>> >>> My data are read from a NTSYSpc file containing 2D coordinates for 10 >>> landmarks for a number of fish specimens, using the readland.nts routine. I >>> have been able to perform a PCA on these data using the shapepca routine in >>> Ian Dryden's shapes R package, but would like to perfom the entire analysis >>> using geomorph. >>> >>> Thanks in advance for any hints! >>> >>> Best regards, >>> >>> -- >>> Dr. Mauro J. Cavalcanti >>> E-mail: mauro...@gmail.com >>> Web: maurobio <http://sites.google.com/site/maurobio> >>> >>> -- >>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org >>> >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to morphmet+unsubscr...@morphometrics.org. >>> >> >> >> -- >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> Emma Sherratt, PhD. >> >> Lecturer in Zoology, >> Zoology Division, School of Environmental and Rural Science, >> Room L120 Bldg C02, >> University of New England, >> Armidale, NSW, Australia, 2351 >> Tel: +61 2 6773 5041 >> email: emma.sherr...@une.edu.au >> Twitter: @DrEmSherratt >> >> Caecilians are legless amphibians... >> >> * __ >> (\ .-. .-. /_") >> \\_//^\\_//^\\_// >> `"` `"` `"`* >> >> learn more about them here: www.emmasherratt.com/caecilians >> >> >> >> >> > > > -- > Dr. Mauro J. Cavalcanti > E-mail: mauro...@gmail.com > Web: http://sites.google.com/site/maurobio > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > > To unsubscribe from this group and stop receiving emails from it, send > an email to morphmet+unsubscr...@morphometrics.org. > > > -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: http://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
