Igor, Yes, you can do that and the help page for that function has examples to do that.
Mike > On Nov 5, 2018, at 5:26 AM, Igor Talijančić <talijancic.i...@gmail.com> wrote: > > Hello everyone, > > Just a question regarding the plotting of deformation grinds of the > trajectory analysis (e.g. pupfish or plethodon data). Can shape.predictor > function be used for visualizing TA$pc.means since TA$pc.data corresponds to > PC scores obtained for Y.gpa$coords? > > > > Thank you for your given time and consideration. > > > > Sincerely, > > Igor > > > Dana srijeda, 25. srpnja 2018. u 14:42:41 UTC+2, korisnik javiersantos3 > napisao je: > Hello Carmelo and Mike, > > Thanks for the quick response! I see things now clearer, especially with the > examples you have both provided. Sometimes one gets disoriented in the > abstractness of shape space and coding ;-P Thanks again! > > > Best wishes, > Javier > > > From: Mike Collyer <mlco...@gmail.com <>> > Sent: Wednesday, July 25, 2018 2:29:38 PM > To: Javier Santos > Cc: Morphomet Mailing List > Subject: Re: Conceptual clarification of plotting shape deformation grids in > geomorph > > Javier, > > First your plotting question. The plot.trajectory.analysis function is an S3 > generic plot function, which means you can modify the plot as you like. You > do this easiest with the points function. Here is an example, using the help > page example, which hopefully makes sense for you: > > data(plethodon) > Y.gpa <- gpagen(plethodon$land) > gdf <- geomorph.data.frame(Y.gpa, species = plethodon$species, site = > plethodon$site) > > TA <- trajectory.analysis(coords ~ species*site, data=gdf) > summary(TA, angle.type = "deg") > plot(TA) > # Augment plot with the following code > points(TA$pc.data, pch=19, col = "blue”) # turn all points blue > points(TA$pc.data, pch=19, col = TA$groups) # change points to different > colors, by group > One can modify plots as desired but you might need to learn how to use > graphical parameters in order to do it. See the help for the function, par, > to know how to do that. > > Second, since PC scores are Procrustes residuals (coordinates) projected onto > PC axes, there is a direct correspondence between an observation’s set of > coordinates and its PC scores. If you perform trajectory analysis, the > $means object has the coordinates for the means (trajectory points). You > simply have to rearrange the values with arrayspecs to generate deformation > grids. The $pc.data is a matrix of PC scores whose rows correspond to the > coordinates in the gpagen object. For example, TA$pc.data[5,] is a set of PC > scores for Y.gpa$coords[,,5]. > > Finally, for your last question, the function shape.predictor does exactly > what you seek. The help page has examples that should help you (on e > specifically for allometry). > > Cheers! > Mike > >> On Jul 25, 2018, at 7:17 AM, Javier Santos <javier...@hotmail.com <>> wrote: >> >> Hello Morphometricians, >> >> I was hoping someone could clarify the concept of plotting shape deformation >> grids from the geomorph output. I am confused at the moment because the >> output of most functions (eg. trajectory.analysis()) gives PC values or >> regression scores, while most of the plotting functions I know (eg. >> plotRefToTarget(), plotTangentSpace(), plotAllSpecimens()) require LM >> coordinates. I am sure that the conceptual framework to plot the shape >> deformation grids corresponding from the PC/regression values of the >> functions' output should not be too complicated, but I am currently lost how >> to do so with the coding and do not have a working example. >> >> I will use my current analysis as an example from which to work upon. I have >> ran a trajectory.analysis() on a three species sample: >> >> ontogeny <- trajectory.analysis(M2d ~ >> species*age,f2=NULL,iter=999,seed=NULL,data=gdf) >> >> and plot the results: >> >> x11(); >> plot(ontogeny,group.cols=c("red","blue","green"),pt.scale=1.5,pt.seq.pattern=c("black","gray","white")) >> >> The following code plots the trajectory in the corresponding PC1-PC2 >> morphospace with each species' trajectory in a different color, however, >> although the lines are different colors, the points corresponding to each >> individual are grey for all species. How can I color these points by species >> group without exporting the data? >> I would also like to plot the shape deformation that corresponds to each PC >> axis like the function plotTangentSpace() does. How can that be coded from >> the output of the trajectory.analysis()? >> And lastly, how do you code, for example, when the shape deformation you >> want to plot corresponds to the $pred.val of the regression in the >> procD.allometry() function output [in contrast to PC values]? >> >> Any help on how to approach coding these circumstances or any explicative >> literature on the topic would be greatly appreciated. >> >> >> Best wishes, >> Javier > -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- 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 morphmet+unsubscr...@morphometrics.org.