plotting shape deformations in trajectory analyis.

[Jamile de Moura Bubadue]

Dear all

I am looking into shape trajectories of the femur from three different families from the terrestrial to arboreal state.

so

fit<-procD.lm(shape~gp*hab,data=fdf,iter=9999)

TA<-trajectory.analysis(fit,groups=gp,traj.pts = hab)

I was wondering if there was any way to use plotRefToTarget from the resulting trajectories, plotting for each group the shape at the tip of the trajectory in one state (red) and then the other (green). This would mean I cannot use shape.predictor into the resulting pca from the trajectory analysis object because then I would get the shape deformations from either PC1 or PC2 rather than a position within the bi-plot. I was looking for a way to do it as in picknplot.shape function (to look at shape deformations at the middle of the plot). Bi-plot attached

Thank you

J

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[Antigoni Kaliontzopoulou]

Jamile, 

the shapes at the tips of the trajectories correspond to group means. You can use a combination of coord.subset to divide your groups, then mshape on each group, and then plotRefToTarget to depict the specific shape changes across your vectors.

Hope this helps

Antigoni

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[Jamile de Moura Bubadue]

Yes! This makes a lot of sense! Thank you!

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[Antigoni Kaliontzopoulou]

Jamile, I just realised I was not fully clear: obviously, what you see in the trajectory analysis scatterplots is a simplified view, i.e. a projection of group means to the PC1-PC2 space. The solution I´m proposing, would provide a visualization of the "real" (i.e. full-shape) vector between points, which is the one being statistically analysed.

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