PCA plotting?

[Candice Neves]

Hi All

Part of my MSc has me looking at shape change in molars using EFA and the analysis portion was conducted in Momocs, but I much prefer the visualisations for PCAs in geomorph. Is there possibly a way to create a PCA of my molar PC axes using geomorph? I'd like to maintain consistency in the way my figures look, so any help on this would be very much appreciated

Thanks

Candice Neves

[Antigoni Kaliontzopoulou]

Dear Candice,

PCA and related graphical support is easily implemented in geomorph using the function plotTangentSpace. The function allows you to calculate the PCA, plot a scatterplot of PCA scores, and visualize associated shape changes. For a more detailed account, you can see the function´s help file, or this short tutorial:

https://github.com/geomorphR/geomorph/wiki/Plotting-PCA-with-TPS-grids

All the best,

Antigoni

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Antigoni Kaliontzopoulou

Assistant Researcher
CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos
University of Porto
Campus Agrário de Vairão, 4485-661 Vairão
PORTUGAL

http://antigonik.wix.com/akaliontzopoulou
http://cibio.up.pt/people/details/akaliont
http://aphylogenetics.wix.com/phylogenetics

[Candice Neves]

Hi Antigoni

I’ve been playing around with the plotTangentSpace function, but my problem is that I’m working with outline points. I can’t simply treat the outlines as landmarks, and if I did the PCAs come out looking completely different (see attached examples). I’m wondering if there is a way to use the PCs from my momocs analysis in a PCA visualisation in Geomorph?

Thanks

Candice

On 22 Jan 2018, at 12:39, Antigoni Kaliontzopoulou <ant...@gmail.com> wrote:

https://github.com/geomorphR/geomorph/wiki/Plotting-PCA-with-TPS-grids

[Antigoni Kaliontzopoulou]

Sorry, Candice, I misunderstood your question. 

geomorph works with landmark shape data. One possibility would be to do a subsampling of your outline data to produce semilandmarks, using the digit.curves() function of geomorph, and possibly complement these with some fixed landmarks, which could then be used in a landmark-based shape analysis. In that case, you would need to superimpose your data using gpagen() with the curves argument, and then do the PCA using plotTangentSpace. But this is an analytically completely different solution compared to outline analysis using EFA.

Alternatively, the PCA and scatter-plotting part of plotTangentSpace are both based on the prcomp() base function of R, so producing plots with your EFA-treated data should be straightforward by setting uniform plot() arguments in R.

Hope this helps,

Antigoni