Helper function for plotting the shapes

Description

Helper function for plotting the projections of the shapes. It displays the projection on the xy plane of the recorded points and mean shape for a given cluster. To that end, first it is needed to carry out a generalized Procrustes analysis in the cluster to obtain the full Procrustes rotated data.

Usage

projShapes(clust,array3D,asig,prototypes)

Arguments

Value

Numerical vector with the percentile values of an archetypoid.

Author(s)

Guillermo Vinue

References

Vinue, G., Simo, A., and Alemany, S., (2014). The k-means algorithm for 3D shapes with an application to apparel design, Advances in Data Analysis and Classification, 1–30.

See Also

LloydShapes, HartiganShapes, trimmedLloydShapes

Examples

landmarksNoNa <- na.exclude(landmarksSampleSpaSurv)
dim(landmarksNoNa) 
#[1] 574 198 
numLandmarks <- (dim(landmarksNoNa)[2]) / 3
#[1] 66
#As a toy example, only the first 15 individuals are used.
landmarksNoNa_First10 <- landmarksNoNa[1:10, ] 
(numIndiv <- dim(landmarksNoNa_First10)[1])
#[1] 10         
    
array3D <- array3Dlandm(numLandmarks, numIndiv, landmarksNoNa_First10)
#shapes::plotshapes(array3D[,,1]) 
#calibrate::textxy(array3D[,1,1], array3D[,2,1], labs = 1:numLandmarks, cex = 0.7) 

numClust <- 2 ; algSteps <- 1 ; niter <- 1 ; stopCr <- 0.0001
resLL <- LloydShapes(array3D, numClust, algSteps, niter, stopCr, FALSE, FALSE)
clust_kmeansProc <- resLL$asig

prototypes <- anthrCases(resLL)

projShapes(1, array3D, clust_kmeansProc, prototypes)
#legend("topleft", c("Registrated data", "Mean shape"), pch = 1, col = 1:2, text.col = 1:2)
#title("Procrustes registrated data for cluster 1 \n with its mean shape superimposed", 
#      sub = "Plane xy")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(Anthropometry)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Anthropometry/projShapes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: projShapes
> ### Title: Helper function for plotting the shapes
> ### Aliases: projShapes
> ### Keywords: math
> 
> ### ** Examples
> 
> landmarksNoNa <- na.exclude(landmarksSampleSpaSurv)
> dim(landmarksNoNa) 
[1] 574 198
> #[1] 574 198 
> numLandmarks <- (dim(landmarksNoNa)[2]) / 3
> #[1] 66
> #As a toy example, only the first 15 individuals are used.
> landmarksNoNa_First10 <- landmarksNoNa[1:10, ] 
> (numIndiv <- dim(landmarksNoNa_First10)[1])
[1] 10
> #[1] 10         
>     
> array3D <- array3Dlandm(numLandmarks, numIndiv, landmarksNoNa_First10)
> #shapes::plotshapes(array3D[,,1]) 
> #calibrate::textxy(array3D[,1,1], array3D[,2,1], labs = 1:numLandmarks, cex = 0.7) 
> 
> numClust <- 2 ; algSteps <- 1 ; niter <- 1 ; stopCr <- 0.0001
> resLL <- LloydShapes(array3D, numClust, algSteps, niter, stopCr, FALSE, FALSE)
> clust_kmeansProc <- resLL$asig
> 
> prototypes <- anthrCases(resLL)
> 
> projShapes(1, array3D, clust_kmeansProc, prototypes)
> #legend("topleft", c("Registrated data", "Mean shape"), pch = 1, col = 1:2, text.col = 1:2)
> #title("Procrustes registrated data for cluster 1 \n with its mean shape superimposed", 
> #      sub = "Plane xy")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>