Plot 3D Wireframes from Morphologika

February 25, 2013
By

(This article was first published on geomorph, and kindly contributed to R-bloggers)


Hi morphometricians,
A quick update: a function to plot Morphologika 3D wireframes using the package geomorph. This routine (or a version of it) will be included in our next package update under the "read.morphologika" function.

Enjoy!

Example:

library(geomorph)
# create an array of 10 random 3D specimens with 6 landmarks each to GPA
data<-array(abs(rnorm(18*10)),c(6,3,5))

# create a simple wireframe, e.g., pt1 connects to pt2, 2-to-3, 3-to-4,...etc.
wireframe<-matrix(c(1,2,2,3,3,4,4,5,5,6),ncol=2,byrow=T)
wireframe
mydata.gpa<-gpagen(data) #gpa landmarks

# choose the largest and/or smallest specimen
max<-which.max(mydata.gpa$Csize) #ID specimen w/largest CS
min<-which.min(mydata.gpa$Csize) #ID specimen w/smallest CS

# wireframe function: wirefun
# Input: 2 matrices: A & W
#  A is the procrustes residualsmatrix
#  W is the wireframe matrix
wirefun<-function(A,W,...){
  plot3d(A,type="n", aspect=FALSE,...)
  for(i in 1:dim(W)[1]){
    points3d(A[W[i,],],...)
    text3d(A[W[i,],],texts=W[i,],...)
    lines3d(rbind(A[W[i,1],],A[W[i,2],]),...)
  }
}

# Plot
wirefun(A=mydata.gpa$coords[,,1],W=wireframe,size=10,adj=2.5,col="black")

To leave a comment for the author, please follow the link and comment on his blog: geomorph.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...



If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.