Use scatterplot3d to plot a tetrahedral color space

tcs_s3d.R

# (very convoluted) function to plot tetrahedral colorspace

require(pavo)
require(scatterplot3d)
require(RColorBrewer)

# get the data
data(sicalis)
tcsdat <- tcs(vismodel(sicalis))

# filter only xyz coordinates
tcsdat.xyz <- tcsdat[,c('x','y','z')]

# make a color palette
pal <- brewer.pal(3, 'Set1')

# TETRAHEDRAL FUNCTION
# note that if points to be plotted are changed, the whole function needs to be
# sourced back into R

tetraplot<-function(Y=NULL,angle=65,scale.y=0.45)

{
par(mar=c(1,1,1,1))

if(!is.null(Y)){
  test<-scatterplot3d(x=Y$x, y=Y$y, z=Y$z, box=TRUE, pch=16, color=rgb(0,0,0,.5), 
    xlim=c(-1.22,.612), ylim=c(-.35,.707), zlim=c(-.25,.75), 
    axis=F, grid=F, angle=angle, scale.y=scale.y, cex.symbols=1, mar=c(1,1,1,1))
  }

if(is.null(Y)){
  test<-scatterplot3d(x=0, y=0, z=0, box=TRUE, pch=16, color=rgb(0,0,0,.5), 
    xlim=c(-1.22,.612), ylim=c(-.35,.707), zlim=c(-.25,.75), 
    axis=F, grid=F, angle=angle, scale.y=scale.y, cex.symbols=1, mar=c(1,1,1,1))
  }

#################################
# INSERT POINT INFORMATION HERE #
#################################

test$points3d(subset(tcsdat.xyz, 'C'), pch=20, col=pal[1])
test$points3d(subset(tcsdat.xyz, 'B'), pch=20, col=pal[2])
test$points3d(subset(tcsdat.xyz, 'T'), pch=20, col=pal[3])

#########################
# END POINT INFORMATION #
#########################

# Vertex coordinates
uv<-test$xyz.convert(0,0,.75)
blue<-test$xyz.convert((-1*sqrt(1.5)),(-1/(2*sqrt(2))),-.25)
green<-test$xyz.convert(0,(1/sqrt(2)),-.25)
red<-test$xyz.convert((.5*sqrt(1.5)),(-1/(2*sqrt(2))),-.25)
no.uv<-test$xyz.convert(0,0,-.25)

# Add text to vertices (can also be changed to points if preferred)
text(red$x,red$y,"red")
text(green$x,green$y,"green")
text(blue$x,blue$y,"blue")
text(uv$x,uv$y,"uv")

# Draw tetrahedron
segments(uv$x,uv$y,red$x,red$y)
segments(uv$x,uv$y,green$x,green$y)
segments(uv$x,uv$y,blue$x,blue$y)
segments(red$x,red$y,green$x,green$y)
segments(green$x,green$y,blue$x,blue$y)
segments(blue$x,blue$y,red$x,red$y)

}

# Call the function to plot
tetraplot()

# angle and scale arguments can be used to modify the plot

tetraplot(, angle=45)

# add legend
legend('topright', pch=20, col=pal, legend=c('crown','breast','throat') )