I'm new to R world and I was trying to do a pca on a dataset; I used rgl library for 3D plots but when I run my code il plots everithing but lines3d and planes3d.
I expected to have a clear result because it was the exact same code as the teacher's one but what I got was only the plots of the points3d function; the problem lies when I use the functions lines3d and planes3d
That's the code I used:
library(rgl)
library(mvtnorm)
#matrix
nobs = 100
sig = rbind(c(9, 1, 1), c(1, 4, 1), c(1, 1, 1))
mu = c(0, 2, 3)
X = rmvnorm(nobs,mu,sig)
X
#mean
M <- colMeans(X)
M
#variance matrix
S <- cov(X)
S # eigen(S)
R = cor(X)
R
open3d()
points3d(X, asp=1, size=4)
axes3d()
#principal components
PC = princomp(X)
PC
PC$loadings
eigen(S)$vectors
PC$scores
open3d()
points3d(X, asp=1, size=4)
axes3d()
#display mean on the graphic
points3d(t(M), col='red', size=6)
#lines to connect the mean to the observations
for(i in 1:nobs)
lines3d(rbind(X[i,], M))
#first principal component
open3d()
points3d(X, asp=1, size=4)
axes3d()
PC1 <- NULL
for (i in 1:nobs) PC1 <- rbind(PC1, PC$loadings[,1]*PC$scores[i,1] + M)
points3d(PC1, col = 'red', size = 6)
for (i in 1:nobs) lines3d(rbind(X[i,], PC1[i,]), col = 'blue')
lines3d(rbind(M + 2*PC$sdev[1]*PC$loadings[,1], M - 2*PC$sdev[1]*PC$loadings[,1]), col = 'green')
#second principal component
open3d()
points3d(X, asp=1, size=4)
axes3d()
PC12 <- NULL
for(i in 1:nobs)PC12 <- rbind(PC12, PC$loadings[,1]*PC$scores[i,1] + PC$loadings[,2]*PC$scores[i,2] + M)
points3d(PC12, col='red', size=6)
for(i in 1:nobs)lines3d(rbind(X[i,], PC12[i,]),col='blue')
library(pracma)
normal = cross(PC$loadings[,1],PC$loadings[,2])
planes3d(a = normal,d = - normal %*% M, col = "orange")
