if (!"FactoMineR" %in% installed.packages()) install.packages("FactoMineR")
if (!"smacof" %in% installed.packages()) install.packages("smacof")
if (!"vegan" %in% installed.packages()) install.packages("vegan")
if (!"Rtsne" %in% installed.packages()) install.packages("Rtsne")


#---------------------------------------------------------------------
# Data download
pot = read.table("https://perso.univ-rennes1.fr/bernard.delyon/data/poterie.dat",header=TRUE)
Four = pot$FOUR
pot = pot[,1:9]

#---------------------------------------------------------------------
# Compute PCA
library(FactoMineR)
pca = PCA(pot,ncp=2) # standardization and plots are by default

dev.new() # open a new figure
plot(pca$ind$coord,col="white",pch=20,xlab="PC1",ylab="PC2")
text(pca$ind$coord,label=Four,col=Four)
title("PCA")

#---------------------------------------------------------------------
# Compute MDS
D = dist(scale(pot)) # euclidean distance
mds = cmdscale(D,k=2) 

dev.new() # open a new figure
plot(mds,col="white",pch=20,xlab="1st axis",ylab="2nd axis")
text(mds,label=Four,col=Four)
title("MDS")


library(smacof)
mds.smacof <- mds(D)
plot(mds.smacof, type = "p", label.conf = list(label = TRUE, col = "darkgray"), pch = 25, col = Four)


#---------------------------------------------------------------------
# Compute isomap
library(vegan)
D = dist(scale(pot)) # euclidean distance
isom = isomap(D, ndim=2,k=10)

dev.new() # open a new figure
plot(isom$points,col="white",pch=20,xlab="1st axis",ylab="2nd axis")
text(isom$points,label=Four,col=Four)
title("Isomap")


#---------------------------------------------------------------------
# Compute tSNE
library(Rtsne)

perplexity = c(1,2,5,10)

set.seed(9)  
dev.new()
par(mfrow=c(1,4))
for (perp in perplexity){
  tsne_model_1 = Rtsne(scale(pot), check_duplicates=FALSE, pca=TRUE, 
                     perplexity=perp, theta=0, dims=2)
  plot(tsne_model_1$Y,col=Four,pch=20,xlab="1st axis",ylab="2nd axis")
  title(perp)
}