data(spcaIllus)
attach(spcaIllus)
opar <- par(no.readonly=TRUE)
## comparison PCA vs sPCA

# PCA
pca2A <- dudi.pca(dat2A$tab,center=TRUE,scale=FALSE,scannf=FALSE)
pca2B <- dudi.pca(dat2B$tab,center=TRUE,scale=FALSE,scannf=FALSE)
pca2C <- dudi.pca(dat2C$tab,center=TRUE,scale=FALSE,scannf=FALSE)
pca3 <- dudi.pca(dat3$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2)
pca4 <- dudi.pca(dat4$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2)

# sPCA
spca2A <-spca(dat2A,xy=dat2A$other$xy,ask=FALSE,type=1,
plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0)

spca2B <- spca(dat2B,xy=dat2B$other$xy,ask=FALSE,type=1,
plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0)

spca2C <- spca(dat2C,xy=dat2C$other$xy,ask=FALSE,
type=1,plot=FALSE,scannf=FALSE,nfposi=0,nfnega=1)

spca3 <- spca(dat3,xy=dat3$other$xy,ask=FALSE,
type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1)

spca4 <- spca(dat4,xy=dat4$other$xy,ask=FALSE,
type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1)

# an auxiliary function for graphics
plotaux <- function(x,analysis,axis=1,lab=NULL,...){
neig <- NULL
if(inherits(analysis,"spca")) neig <- nb2neig(analysis$lw$neighbours)
xrange <- range(x$other$xy[,1])
xlim <- xrange + c(-diff(xrange)*.1 , diff(xrange)*.45)
yrange <- range(x$other$xy[,2])
ylim <- yrange + c(-diff(yrange)*.45 , diff(yrange)*.1)

s.value(x$other$xy,analysis$li[,axis],include.ori=FALSE,addaxes=FALSE,
cgrid=0,grid=FALSE,neig=neig,cleg=0,xlim=xlim,ylim=ylim,...)

par(mar=rep(.1,4))
if(is.null(lab)) lab = gsub("[P]","",x$pop)
text(x$other$xy, lab=lab, col="blue", cex=1.2, font=2)
add.scatter({barplot(analysis$eig,col="grey");box();
title("Eigenvalues",line=-1)},posi="bottomright",ratio=.3)
}

# plots
plotaux(dat2A,pca2A,sub="dat2A - PCA",pos="bottomleft",csub=2)
plotaux(dat2A,spca2A,sub="dat2A - sPCA glob1",pos="bottomleft",csub=2)

plotaux(dat2B,pca2B,sub="dat2B - PCA",pos="bottomleft",csub=2)
plotaux(dat2B,spca2B,sub="dat2B - sPCA glob1",pos="bottomleft",csub=2)

plotaux(dat2C,pca2C,sub="dat2C - PCA",pos="bottomleft",csub=2)
plotaux(dat2C,spca2C,sub="dat2C - sPCA loc1",pos="bottomleft",csub=2,axis=2)

par(mfrow=c(2,2))
plotaux(dat3,pca3,sub="dat3 - PCA axis1",pos="bottomleft",csub=2)
plotaux(dat3,spca3,sub="dat3 - sPCA glob1",pos="bottomleft",csub=2)
plotaux(dat3,pca3,sub="dat3 - PCA axis2",pos="bottomleft",csub=2,axis=2)
plotaux(dat3,spca3,sub="dat3 - sPCA loc1",pos="bottomleft",csub=2,axis=2)

plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis1",
pos="bottomleft",csub=2)
plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA glob1",
pos="bottomleft",csub=2)
plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis2",
pos="bottomleft",csub=2,axis=2)
plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA loc1",
pos="bottomleft",csub=2,axis=2)

# color plot
par(opar)
colorplot(spca3, cex=4, main="colorplot sPCA dat3")
text(spca3$xy[,1], spca3$xy[,2], dat3$pop)

colorplot(spca4, cex=4, main="colorplot sPCA dat4")
text(spca4$xy[,1], spca4$xy[,2], dat4$other$sup.pop)

# detach data
detach(spcaIllus)