Nothing
pcoa <- function(DM, groups, inds, name,surname){
ntt <- length(levels(groups))
#PCoA
pcol <- cmdscale(DM, k=length(inds)-1, eig=T)
var <- pcol$eig / sum(pcol$eig) *100
var
var1 <- round(var[1], digits=1)
var2 <- round(var[2], digits=1)
pcol$points<-as.data.frame(pcol$points)
spcoo<-split(pcol$points, groups)
maxX <- max(pcol$points$V1)
minX <- min(pcol$points$V1)
maxY <- max(pcol$points$V2)
minY <- min(pcol$points$V2)
fullname <- paste(name,surname, sep='-')
cat("- Saving PCoA figure for ", surname, " in file: ", paste(fullname,"png",sep='.'),".....")
png(filename=paste(fullname,"png",sep='.'))
par(bty = 'n')
plot(0,0, main=paste(name,surname, sep=": "), type = "n",xlab=paste("C1 (",var1,"%)"),ylab=paste("C2 (",var2,"%)"), xlim=c(minX-10^floor(log10(abs(minX))),maxX+10^floor(log10(abs(maxX)))), ylim=c(minY-10^floor(log10(abs(minY))),maxY+10^floor(log10(abs(maxY)))), frame=TRUE, cex=1.5)
bgcolors<-rainbow(ntt+1)[-2] #No yellow?
symbs <- c(21,22,23,24,25) #What if we have > 7 groups???
for(i in 1:ntt){
points(spcoo[[i]], pch=21, col="black", bg=bgcolors[i])
}
s.class(pcol$points, groups, cpoint=0, col=bgcolors, add.plot=TRUE)
dev.off()
cat("Ok!\n")
prefix <- paste(name,surname,sep='-')
write.csv(data.frame(Group=groups,ind=inds,pcol$points), file=paste(prefix,"PCoA.coor.csv", sep='-'))
write.csv(data.frame(pcol$eig), file=paste(prefix,"PCoA.eige.csv", sep='-'))
}
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