complots <- function(ident, scale, ncols, save=F, subsamp=-1, complete=T)
{
	### Define colors
	cols <-(colorRamp(c(rgb(255/255, 249/255,121/255),rgb(106/255,0,0) ) )( (0:100)/100 ) )	
	cols <- cols/255
	colgrad<-NA
	for (i in 1:101) colgrad[i] <- rgb(cols [i,1] , cols[i,2], cols[i,3])

  #define the layout for the plot
	par(mfrow=c(2,3))
	
	nt <- length(spec)
	index <- which(substr(colnames(specdat),1,nchar(ident))==ident) 
	dats<- matrix(NA, ncol=nt, nrow=nrow(specdat))
	sums<-0
	cols <- colorRampPalette(c("yellow", "red"))(ncols+1)
	for (i in 1:nt)
	{
		mm <- max(specdat[,index[i]],na.rm=T) 
		if (scale)  dats[,i] <- specdat[,index[i]]/mm else dats[,i] <- specdat[,index[i]]
		if (subsamp!=-1) 
		{
			sindex <- dats[,i] < subsamp
			dats[sindex,i] <- NA
		}
		fn <- paste(ident,names(spec)[i],sep="-")
		ddat <- cbind(specdat[,2], specdat[,3],specdat[,index[i] ])
		ddat <- ddat[!is.na(rowSums(ddat)),]
		r <-rasterFromXYZ(ddat )
		
		if (save) 
		{
			png(paste(fn,".png",sep=""))
			plot(r, col=colgrad, main=fn)
			plot(map, add=T)
			dev.off()
		}
		plot(r, col=colgrad, ext=extent(r), main=fn)
		plot(map, add=T)
	
		
	}
	
	sums <- rowMeans(dats , na.rm=T)
	if (complete==F) sums <- rowMeans(dats) #use only an entry if all species have data 
	
	#standardise by the range
	ranges<- NA
	for (ii in 1:length(sums))
	{
		if (sum(!is.na(dats[ii,])))
		{
			ranges[ii] <- diff(range(dats[ii,], na.rm=T))
		} #else ranges[ii]<-NA
		
	}
	sum_range <- sums/ranges
	sum_range <- (sum_range - min(sum_range, na.rm=T))/(max(sum_range, na.rm=T)-min(sum_range,na.rm=T))
	#plot(specdat[,2], specdat[,3], col = colgrad[sum_range*ncols+1], pch=15, main="av. sum/range")
	ddat <- cbind(specdat[,2], specdat[,3],sum_range*ncols/100)
	ddat <- ddat[!is.na(rowSums(ddat)),]
	r <-rasterFromXYZ(ddat )

	if (save) 
	{
		png(paste(ident[i],"_all.png",sep=""))
		plot(r, col=colgrad, main=paste(ident," of all species"))
		plot(map, add=T)
		dev.off()
	}
	plot(r, col=colgrad, main=paste(ident," of all species"))
	plot(map, add=T)
}