Reads TA data and plots piechart and chao1/rarefaction line graphs3

plot_morphospecies.R

library(vegan)
class <- "Anthony"

dat <- read.table(paste(class,".dat", sep=""), sep = "\t", header=TRUE)

#######PieChart############

piedata <- matrix(ncol=1, nrow=length(unique(dat[,1])))
names <- levels(unique(dat[,1]))
rownames(piedata) <- names


######Total number of morphospecies per order#####
for (i in 1:length(names)){
	sum <- 0
	for (j in 1:nrow(dat)){
		if (dat[j,1]==names[i])
			{sum <- sum + 1}	
	}
	piedata[i] <- sum
}



#####Total number of insects per order#########
#for (i in 1:length(names)){
#	sum <- 0
#	for (j in 1:nrow(dat)){
#		if (dat[j,1]==names[i])
#			{sum <- sum + dat[j,(ncol(dat))]}	
#	}
#	piedata[i] <- sum
#}

pdf(file=paste(class,"_pie.pdf", sep=""))
pie(piedata, labels = rownames(piedata), col=rainbow(nrow(piedata)), main=paste(class,"'s class",sep=""))
dev.off()



###########Rarefaction and Chao############
tdat <- t(dat[3:(ncol(dat)-1)])

### create a matrix of chao and rarefyed data #######
#rdat <- rrarefy(tdat, (nrow(tdat)))
pdf(file=paste(class,"_chao.pdf", sep=""))
plot(specaccum(tdat)$sites, specaccum(tdat)$richness, ylim=c(0,300), ylab="# of Morphospecies", xlab="# of Group Samples", type="b", pch=1, col=2, cex=2, cex.lab=1.5, main=paste(class,"'s class",sep=""))


chao <- matrix(ncol=2, nrow=nrow(tdat))
for (i in (nrow(tdat)):1)
	{
	chao[i,2] <- specpool(tdat[1:i,])$chao
	chao[i,1] <- i
	}

lines(chao, lty=2, type="b", pch=0, col=4, cex=2)
legend("topright", legend=c("Observed", "Chao1"),lty=c(1,2), pch=c(1,0), col=c(2,4))
dev.off()