R tutorial for Mothur results plot

#	--Dot/Line graphs--
#	We might be interested in plotting the first two dimensions of a PCoA or 
#	NMDS plot.  Let's do this with data generated in the Costello stool analysis
#	tutorial.  The necessary file is in your folder.

nmds<-read.table(file="stool.final.an.thetayc.0.03.lt.nmds.axes", header=T)
plot(nmds$axis1, nmds$axis2)

#	or

plot(nmds$axis2~nmds$axis1)

#	Looking at the group names in the nmds table we see that the first 12 sample
#	names are from women ("F") and the last 12 are from men ("M").  There are
#	more elegant ways to do this, but for beginners, this will work...

nmds.col<-c(rep("pink", 12), rep("blue", 12))

plot(nmds$axis2~nmds$axis1, col=nmds.col, xlab="Axis 1", ylab="Axis 2")
legend(x=0.3, y=0.6, legend=c("Female", "Male"), pch=1, col=c("pink", "blue"))

plot(nmds$axis2~nmds$axis1, col=nmds.col, xlab="Axis 1", ylab="Axis 2", pch=18,
	cex=2)
legend(x=0.3, y=0.6, legend=c("Female", "Male"), pch=18, cex=1, col=c("pink", 
	"blue"))

#	Although these points aren't linked you could connect them...

plot(nmds$axis2~nmds$axis1, col=nmds.col, xlab="Axis 1", ylab="Axis 2", pch=18, 
	cex=2, type="b")
legend(x=0.3, y=0.6, legend=c("Female", "Male"), pch=18, cex=1, lty=1, 
	col=c("pink", "blue"))

#	You can also overlay two graphs on top of each other using the points
#	command.  Here we'll put the cumulative number of sequences that have that 
#	sequence length or higher.

hist(seq.sum$nbases, col="skyblue", freq=T, xlab="Sequence Length",
	main="Distribution of Sequence Lengths", ylim=c(0,length(seq.sum$nbases)))
points(sort(seq.sum$nbases), length(seq.sum$nbases):1, type="l")
box()