Hi,
I am trying to plot a 3D NMDS, which I can do it using the following codes;
nmds<-read.table(file="my.file", header=T)nmds.col<-c(rep("green", 10),
rep("blue", 8), rep("red", 8))plot3d(nmds$axis1, nmds$axis2, nmds$axis3,
col=nmds.col, xlab="1st Dimension", ylab="2nd Dimension", zlab="3rd Dimension",
type="s", size=2)
however, I intend to draw lines to group up dots of same categories, which I
able to do but only with 2D NMDS using the following codes;
nmds<-read.table(file="my.file",header=T)nmds.col<-c(rep("green",10),rep("blue",8),rep("red",8))nmds.group<-c(rep("group1",9),rep("group2",8))plot(nmds$axis1,
nmds$axis2, col=nmds.col, xlab="1st Dimension", ylab="2nd Dimension",
type="p", pch=5,
cex=1)ordihull(nmds,groups=nmds.group,draw="lines",col="grey75",label=F)legend(x=0.2,
y=0.15, legend=c("group1", "group2"), pch=18, cex=1, col=c("red", "green",
"blue"))ordihull(nmds,groups=nmds.group,draw="lines",col="grey75",label=F)
Is there any codes I can use to have similar action like ordihull for 3D NMDS
plot?
P/S: My NMDS calculations were done using mothur software, which will produce
text files of NMDS axes and stress level.
Feng
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