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$axis2, col=nmds.col, xlab="1st Dimension", ylab="2nd
Dimension", type="p", pch=5, cex=1)
ordihull(nmds,groups=nmds.group,draw="lines",col="grey75",label=F)
legend(x=0.2, y=0.15, legend=c("group1", "group2"), pch=18, cex=1, col=c("red",
"green", "blue"))
ordihull(nmds,groups=nmds.group,draw="lines",col="grey75",label=F)
Is there any codes I can use to have similar action like ordihull for 3D NMDS
plot?
P/S: My NMDS calculations were done using mothur software, which will produce
text files of NMDS axes and stress level.
Feng
> From: [email protected]
> To: [email protected]
> Date: Tue, 25 Mar 2014 00:38:46 +0800
> Subject: [R-sig-phylo] Help with 3D NMDS Plot
>
> Hi,
> I am trying to plot a 3D NMDS, which I can do it using the following codes;
> nmds<-read.table(file="my.file", header=T)nmds.col<-c(rep("green", 10),
> rep("blue", 8), rep("red", 8))plot3d(nmds$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
>
>
>
>
> [[alternative HTML version deleted]]
>
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