How to plot PCoA, NMDS... directly from mothur?

I am follwing MiSeq_SOP and I have reached the PCoA (from OTUs and phylogenetic approaches) and NMDS generation steps.

I have obtained the files with the distances (.axes, and so on) and all the other files from these commands. However, I do not know how can I plot the results to get some beautiful figures for my future publications.

Is there any way to have these plots directly from MOTHUR?
Is there any other way to do so in a straightforward manner?

Thanks a lot

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Within mothur, no. But the .axes files are easy to load into Excel or R and plot. There’s a nice R tutorial on the wiki (here) that has a worked example of plotting an NMDS near the bottom of the page.

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Thanks dwaite!

I have searched the R tutorial for mothur and I have found the functions you said.

However, they didn’t work as I needed, so I generate new R code for having a plot of the nmds/PCoA distances, just having the points and their names in black:

nmds<-read.table(file="nmds.axes", header=T)
rownames(nmds)<- nmds[,1]
sample_names.nmds<-factor(rownames(nmds))
plot(nmds$axis2~nmds$axis1, xlab="Axis 1", ylab="Axis 2")
with(nmds, text(x = axis1, y = axis2, labels = sample_names.nmds))

Hope it will help someone!!

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