NMDS biplot to show both samples and species using R

Integrating mothur with other programs
1

Dear Pat,
I have successfully plotted NMDS to show sample sites using following functions.

nmds<-read.table(file=“stool.final.an.thetayc.0.03.lt.nmds.axes”, header=T)
plot(nmds$axis1, nmds$axis2)
Then I changed the colors for different sites using functions mentioned in the R tutorial (https://www.mothur.org/wiki/R_tutorial)
Now, I want to show both samples and the species(or OTUs) on the same plot using R functions.

I couldn’t find any related document to do this, so could you please advise me to do this wit R( I know Vegan and Phyloseq packages can be used for this, but I want to plot the NMDS with mothur output values).

Many thanks.
DilhanideSri

2

You can certainly do that in R, but I’m afraid it’s a bit beyond the scope of what we have time for in the forum.

Pat

3

as far as I know this isn’t implemented in ggord yet. Here is how I’ve done it


look at this question, it's how I started. http://stackoverflow.com/questions/14711470/plotting-envfit-vectors-vegan-package-in-ggplot2 
scrs <- as.data.frame(scores(bc.nms, display ='sites'))
scrs <- cbind(scrs, DiagnosisGroup = alpha.clin$DiagnosisGroup)
spec <- envfit(bc.nms, otu, perm=999)

spp.scrs <- as.data.frame((scores(spec, display="vectors")))
spp.scrs <- cbind(spp.scrs, Species =rownames(spp.scrs))
spp.scrs <- cbind(spp.scrs, pVal=spec$vectors$pvals)
# spp.scrs <- cbind(spp.scrs, Taxa=taxa$prefered, phy.col=taxa$phy.col)
spp.scrs <- cbind(spp.scrs, Phyla=taxa$class)

###color vectors by phyla

ggplot(scrs)+
    coord_fixed()+
    geom_segment(data=spp.scrs[spp.scrs$pVal<0.005,], 
                 aes(x=0, xend=NMDS1, y=0, yend=NMDS2, color = Phyla),
                 arrow=arrow(length=unit (0.25, "cm")), size=1.5)+
    geom_point(mapping=aes(x=NMDS1, y=NMDS2, shape = as.factor(DiagnosisGroup)), size=2)+
    geom_text(data=scrs, aes(x=NMDS1-.02, y=NMDS2-.02, label=row.names(scrs)), size=4)+
    theme_bw()