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I am trying to plot an NMDS plot of species community composition data with ellipses which represent 95% confidence intervals. I generated the data for my NMDS plot using metaMDS and successfully have ordinations generated using the basic plot functions in R (see code below). However, I am struggling to get my data to plot successfully using ggplot2 and this is the only way I have seen 95% CIs plotted on NMDS plots. I am hoping someone is able to help me correct my code so the ellipses show 95% CIs, or could point me in the right direction for achieving this using other methods?

My basic code for plotting my NMDS plot:

orditorp(dung.families.mds, display = "sites", labels = F, pch = c(16, 8, 17, 18) [as.numeric(group.variables$Heating)], col = c("green", "blue", "orange", "black") [as.numeric(group.variables$Dungfauna)], cex = 1.3)
ordiellipse(dung.families.mds, groups = group.variables$Dungfauna, draw = "polygon", lty = 1, col = "grey90")
legend("topleft", "stress = 0.1329627", bty = "n", cex = 1)

My ordination: NMDS ordination plot

Katie Jones
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1 Answers1

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I realize this question is old, but I found this post useful for plotting confidence ellipses during my work, and maybe it will help you. Plotting ordiellipse function from vegan package onto NMDS plot created in ggplot2

Edit: Below I have copied the code from the second part of Didzis Elferts's answer on the link above. Where "sol" is the metaMDS object:

First, make NMDS data frame with group column.

NMDS = data.frame(MDS1 = sol$points[,1], MDS2 = >sol$points[,2],group=MyMeta$amt)

Next, save result of function ordiellipse() as some object.

ord<-ordiellipse(sol, MyMeta$amt, display = "sites", >kind = "se", conf = 0.95, label = T)

Data frame df_ell contains values to show ellipses. It is calculated again with function veganCovEllipse which is hidden in vegan package. This function is applied to each level of NMDS (group) and now it uses arguments stored in ord object - cov, center and scale of each level.

df_ell <- data.frame()
for(g in levels(NMDS$group)){
  df_ell <- rbind(df_ell, cbind(as.data.frame(with(NMDS[NMDS$group==g,],
                  veganCovEllipse(ord[[g]]$cov,ord[[g]]$center,ord[[g]]$scale)))
                                ,group=g))
}

Plotting is done the same way as in previous example. As for the calculating of coordinates for elipses object of ordiellipse() is used, this solution will work with different parameters you provide for this function.

ggplot(data = NMDS, aes(MDS1, MDS2)) + geom_point(aes(color = group)) +
  geom_path(data=df_ell, aes(x=NMDS1, y=NMDS2,colour=group), size=1, linetype=2)
HarMe
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