Plotting ordiellipse function from vegan package onto NMDS plot created in ggplot2

First of all, I added column group to your NMDS data frame.

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

Second data frame contains mean MDS1 and MDS2 values for each group and it will be used to show group names on plot

  NMDS.mean=aggregate(NMDS[,1:2],list(group=group),mean)

Data frame df_ell contains values to show ellipses. It is calculated with function veganCovEllipse which is hidden in vegan package. This function is applied to each level of NMDS (group) and it uses also function cov.wt to calculate covariance matrix.

  veganCovEllipse<-function (cov, center = c(0, 0), scale = 1, npoints = 100)   {    theta <- (0:npoints) * 2 * pi/npoints    Circle <- cbind(cos(theta), sin(theta))    t(center + scale * t(Circle %*% chol(cov)))  }  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(cov.wt(cbind(MDS1,MDS2),wt=rep(1/length(MDS1),length(MDS1)))$cov,center=c(mean(MDS1),mean(MDS2)))))                    ,group=g))  }

Now ellipses are plotted with function geom_path() and annotate() used to plot group names.

  ggplot(data = NMDS, aes(MDS1, MDS2)) + geom_point(aes(color = group)) +    geom_path(data=df_ell, aes(x=MDS1, y=MDS2,colour=group), size=1, linetype=2)+    annotate("text",x=NMDS.mean$MDS1,y=NMDS.mean$MDS2,label=NMDS.mean$group)

Idea for ellipse plotting was adopted from another stackoverflow question.

UPDATE - solution that works in both cases

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)

Two updates:

1.NMDS.mean=aggregate(NMDS[,1:2],list(group=group),mean)

should be updated to

NMDS.mean=aggregate(NMDS[,1:2],list(group=NMDS$group),"mean")

NMDS$group is not a factor, so looping over levels of NMDS$group does not work. Df_ell returns zero observations in zero variables.

 NMDS$group <- as.factor(NMDS$group)

fixes this.