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2012-12-10T12:36:45.590
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First of all, I added column group to your NMDS data frame. <pre><code> NMDS = data.frame(MDS1 = sol$points[,1], MDS2 = sol$points[,2],group=MyMeta$amt) </code></pre> Second data frame contains mean MDS1 and MDS2 values for each group and it will be used to show group names on plot <pre><code> NMDS.mean=aggregate(NMDS[,1:2],list(group=group),mean) </code></pre> Data frame <code>df_ell</code> contains values to show ellipses. It is calculated with function <code>veganCovEllipse</code> which is hidden in <code>vegan</code> package. This function is applied to each level of NMDS (group) and it uses also function <code>cov.wt</code> to calculate covariance matrix. <pre><code> veganCovEllipse<-function (cov, center = c(0, 0), scale = 1, npoints = 100) { theta <- (0:npoints) * 2 * pi/npoints Circle <- cbind(cos(theta), sin(theta)) t(center + scale * t(Circle %*% chol(cov))) } df_ell <- data.frame() for(g in levels(NMDS$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)) } </code></pre> Now ellipses are plotted with function <code>geom_path()</code> and <code>annotate()</code> used to plot group names. <pre><code> 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$group) </code></pre> Idea for ellipse plotting was adopted from another stackoverflow <a href="https://stackoverflow.com/questions/2397097/how-can-a-data-ellipse-be-superimposed-on-a-ggplot2-scatterplot">question</a>. <img src="https://i.stack.imgur.com/nhva1.jpg" alt="enter image description here"> <h2>UPDATE - solution that works in both cases</h2> First, make NMDS data frame with group column. <pre><code>NMDS = data.frame(MDS1 = sol$points[,1], MDS2 = sol$points[,2],group=MyMeta$amt) </code></pre> Next, save result of function <code>ordiellipse()</code> as some object. <pre><code>ord<-ordiellipse(sol, MyMeta$amt, display = "sites", kind = "se", conf = 0.95, label = T) </code></pre> Data frame <code>df_ell</code> contains values to show ellipses. It is calculated again with function <code>veganCovEllipse</code> which is hidden in <code>vegan</code> package. This function is applied to each level of NMDS (group) and now it uses arguments stored in <code>ord</code> object - <code>cov</code>, <code>center</code> and <code>scale</code> of each level. <pre><code>df_ell <- data.frame() for(g in levels(NMDS$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)) } </code></pre> Plotting is done the same way as in previous example. As for the calculating of coordinates for elipses object of <code>ordiellipse()</code> is used, this solution will work with different parameters you provide for this function. <pre><code>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) </code></pre> <img src="https://i.stack.imgur.com/Q5NPs.png" alt="enter image description here">
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