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

Question

Instead of the normal plot function I am using `ggplot2` to create NMDS plots. I would like to display groups in the NMDS plot using the function `ordiellipse()` from the `vegan` package. Example data: ``` library(vegan) library(ggplot2) data(dune) # calculate distance for NMDS sol <- metaMDS(dune) # Create meta data for grouping MyMeta = data.frame( sites = c(2,13,4,16,6,1,8,5,17,15,10,11,9,18,3,20,14,19,12,7), amt = c("hi", "hi", "hi", "md", "lo", "hi", "hi", "lo", "md", "md", "lo", "lo", "hi", "lo", "hi", "md", "md", "lo", "hi", "lo"), row.names = "sites") # plot NMDS using basic plot function and color points by "amt" from MyMeta plot(sol$points, col = MyMeta$amt) # draw dispersion ellipses around data points ordiellipse(sol, MyMeta$amt, display = "sites", kind = "sd", label = T) # same in ggplot2 NMDS = data.frame(MDS1 = sol$points[,1], MDS2 = sol$points[,2]) ggplot(data = NMDS, aes(MDS1, MDS2)) + geom_point(aes(data = MyMeta, color = MyMeta$amt)) ``` How can I add ordiellipse to…

Accepted Answer

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)
```

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

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