Plotting envfit vectors (vegan package) in ggplot2

Question

I am working on finalizing a NMDS plot that I created in vegan and ggplot2 but cannot figure out how to add envfit species-loading vectors to the plot. When I try to it says "invalid graphics state". The example below is slightly modified from another question (Plotting ordiellipse function from vegan package onto NMDS plot created in ggplot2) but it expressed exactly the example I wanted to include since I used this question to help me get metaMDS into ggplot2 in the first place: ``` library(vegan) library(ggplot2) data(dune) # calculate distance for NMDS NMDS.log<-log(dune+1) sol <- metaMDS(NMDS.log) # 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) # same in gg…

Accepted Answer

Start with adding libraries. Additionally library `grid` is necessary.

```
library(ggplot2)
library(vegan)
library(grid)
data(dune)
```

Do metaMDS analysis and save results in data frame.

```
NMDS.log<-log(dune+1)
sol <- metaMDS(NMDS.log)

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

Add species loadings and save them as data frame. Directions of arrows cosines are stored in list `vectors` and matrix `arrows`. To get coordinates of the arrows those direction values should be multiplied by square root of `r2` values that are stored in `vectors$r`. More straight forward way is to use function `scores()` as provided in answer of @Gavin Simpson. Then add new column containing `species` names.

```
vec.sp<-envfit(sol$points, NMDS.log, perm=1000)
vec.sp.df<-as.data.frame(vec.sp$vectors$arrows*sqrt(vec.sp$vectors$r))
vec.sp.df$species<-rownames(vec.sp.df)
```

Arrows are added with `geom_segment()` and species names with `geom_text()`. For both tasks data frame `vec.sp.df` is used.

```
ggplot(data = NMDS, aes(MDS1, MDS2)) + 
  geom_point(aes(data = MyMeta, color = MyMeta$amt))+
  geom_segment(data=vec.sp.df,aes(x=0,xend=MDS1,y=0,yend=MDS2),
      arrow = arrow(length = unit(0.5, "cm")),colour="grey",inherit_aes=FALSE) + 
  geom_text(data=vec.sp.df,aes(x=MDS1,y=MDS2,label=species),size=5)+
  coord_fixed()
```

Plotting envfit vectors (vegan package) in ggplot2

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