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 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$amt))
#Add species loadings
vec.sp<-envfit(sol$points, NMDS.log, perm=1000)
plot(vec.sp, p.max=0.1, col="blue")
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()