labeling nmds plot by column values in r

Question

I ran metaMDS and want to plot and color code by a grouping based on certain data frame characters. In my original data frame, df$yr are years and df$2 are sites. I want to color by the years.

caltmds <- metaMDS(df[,3:12], k=3)
plot(caltmds, type = 'n')
cols <- c("red2", "mediumblue")
points(caltmds, col = cols[df$yr])

I also tried from this post:

scl <- 3
colvec <- c("red2", "mediumblue")
plot(caltmds, type = "n", scaling = scl) 
with(df, points(caltmds, display = "sites", col = colvec[yr], pch = 21, bg = colvec[yr]))
text(caltmds, display = "species", cex = 0.8, col = "darkcyan")
with(df, legend("topright", legend = levels(yr), bty = "n", col = colvec, pch = 21, pt.bg = colvec))

Nothing plots

Can you add `dput(df)` output, so we can reproduce your case? — Istrel, Feb 22 '19 at 22:44
It is a massive data frame which is why I didn't provide any data..which I guess limits the help — KNN, Feb 23 '19 at 17:00

score 0 · Accepted Answer · answered Feb 22 '19 at 23:09

0

#DATA
df1 = mtcars

mycolors = df1$cyl   #Identify the grouping vector

library(vegan)
m = metaMDS(df1)

x = scores(m)  #Extract co-ordinates

plot(x, col = as.numeric(as.factor(mycolors)))

answered Feb 22 '19 at 23:09

d.b

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Your code: `x = scores(m) #Extract co-ordinates` is what I was missing! This colors the points on the plot by the two years - as I wanted. I will see if I can build out from here now to add on labels, legend, etc. – KNN Feb 23 '19 at 16:56

labeling nmds plot by column values in r

1 Answers1