How to add point labels to ggplot object?

Question

I'm having trouble with this one here. I'm trying to add labels to my CCA plot, only for the species category. Normally I would include that in the aes function, however, ggplot2 isn't capable to creating cca plots, so I had to use the vegan package to create the plot, ggvegan to convert it to an object recognizable by ggplot, and then edit it as an object from there.

cca <- cca(sp_matrix~average+bpi_st_fi+northing+easting+slope+depth, 
data=mollusca)
plot(cca)
summary(cca)
ccaplot <- autoplot(cca)
ccaplot + 
  lims(x = c(-2.5, 2.5)) + lims(y = c(-2.5,2.5)) +  
  theme(panel.background = element_blank()) + geom_hline(aes(yintercept=0), 
colour="#8c8c8c") +
  geom_vline(aes(xintercept=0), colour="#8c8c8c")

This is the resulting CCA plot that is generated

When I create the original plot using "vegan", it labels the species, but when I convert it to a ggplot object it deletes them. Will I have to edit the plot using base R code, or is there a way to both get the species labels back and edit their size, font and colour with ggplot2?

use fortify(cca, display = "sp") to get just the species scores and then give this data.frame to geom_label — Richard Telford
I'm sorry, I'm not very proficient in R, how do I make it a data frame and give it to geom_label? — Sara Fritsch

Richard Telford Richard Telford · Accepted Answer · 2018-03-26T10:27:03

This is one way to do it. I've used ggrepel to reduce overlapping labels. In practice, you will probably have to select just a few species to label, unless your system is species poor

library("vegan")
library("ggvegan")
library("ggrepel")
data("dune")
data("dune.env")


CCA <- cca(dune ~ ., data = dune.env[,1:3])

sp <- fortify(CCA, display = "sp")

autoplot(CCA) +
  geom_text_repel(data = sp, mapping = aes(x = CCA1, y = CCA2, label = Label))

How to add point labels to ggplot object?

1 Answers