Convert rarefaction plots from Vegan to ggplot2 in R?

1
votes

Hi I am running species estimator calculations in the package 'vegan'.

The code I'm running is very simple:

library(vegan)    
data(BCI)
p<-poolaccum(BCI, permutations = 50)
p.plot<-plot(p, display = c("chao", "jack1", "jack2"))

The object p.plot is a trellis type object. So I was not able to convert it to a dataframe to for ggplot. The reason why I want to be able to use ggplot is because I want all the estimator curves to be on the same graph with labels. I'm also doing these plots for other datasets and I want to consolidate space as much as possible.

Any help would be great! Thank you

1
rggplot2vegan
Maybe this github.com/gavinsimpson/ggvegan? – Tung

1 Answers

3
votes

summary(p) can help you get input data for ggplot2. I demonstrate Chao plot here:

library(ggplot2)
library(reshape2)
chao <- data.frame(summary(p)$chao,check.names = FALSE)
colnames(chao) <- c("N", "Chao", "lower2.5", "higher97.5", "std")
chao_melt <- melt(chao, id.vars = c("N","std"))
ggplot(data = chao_melt, aes(x = N, y = value, group = variable)) +
  geom_line(aes(color = variable))

p is what you got in p<-poolaccum(BCI, permutations = 50) The output is like this, you can make some adjustment for multiple plots and theme.