Hello,

I am performing a pangenomic analysis on a set of bacterial strains and would like to plot pangenome and core genome accumulation curves using vegan in R.

For the pangenome accumulation/rarefaction curve, I used a gene presence-absence table to do the following:

library(vegan)
specaccum(matrix,"random",permutations=1000)

(and plotting the resultant object with ggplot)

Can someone help me make a similar curve to show a core gene accumulation/rarefaction curve?

Thanks so much for your time!