I'm trying to generate a rarefaction curve plot from a phyloseq object. I'm using the function ggrare using rarecurve function from the vegan package:
The function rarecurve allow the ploting of all the samples but I can't group the samples by metadata variable
Here is my code for the rarefaction curve plot
pRare <- ggrare(epi_physeq_3.5ans, step = 100,color = "cluster_3a", label = "cluster_3a") plot(pRare) #epi_physeq_3.5ans : phyloseq object #cluster_3a : metadata variable
This give me the curve for all samples with different colors according to the cluster_3a variable.
Howerver I want to plot only 2 curves wich are the average species richness with standar error bars for each group.
Something like from : https://doi.org/10.1038/srep08397
I can't find any package in R that allow grouping samples for plotting rarefaction curves.
Do you know any package or any idea of how that can be done ?