subset_taxa in loop

[jeremysutherland]

Does anyone know why this doesn't work?

PHYLA <- unique(ps.rare@tax_table$phylum)
for (n in PHYLA){
  ps <- subset_taxa(ps.rare, phylum == n) ### This doesn't work. Error in eval(e, x, parent.frame()) : object 'n' not found
  print(ps) 
  }

This script is just for example purposes. The issue seems to be passing the "n" variable to the '=='. I've tried str(n), as.character(n), print(n). Nothing seems to do the trick.

[jeremysutherland]

This is the solution:

PHYLA <- unique(ps.rare@tax_table$phylum)
for (i in PHYLA){
ASV <- as.data.frame(ps.rare@otu_table)
TAXA <- as.data.frame(ps.rare@tax_table)
TAXA <- subset(TAXA, phylum == i)
print(dim(ASV))
ASV <- subset(ASV, rownames(ASV) %in% rownames(TAXA))
print(dim(ASV))
}