Aggregate Top Taxa v2 — aggregate_top_taxa2 • microbiomeutilities

Summarize phyloseq: combine other than the most abundant taxa.

aggregate_top_taxa2(x, top, level)

Arguments

x: phyloseq-class object
top: Keep the top-n taxa, and merge the rest under the category 'Other'. Instead of top-n numeric this can also be a character vector listing the groups to combine.
level: Summarization level (from rank_names(pseq))

phyloseq-class object

Backup from microbiome R pkg. This function is replaced by aggregate_rare function.

See citation('microbiome')

data(dietswap)
s <- aggregate_top_taxa2(dietswap, top = 3, "Phylum")