taxa_level: Taxa level collating

In umerijaz/microbiomeSeq: Microbial community analysis in an environmental context.

Description

This function takes a physeq object and returns a physeq object with taxa at a specified taxonomic level. It extends the tax_glom to include names of corresponding taxa at a specified taxonomy level and updating tree tip labels accordingly.

Usage

taxa_level(physeq, which_level)

Arguments

physeq	(Required). A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.
which_level	(Required). Character string specifying taxonomic level.

Value

physeq object at specified taxonomic level.

Examples

data(pitlatrine)
physeq<-data(physeq)
physeq <- taxa_level(physeq = physeq,which_level = "Family")

umerijaz/microbiomeSeq documentation built on May 30, 2019, 3:13 p.m.