rank_tax: Generate a ranked vector of OTUs or other taxonomic level.

In cb-42/cbmbtools: R Functions for Facilitating Microbiome Analyses

Description

Generate a ranked vector of OTUs or other taxonomic level.

Usage

rank_tax(df, desc = TRUE, tax_level = "OTU", tax_df = otu_good_taxonomy)

Arguments

df	A dataframe containing OTU data to be used to determine ranking.
desc	Boolean for determining whether the OTUs should be sorted in descending (default) or ascending order.
tax_level	Taxonomic level in tax_df to be utilized for ranking. The values within tax_level should also be column names in df. Defaults to OTU.
tax_df	Taxonomy table. Defaults to otu_good_taxonomy.

Value

A ranked character vector based on the mean abundance corresponding to levels in tax_df[, tax_level].

Examples

rank_tax(df = dplyr::filter(otu_df, Experiment == "Amx"))
rank_tax(phy_filt, tax_level = "Phylum")

cb-42/cbmbtools documentation built on Jan. 9, 2021, 1:38 a.m.