get_top_taxa-deprecated: Get the most abundant taxa from a phyloseq object

In gmteunisse/Fantaxtic: Fantaxtic - nested bar plots for phyloseq data

Get the most abundant taxa from a phyloseq object

Description

This function subsets a phyloseq object to the top n most abundant taxa. Users can choose whether to select by absolute counts or relative counts, and whether to discard or collapse remaining taxa.

Usage

get_top_taxa(physeq_obj, n, relative = T, discard_other, other_label)

Arguments

physeq_obj	A phyloseq object with an otu_table and a tax_table.
n	The number of top taxa to subset to.
relative	Select taxa based on relative abundance? (default = TRUE)
discard_other	Discard remainig taxa? (default = FALSE)
other_label	Label to give to collapsed taxa.

Value

A phyloseq object

See Also

fantaxtic-deprecated

Examples

data(GlobalPatterns)
get_top_taxa(GlobalPatterns, 10)
get_top_taxa(GlobalPatterns, 10, relative = FALSE)
get_top_taxa(GlobalPatterns, 10, relative = TRUE, discard_other = TRUE)
get_top_taxa(GlobalPatterns, 10, relative = TRUE, other_label = "Non-abundant taxa")

gmteunisse/Fantaxtic documentation built on June 7, 2024, 8:47 a.m.