phyloseq_taxonomic_resolution: Estimate taxonomic resolution of data

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Estimate taxonomic resolution of data

Description

Estimate taxonomic resolution of data

Usage

phyloseq_taxonomic_resolution(physeq, add_counts = TRUE, justDF = FALSE)

Arguments

physeq	A phyloseq-class object
add_counts	Logical, add read and OTU counts on top of the bars (default, TRUE)
justDF	Logical, just return the data.frame, do not plot (default, FALSE)

Details

This function counts the number of OTUs and reads annotated at the lowest level of taxonomic classification and shows it on a barplot.

Value

ggplot-object (if justDF = FALSE) or a data.frame (if justDF = TRUE).

See Also

get_max_taxonomic_rank

Examples

data(GlobalPatterns)
gpt <- phyloseq_taxonomic_resolution(GlobalPatterns)
gpt
gpt$data_wide

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.