phyloseq_prevalence_plot: Prevalence plot (total OTU abundance vs OTU prevalence).

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Prevalence plot (total OTU abundance vs OTU prevalence).

Description

This function will plot total OTU abundance vs the fraction of samples in which an OTU is observed.

Usage

phyloseq_prevalence_plot(
  physeq,
  prev.trh = NULL,
  taxcolor = NULL,
  facet = FALSE,
  point_alpha = 0.7,
  showplot = T
)

Arguments

physeq	A phyloseq-class object
prev.trh	Add horizontal line with prevalence threshold (default is NULL, but 0.05 = 5% of samples)
taxcolor	Taxonomy rank for coloring the points (e.g. "Phylum")
facet	Logical, split to separate panels by taxonomy rank used for coloring the points
point_alpha	Point transparency value
showplot	Logical, show plot on screen

Value

Plot of class 'ggplot'.

See Also

phyloseq_filter_prevalence

Examples

data(GlobalPatterns)
# Subset data
GP <- subset_taxa(GlobalPatterns, Phylum %in% c("Acidobacteria", "Actinobacteria", "Firmicutes", "Verrucomicrobia"))
phyloseq_prevalence_plot(GP, taxcolor = "Phylum", facet = TRUE, point_alpha = 0.5, prev.trh = 0.05)

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