plot_taxa_prevalence: Visualize Prevalence Distributions for Taxa

In microbiome/microbiome: Microbiome Analytics

Visualize Prevalence Distributions for Taxa

Description

Create taxa prevalence plots at various taxonomic levels.

Usage

plot_taxa_prevalence(x, level, detection = 0)

Arguments

x	phyloseq-class object, OTU data must be counts and not relative abundance or other transformed data.
level	Phylum/Order/Class/Family
detection	Detection threshold for presence (prevalance)

Details

This helps to obtain first insights into how is the taxa distribution in the data. It also gives an idea about the taxonomic affiliation of rare and abundant taxa in the data. This may be helpful for data filtering or other downstream analysis.

Value

A ggplot plot object.

Author(s)

Sudarshan A. Shetty [e-mail]

Examples

data(atlas1006)
# Pick data subset just to speed up example
p0 <- subset_samples(atlas1006, DNA_extraction_method == "r")
p0 <- prune_taxa(taxa(p0)[grep("Bacteroides", taxa(p0))], p0)
# Detection threshold (0 by default; higher especially with HITChip)
p <- plot_taxa_prevalence(p0, 'Phylum', detection = 1)
print(p)

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.