plot_taxa_prevalence: Visualize Prevalence Distributions for Taxa

Description Usage Arguments Details Value Author(s) Examples

View source: R/plot_taxa_prevalence.R

Description

Create taxa prevalence plots at various taxonomic levels.

Usage

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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 sudarshanshetty9@gmail.com

Examples

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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 documentation built on Nov. 8, 2020, 5:08 p.m.