plot_taxa_prevalence {microbiome} | R Documentation

## 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 sudarshanshetty9@gmail.com

### 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)

[Package microbiome version 1.12.0 Index]