phyloseq: plot_phyloseq-methods – R documentation

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plot_phyloseq-methods

Generic plot defaults for phyloseq.

Description

There are many useful examples of phyloseq graphics functions in the phyloseq online tutorials. The specific plot type is chosen according to available non-empty slots. This is mainly for syntactic convenience and quick-plotting. See links below for some examples of available graphics tools available in the phyloseq-package.

Usage

plot_phyloseq(physeq, ...)

## S4 method for signature 'phyloseq'
plot_phyloseq(physeq, ...)

Arguments

`physeq`	(Required). `phyloseq-class`. The actual plot type depends on the available (non-empty) component data types contained within.
`...`	(Optional). Additional parameters to be passed on to the respective specific plotting function. See below for different plotting functions that might be called by this generic plotting wrapper.

Value

A plot is created. The nature and class of the plot depends on the physeq argument, specifically, which component data classes are present.

Examples

data(esophagus)
plot_phyloseq(esophagus)

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23