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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(phyloseq)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/phyloseq/plot_phyloseq-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot_phyloseq
> ### Title: Generic plot defaults for phyloseq.
> ### Aliases: plot_phyloseq plot_phyloseq,phyloseq-method
>
> ### ** Examples
>
> data(esophagus)
> plot_phyloseq(esophagus)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.