cca-rda-phyloseq-methods: Constrained Correspondence Analysis and Redundancy Analysis.

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

Constrained Correspondence Analysis and Redundancy Analysis.

Description

This is the internal function that simplifies getting phyloseq data into the constrained ordination functions, cca and rda. Unlike capscale.phyloseq, the formula argument to these methods is optional, and results in an unconstrained ordination.

Usage

cca.phyloseq(physeq, formula = NULL, method = "CCA", ...)

## S4 method for signature 'phyloseq,formula'
cca.phyloseq(physeq, formula = NULL,
  method = "CCA", ...)

## S4 method for signature 'otu_table,ANY'
cca.phyloseq(physeq, formula = NULL,
  method = "CCA", ...)

## S4 method for signature 'phyloseq,'NULL''
cca.phyloseq(physeq, formula = NULL,
  method = "CCA", ...)

Arguments

physeq	(Required). Phylogenetic sequencing data (phyloseq-class). The data on which you want to perform the ordination.
formula	(Optional). A formula, specifying the contraining variable(s) format, with variable names corresponding to sample_data (RHS) from within physeq.
method	(Optional). A single character string, specifying "RDA" or "CCA". Default is "CCA".
...	(Optional). Additional named arguments passed to capscale.

Value

same output as cca or rda, respectively.

See Also

plot_ordination, rda, cca

Examples

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# cca.phyloseq(physeq, formula, method, ...)

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.