phy_tree {phyloseq} | R Documentation

## Retrieve phylogenetic tree (`phylo`-class) from object.

### Description

This is the suggested method for accessing the phylogenetic tree, (`phylo`-class) from a `phyloseq-class`. Like other accessors (see See Also, below), the default behavior of this method is to stop with an error if `physeq` is a `phyloseq-class` but does not contain a phylogenetic tree (the component data you are trying to access in this case).

### Usage

    phy_tree(physeq, errorIfNULL=TRUE)

    ## S4 method for signature 'ANY'
    phy_tree(physeq, errorIfNULL = TRUE)

    ## S4 method for signature 'phylo'
    phy_tree(physeq)

### Arguments

`physeq` | (Required). An instance of phyloseq-class that contains a phylogenetic tree. If physeq is a phylogenetic tree (a component data class), then it is returned as-is.
`errorIfNULL` | (Optional). Logical. Should the accessor stop with an error if the slot is empty (`NULL`)? Default `TRUE`.

### Details

Note that the tip labels should be named to match the `taxa_names` of the other objects to which it is going to be paired. The `phyloseq` constructor automatically checks for exact agreement in the set of species described by the phlyogenetic tree and the other components (taxonomyTable, otu_table), and trims as-needed. Thus, the tip.labels in a phylo object must be named to match the results of `taxa_names` of the other objects to which it will ultimately be paired.

### Value

The `phylo`-class object contained within `physeq`; or NULL if `physeq` does not have a tree. This method stops with an error in the latter NULL case be default, which can be over-ridden by changing the value of `errorIfNULL` to `FALSE`.

### See Also

`otu_table`, `sample_data`, `tax_table` `refseq`, `phyloseq`, `merge_phyloseq`

### Examples

     data(GlobalPatterns)
     phy_tree(GlobalPatterns)

[Package phyloseq version 1.38.0 Index]