Retrieve phylogenetic tree (phylo-class) from object.
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).
phy_tree(physeq, errorIfNULL=TRUE) ## S4 method for signature 'ANY' phy_tree(physeq, errorIfNULL = TRUE) ## S4 method for signature 'phylo' phy_tree(physeq)
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 ( |
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.
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.
data(GlobalPatterns) phy_tree(GlobalPatterns)
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