tip_glom {phyloseq} | R Documentation

## Agglomerate closely-related taxa using single-linkage clustering.

### Description

All tips of the tree separated by a cophenetic distance smaller than `h` will be agglomerated into one taxa using `merge_taxa`.

### Usage

    tip_glom(physeq, h = 0.2, hcfun = agnes, ...)

### Arguments

`physeq` | (Required). A `phyloseq-class`, containing a phylogenetic tree. Alternatively, a phylogenetic tree `phylo` will also work.
`h` | (Optional). Numeric scalar of the height where the tree should be cut. This refers to the tree resulting from hierarchical clustering of `cophenetic.phylo(phy_tree(physeq))`, not necessarily the original phylogenetic tree, `phy_tree(physeq)`. Default value is `0.2`. Note that this argument used to be named `speciationMinLength`, before this function/method was rewritten.
`hcfun` | (Optional). A function. The (agglomerative, hierarchical) clustering function to use. Good examples are `agnes` and `hclust`. The default is `agnes`.
`...` | (Optional). Additional named arguments to pass to `hcfun`.

### Details

Can be used to create a non-trivial OTU Table, if a phylogenetic tree is available.

For now, a simple, “greedy”, single-linkage clustering is used. In future releases it should be possible to specify different clustering approaches available in `R`, in particular, complete-linkage clustering appears to be used more commonly for OTU clustering applications.

### Value

An instance of the `phyloseq-class`. Or alternatively, a `phylo` object if the `physeq` argument was just a tree. In the expected-use case, the number of OTUs will be fewer (see `ntaxa`), after merging OTUs that are related enough to be called the same OTU.

### See Also

`merge_taxa`

`agnes`

`hclust`

`cophenetic.phylo`

`phylo`

### Examples

    data("esophagus")
    # for speed
    esophagus = prune_taxa(taxa_names(esophagus)[1:25], esophagus)
    plot_tree(esophagus, label.tips="taxa_names", size="abundance", title="Before tip_glom()")
    plot_tree(tip_glom(esophagus, h=0.2), label.tips="taxa_names", size="abundance", title="After tip_glom()")

[Package phyloseq version 1.38.0 Index]