Agglomerate closely-related taxa using single-linkage clustering.
All tips of the tree separated by a cophenetic distance smaller than
h will be agglomerated into one taxa using merge_taxa.
tip_glom(physeq, h = 0.2, hcfun = agnes, ...)
physeq |
(Required). A |
h |
(Optional). Numeric scalar of the height where the tree should be cut.
This refers to the tree resulting from hierarchical clustering
of |
hcfun |
(Optional). A function.
The (agglomerative, hierarchical) clustering function to use.
Good examples are
|
... |
(Optional). Additional named arguments to pass
to |
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.
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.
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()")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.