phyloseq: tax_glom – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

tax_glom

Agglomerate taxa of the same type.

Description

This method merges species that have the same taxonomy at a certain taxonomic rank. Its approach is analogous to tip_glom, but uses categorical data instead of a tree. In principal, other categorical data known for all taxa could also be used in place of taxonomy, but for the moment, this must be stored in the taxonomyTable of the data. Also, columns/ranks to the right of the rank chosen to use for agglomeration will be replaced with NA, because they should be meaningless following agglomeration.

Usage

tax_glom(physeq, taxrank=rank_names(physeq)[1], NArm=TRUE, bad_empty=c(NA, "", " ", "\t"))

Arguments

`physeq`	(Required). `phyloseq-class` or `otu_table`.
`taxrank`	A character string specifying the taxonomic level that you want to agglomerate over. Should be among the results of `rank_names(physeq)`. The default value is `rank_names(physeq)[1]`, which may agglomerate too broadly for a given experiment. You are strongly encouraged to try different values for this argument.
`NArm`	(Optional). Logical, length equal to one. Default is `TRUE`. CAUTION. The decision to prune (or not) taxa for which you lack categorical data could have a large effect on downstream analysis. You may want to re-compute your analysis under both conditions, or at least think carefully about what the effect might be and the reasons explaining the absence of information for certain taxa. In the case of taxonomy, it is often a result of imprecision in taxonomic designation based on short phylogenetic sequences and a patchy system of nomenclature. If this seems to be an issue for your analysis, think about also trying the nomenclature-agnostic `tip_glom` method if you have a phylogenetic tree available.
`bad_empty`	(Optional). Character vector. Default: `c(NA, "", " ", "\t")`. Defines the bad/empty values that should be ignored and/or considered unknown. They will be removed from the internal agglomeration vector derived from the argument to `tax`, and therefore agglomeration will not combine taxa according to the presence of these values in `tax`. Furthermore, the corresponding taxa can be optionally pruned from the output if `NArm` is set to `TRUE`.

Value

A taxonomically-agglomerated, optionally-pruned, object with class matching the class of physeq.

Examples

# data(GlobalPatterns)
# ## print the available taxonomic ranks
# colnames(tax_table(GlobalPatterns))
# ## agglomerate at the Family taxonomic rank
# (x1 <- tax_glom(GlobalPatterns, taxrank="Family") )
# ## How many taxa before/after agglomeration?
# ntaxa(GlobalPatterns); ntaxa(x1)
# ## Look at enterotype dataset...
# data(enterotype)
# ## print the available taxonomic ranks. Shows only 1 rank available, not useful for tax_glom
# colnames(tax_table(enterotype))

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23