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
taxonomyTableof 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.
tax_glom(physeq, taxrank=rank_names(physeq), NArm=TRUE, bad_empty=c(NA, "", " ", "\t"))
rank_names(physeq). The default value is
rank_names(physeq), which may agglomerate too broadly for a given experiment. You are strongly encouraged to try different values for this argument.
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_glommethod if you have a phylogenetic tree available.
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
NArmis set to
# 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))