rbiom (version 2.1.2)

taxa_map: Map OTUs names to taxa names at a given rank.

Description

Map OTUs names to taxa names at a given rank.

Usage

taxa_map(
  biom,
  rank = NULL,
  taxa = Inf,
  unc = "singly",
  lineage = FALSE,
  other = FALSE
)

Value

A tibble data.frame when rank=NULL, or a character vector named with the OTU names.

Arguments

biom

An rbiom object, such as from as_rbiom(). Any value accepted by as_rbiom() can also be given here.

rank

When NULL, the entire biom$taxonomy data.frame is returned, transformed as per unc. Alternatively, a single taxonomic rank (rank name or integer position in biom$ranks) which returns a named character vector for mapping OTUs to taxa names.

taxa

Which taxa to display. An integer value will show the top n most abundant taxa. A value 0 <= n < 1 will show any taxa with that mean abundance or greater (e.g. 0.1 implies >= 10%). A character vector of taxa names will show only those named taxa. Default: 6.

unc

How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are:

"singly" -

Replaces them with the OTU name.

"grouped" -

Replaces them with a higher rank's name.

"drop" -

Excludes them from the result.

"asis" -

To not check/modify any taxa names.

Abbreviations are allowed. Default: "singly"

lineage

Include all ranks in the name of the taxa. For instance, setting to TRUE will produce Bacteria; Actinobacteria; Coriobacteriia; Coriobacteriales. Otherwise the taxa name will simply be Coriobacteriales. You want to set this to TRUE when unc = "asis" and you have taxa names (such as Incertae_Sedis) that map to multiple higher level ranks. Default: FALSE

other

Sum all non-itemized taxa into an "Other" taxa. When FALSE, only returns taxa matched by the taxa argument. Specifying TRUE adds "Other" to the returned set. A string can also be given to imply TRUE, but with that value as the name to use instead of "Other". Default: FALSE

See Also

pull.rbiom()

Examples

    library(rbiom)
    library(dplyr, warn.conflicts = FALSE)
    
    # In $taxonomy, .otu is the first column (like a row identifier)  -----
    hmp50$taxonomy %>% head(4)
    
    # In taxa_map, .otu is the last column (most precise rank)  -----------
    taxa_map(hmp50) %>% head(4)
    
    # Generate an OTU to Genus mapping  -----------------------------------
    taxa_map(hmp50, "Genus") %>% head(4)
    
    # Sometimes taxonomic names are incomplete ----------------------------
    otus <- c('GemAsacc', 'GcbBacte', 'Unc58411')
    taxa_map(hmp50, unc = "asis") %>% filter(.otu %in% otus) %>% select(Phylum:.otu)
    
    # rbiom can replace them with unique placeholders ---------------------
    taxa_map(hmp50, unc = "singly") %>% filter(.otu %in% otus) %>% select(Class:.otu)
    
    # Or collapse them into groups ----------------------------------------
    taxa_map(hmp50, unc = "grouped") %>% filter(.otu %in% otus) %>% select(Class:Genus)