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Map OTUs names to taxa names at a given rank.

Source: R/taxa_map.r
taxa_map.Rd

Map OTUs names to taxa names at a given rank.

Usage

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

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.

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.

Default: "singly"

Abbreviations are allowed.

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

Value

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

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)
#> # A tibble: 4 × 7
#>   .otu     Kingdom  Phylum         Class          Order             Family Genus
#>   <chr>    <fct>    <fct>          <fct>          <fct>             <fct>  <fct>
#> 1 Unc01yki Bacteria Firmicutes     Bacilli        Lactobacillales   Lacto… Lact…
#> 2 Unc53100 Bacteria Firmicutes     Bacilli        Lactobacillales   Strep… Stre…
#> 3 LtbAci52 Bacteria Firmicutes     Bacilli        Lactobacillales   Lacto… Lact…
#> 4 CnbTube3 Bacteria Actinobacteria Actinobacteria Corynebacteriales Coryn… Cory…
    
    # In taxa_map, .otu is the last column (most precise rank)  -----------
    taxa_map(hmp50) %>% head(4)
#> # A tibble: 4 × 7
#>   Kingdom  Phylum         Class          Order             Family    Genus .otu 
#>   <fct>    <fct>          <fct>          <fct>             <fct>     <fct> <chr>
#> 1 Bacteria Firmicutes     Bacilli        Lactobacillales   Lactobac… Lact… Unc0…
#> 2 Bacteria Firmicutes     Bacilli        Lactobacillales   Streptoc… Stre… Unc5…
#> 3 Bacteria Firmicutes     Bacilli        Lactobacillales   Lactobac… Lact… LtbA…
#> 4 Bacteria Actinobacteria Actinobacteria Corynebacteriales Coryneba… Cory… CnbT…
    
    # Generate an OTU to Genus mapping  -----------------------------------
    taxa_map(hmp50, "Genus") %>% head(4)
#>          Unc01yki          Unc53100          LtbAci52          CnbTube3 
#>     Lactobacillus     Streptococcus     Lactobacillus Corynebacterium 1 
#> 251 Levels: Abiotrophia Acidaminococcus Acinetobacter ... Veillonella
    
    # Sometimes taxonomic names are incomplete ----------------------------
    otus <- c('GemAsacc', 'GcbBacte', 'Unc58411')
    taxa_map(hmp50) %>% filter(.otu %in% otus) %>% select(Phylum:.otu)
#> # A tibble: 3 × 6
#>   Phylum          Class         Order          Family        Genus         .otu 
#>   <fct>           <fct>         <fct>          <fct>         <fct>         <chr>
#> 1 Gracilibacteria Unc. GcbBacte Unc. GcbBacte  Unc. GcbBacte Unc. GcbBacte GcbB…
#> 2 Tenericutes     Mollicutes    Mollicutes RF9 Unc. Unc58411 Unc. Unc58411 Unc5…
#> 3 Firmicutes      Bacilli       Bacillales     Bacillales XI Gemella       GemA…
    
    # rbiom can replace them with unique placeholders ---------------------
    taxa_map(hmp50, unc = "singly") %>% filter(.otu %in% otus) %>% select(Class:.otu)
#> # A tibble: 3 × 5
#>   Class         Order          Family        Genus         .otu    
#>   <fct>         <fct>          <fct>         <fct>         <chr>   
#> 1 Unc. GcbBacte Unc. GcbBacte  Unc. GcbBacte Unc. GcbBacte GcbBacte
#> 2 Mollicutes    Mollicutes RF9 Unc. Unc58411 Unc. Unc58411 Unc58411
#> 3 Bacilli       Bacillales     Bacillales XI Gemella       GemAsacc
    
    # Or collapse them into groups ----------------------------------------
    taxa_map(hmp50, unc = "grouped") %>% filter(.otu %in% otus) %>% select(Class:Genus)
#> # A tibble: 3 × 4
#>   Class                Order                Family               Genus          
#>   <fct>                <fct>                <fct>                <fct>          
#> 1 Unc. Gracilibacteria Unc. Gracilibacteria Unc. Gracilibacteria Unc. Graciliba…
#> 2 Mollicutes           Mollicutes RF9       Unc. Mollicutes RF9  Unc. Mollicute…
#> 3 Bacilli              Bacillales           Bacillales XI        Gemella