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Simplify taxonomy by removing some unused characters such as "k__"

Source: R/miscellanous.R
simplify_taxo.Rd

lifecycle-maturing

Internally used in clean_pq()

Usage

simplify_taxo(
  physeq,
  pattern_to_remove = c(".__", ".*:"),
  ranks_for_pattern_to_remove = phyloseq::rank_names(physeq),
  ranks_to_remove_space = phyloseq::rank_names(physeq)[!grepl("Species",
    phyloseq::rank_names(physeq))],
  ranks_to_remove_NA = phyloseq::rank_names(physeq),
  pattern_to_NA = NULL,
  ranks_for_pattern_to_NA = phyloseq::rank_names(physeq)
)

Arguments

physeq

(required) a phyloseq-class object obtained using the phyloseq package.

pattern_to_remove

(a vector of character) regex patterns passed to base::gsub(): the matched substring is deleted from the cell value and the rest of the string is kept (e.g. ".__" turns "k__Fungi" into "Fungi").

ranks_for_pattern_to_remove

(character vector or NULL; default all ranks) column names in tax_table to which pattern_to_remove is applied. Pass NULL to skip this operation on all columns.

ranks_to_remove_space

(character vector or NULL; default all ranks whose name does not contain "Species") column names from which ASCII spaces and non-breaking spaces (U+00A0) are stripped. Pass NULL to skip space removal entirely.

ranks_to_remove_NA

(character vector or NULL; default all ranks) column names from which the literal string "NA" (case-sensitive) is removed. Pass NULL to skip this operation. Breaking change from v0.16: the old remove_NA = FALSE default is now ranks_to_remove_NA defaulting to all ranks; pass NULL to reproduce the old behaviour.

pattern_to_NA

(character; default NULL): a regex; if an entire cell value matches, the whole cell is replaced with NA (nothing from the original value is kept). Designed for PR2-style placeholder unknowns such as Embryophyceae_X, Embryophyceae_XX, Embryophyceae_XXX, Embryophyceae_XXX_sp., or Mortierella_sp.. Use "_X+$|_sp\\.$" to cover all such patterns: _X+$ catches rank-filler X's; _sp\\.$ catches any genus-only species placeholder.

ranks_for_pattern_to_NA

(character vector or NULL; default all ranks) column names to which pattern_to_NA is applied. Pass NULL to skip this operation on all columns.

Value

A phyloseq-class object with simplified taxonomy

Author

Adrien Taudière

Examples

d_fm <- data_fungi_mini
d_fm@tax_table[, "Species"] <- paste0(rep(
  c("s__", "s:"),
  ntaxa(d_fm) / 2
), d_fm@tax_table[, "Species"])

# First column is the new vector of Species,
# second column is the column before simplification
cbind(
  simplify_taxo(d_fm)@tax_table[, "Species"],
  d_fm@tax_table[, "Species"]
)
#>        Species         Species           
#> ASV7   ""              "s__NA"           
#> ASV8   "ostrea"        "s:ostrea"        
#> ASV12  "raduloides"    "s__raduloides"   
#> ASV18  "ostrea"        "s:ostrea"        
#> ASV25  "lachnopus"     "s__lachnopus"    
#> ASV26  "hirsutum"      "s:hirsutum"      
#> ASV27  "brasiliensis"  "s__brasiliensis" 
#> ASV29  "eyrei"         "s:eyrei"         
#> ASV32  "oblongisporum" "s__oblongisporum"
#> ASV34  ""              "s:NA"            
#> ASV35  "fomentarius"   "s__fomentarius"  
#> ASV41  "renati"        "s:renati"        
#> ASV42  "lachnopus"     "s__lachnopus"    
#> ASV46  "pellucida"     "s:pellucida"     
#> ASV47  "molaris"       "s__molaris"      
#> ASV48  "caryae"        "s:caryae"        
#> ASV49  "livescens"     "s__livescens"    
#> ASV50  "analogum"      "s:analogum"      
#> ASV53  "fomentarius"   "s__fomentarius"  
#> ASV54  ""              "s:NA"            
#> ASV58  "fomentarius"   "s__fomentarius"  
#> ASV59  "roseocremeum"  "s:roseocremeum"  
#> ASV61  "setigerum"     "s__setigerum"    
#> ASV62  ""              "s:NA"            
#> ASV63  ""              "s__NA"           
#> ASV64  "versicolor"    "s:versicolor"    
#> ASV67  "raduloides"    "s__raduloides"   
#> ASV68  "lachnopus"     "s:lachnopus"     
#> ASV71  ""              "s__NA"           
#> ASV72  ""              "s:NA"            
#> ASV75  "versiformis"   "s__versiformis"  
#> ASV77  "lachnopus"     "s:lachnopus"     
#> ASV82  "glandulosa"    "s__glandulosa"   
#> ASV83  ""              "s:NA"            
#> ASV85  "pubera"        "s__pubera"       
#> ASV91  "mesenterica"   "s:mesenterica"   
#> ASV93  ""              "s__NA"           
#> ASV94  "ostrea"        "s:ostrea"        
#> ASV99  "fomentarius"   "s__fomentarius"  
#> ASV100 ""              "s:NA"            
#> ASV101 "buckii"        "s__buckii"       
#> ASV104 "coralloides"   "s:coralloides"   
#> ASV105 "flaviporus"    "s__flaviporus"   
#> ASV107 "raduloides"    "s:raduloides"    
#> ASV108 "glandulosa"    "s__glandulosa"   
# Apply pattern_to_remove only to Genus and Species columns
cbind(
  simplify_taxo(d_fm,
    ranks_for_pattern_to_remove = c("Genus", "Species")
  )@tax_table[, "Species"],
  d_fm@tax_table[, "Species"]
)
#>        Species         Species           
#> ASV7   ""              "s__NA"           
#> ASV8   "ostrea"        "s:ostrea"        
#> ASV12  "raduloides"    "s__raduloides"   
#> ASV18  "ostrea"        "s:ostrea"        
#> ASV25  "lachnopus"     "s__lachnopus"    
#> ASV26  "hirsutum"      "s:hirsutum"      
#> ASV27  "brasiliensis"  "s__brasiliensis" 
#> ASV29  "eyrei"         "s:eyrei"         
#> ASV32  "oblongisporum" "s__oblongisporum"
#> ASV34  ""              "s:NA"            
#> ASV35  "fomentarius"   "s__fomentarius"  
#> ASV41  "renati"        "s:renati"        
#> ASV42  "lachnopus"     "s__lachnopus"    
#> ASV46  "pellucida"     "s:pellucida"     
#> ASV47  "molaris"       "s__molaris"      
#> ASV48  "caryae"        "s:caryae"        
#> ASV49  "livescens"     "s__livescens"    
#> ASV50  "analogum"      "s:analogum"      
#> ASV53  "fomentarius"   "s__fomentarius"  
#> ASV54  ""              "s:NA"            
#> ASV58  "fomentarius"   "s__fomentarius"  
#> ASV59  "roseocremeum"  "s:roseocremeum"  
#> ASV61  "setigerum"     "s__setigerum"    
#> ASV62  ""              "s:NA"            
#> ASV63  ""              "s__NA"           
#> ASV64  "versicolor"    "s:versicolor"    
#> ASV67  "raduloides"    "s__raduloides"   
#> ASV68  "lachnopus"     "s:lachnopus"     
#> ASV71  ""              "s__NA"           
#> ASV72  ""              "s:NA"            
#> ASV75  "versiformis"   "s__versiformis"  
#> ASV77  "lachnopus"     "s:lachnopus"     
#> ASV82  "glandulosa"    "s__glandulosa"   
#> ASV83  ""              "s:NA"            
#> ASV85  "pubera"        "s__pubera"       
#> ASV91  "mesenterica"   "s:mesenterica"   
#> ASV93  ""              "s__NA"           
#> ASV94  "ostrea"        "s:ostrea"        
#> ASV99  "fomentarius"   "s__fomentarius"  
#> ASV100 ""              "s:NA"            
#> ASV101 "buckii"        "s__buckii"       
#> ASV104 "coralloides"   "s:coralloides"   
#> ASV105 "flaviporus"    "s__flaviporus"   
#> ASV107 "raduloides"    "s:raduloides"    
#> ASV108 "glandulosa"    "s__glandulosa"   
if (FALSE) { # \dontrun{
# Replace PR2 placeholder unknowns (_X, _XX, _XXX, _XXX_sp., Genus_sp.) with NA
simplify_taxo(pq_pr2, pattern_to_NA = "_X+$|_sp\\.$")
# Apply pattern_to_NA only to the Species column
simplify_taxo(pq_pr2,
  pattern_to_NA = "_X+$|_sp\\.$",
  ranks_for_pattern_to_NA = "Species"
)
} # }