Function for renaming taxa in a taxonomic table, which can be
given as matrix or phyloseq object.
It comes with functionality for making unknown
and unclassified taxa unique and substituting them by the next higher known
taxonomic level, e.g., an unknown genus "g__" can automatically be renamed
to "1_Streptococcaceae(F)".
User-defined patterns determine the format of known and substituted names.
Unknown names (e.g., NAs) and unclassified taxa can be
handled separately. Duplicated names within one or more chosen ranks can
also be made unique by numbering them consecutively.
Usage
renameTaxa(
taxtab,
pat = "<r>_<name>",
substPat = "<r>_<name>_<subst_r>_<subst_name>",
unknown = c(NA, "", " ", "__"),
numUnknown = TRUE,
unclass = c("unclassified", "Unclassified"),
numUnclass = TRUE,
numUnclassPat = "<name><num>",
numDupli = NULL,
numDupliPat = "<name><num>",
ranks = NULL,
ranksAbb = NULL,
ignoreCols = NULL
)Arguments
- taxtab
taxonomic table (matrix containing the taxonomic names; columns must be taxonomic ranks) or phyloseq object.
- pat
character specifying the pattern of new taxonomic names if the current name is KNOWN. See the examples and default value for a demo. Possible space holders are:
<name>Taxonomic name (either the original or replaced one)
<rank>Taxonomic rank in lower case
<Rank>Taxonomic rank with first letter in upper case
<r>Abbreviated taxonomic rank in lower case
<R>Abbreviated taxonomic rank in upper case
- substPat
character specifying the pattern of new taxonomic names if the current name is UNKNOWN. The current name is substituted by the next higher existing name. Possible space holders (in addition to that of
pat):<subst_name>Substituted taxonomic name (next higher existing name)
<subst_rank>Taxonomic rank of substitute name in lower case
<subst_Rank>Taxonomic rank of substitute name with first letter in upper case
<subst_r>Abbreviated taxonomic rank of substitute name in lower case
<subst_R>Abbreviated taxonomic rank of substitute name in upper case
- unknown
character vector giving the labels of unknown taxa, without leading rank label (e.g., "g_" or "g__" for genus level). If
numUnknown = TRUE, unknown names are replaced by a number.- numUnknown
logical. If
TRUE, a number is assigned to all unknown taxonomic names (defined byunknown) to make them unique.- unclass
character vector giving the label of unclassified taxa, without leading rank label (e.g., "g_" or "g__" for genus level). If
numUnclass = TRUE, a number is added to the names of unclassified taxa. Note that unclassified taxa and unknown taxa get a separate numbering ifunclassis set. To replace all unknown and unclassified taxa by numbers, add "unclassified" (or the appropriate counterpart) tounknownand setunclasstoNULL.- numUnclass
logical. If
TRUE, a number is assigned to all unclassified taxa (defined byunclass) to make them unique. The pattern is defined vianumUnclassPat.- numUnclassPat
character defining the pattern used for numbering unclassified taxa. Must include a space holder for the name ("<name>") and one for the number ("<num>"). Default is "<name><num>" resulting e.g., in "unclassified1".
- numDupli
character vector giving the ranks that should be made unique by adding a number. Elements must match column names. The pattern is defined via
numDupliPat.- numDupliPat
character defining the pattern used for numbering duplicated names (if
numDupliis given). Must include a space holder for the name ("<name>") and one for the number ("<num>"). Default is "<name><num>" resulting e.g., in "Ruminococcus1".- ranks
character vector giving rank names used for renaming the taxa. If
NULL, the functions tries to automatically set rank names based on common usage.- ranksAbb
character vector giving abbreviated rank names, which are directly used for the place holders <r>, <subst_r>, <R>, and <subst_R> (the former two in lower case and the latter two in upper case). If
NULL, the first letter of the rank names is used.- ignoreCols
numeric vector with columns to be ignored. Names remain unchanged for these columns. Columns containing
NAs are ignored automatically only ifignoreCols = NULL. Note: length ofranksandranksAbbmust match the number of non-ignored columns.
Examples
#--- Load and edit data -----------------------------------------------------
library(phyloseq)
data("GlobalPatterns")
global <- subset_taxa(GlobalPatterns, Kingdom == "Bacteria")
taxtab <- global@tax_table@.Data[1:10, ]
# Add some unclassified taxa
taxtab[c(2,3,5), "Species"] <- "unclassified"
taxtab[c(2,3), "Genus"] <- "unclassified"
taxtab[2, "Family"] <- "unclassified"
# Add some blanks
taxtab[7, "Genus"] <- " "
taxtab[7:9, "Species"] <- " "
# Add taxon that is unclassified up to Kingdom
taxtab[9, ] <- "unclassified"
taxtab[9, 1] <- "Unclassified"
# Add row names
rownames(taxtab) <- paste0("OTU", 1:nrow(taxtab))
print(taxtab)
#> Kingdom Phylum Class Order
#> OTU1 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU2 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU3 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU4 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU5 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU6 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU7 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU8 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU9 "Unclassified" "unclassified" "unclassified" "unclassified"
#> OTU10 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> Family Genus Species
#> OTU1 "Propionibacteriaceae" "Propionibacterium" "Propionibacteriumacnes"
#> OTU2 "unclassified" "unclassified" "unclassified"
#> OTU3 "Propionibacteriaceae" "unclassified" "unclassified"
#> OTU4 "Propionibacteriaceae" "Tessaracoccus" NA
#> OTU5 "Propionibacteriaceae" "Aestuariimicrobium" "unclassified"
#> OTU6 NA NA NA
#> OTU7 "Nocardioidaceae" " " " "
#> OTU8 "Nocardioidaceae" "Propionicimonas" " "
#> OTU9 "unclassified" "unclassified" "unclassified"
#> OTU10 NA NA NA
#--- Example 1 (default setting) --------------------------------------------
# Example 1 (default setting)
# - Known names are replaced by "<r>_<name>"
# - Unknown names are replaced by "<r>_<name>_<subst_r>_<subst_name>"
# - Unclassified taxa have separate numbering
# - Ranks are taken from column names
# - e.g., unknown genus -> "g_1_f_Streptococcaceae"
renamed1 <- renameTaxa(taxtab)
renamed1
#> Kingdom Phylum
#> OTU1 "k_Bacteria" "p_Actinobacteria"
#> OTU2 "k_Bacteria" "p_Actinobacteria"
#> OTU3 "k_Bacteria" "p_Actinobacteria"
#> OTU4 "k_Bacteria" "p_Actinobacteria"
#> OTU5 "k_Bacteria" "p_Actinobacteria"
#> OTU6 "k_Bacteria" "p_Actinobacteria"
#> OTU7 "k_Bacteria" "p_Actinobacteria"
#> OTU8 "k_Bacteria" "p_Actinobacteria"
#> OTU9 "k_Unclassified1" "p_unclassified1_k_Unclassified1"
#> OTU10 "k_Bacteria" "p_Actinobacteria"
#> Class Order
#> OTU1 "c_Actinobacteria" "o_Actinomycetales"
#> OTU2 "c_Actinobacteria" "o_Actinomycetales"
#> OTU3 "c_Actinobacteria" "o_Actinomycetales"
#> OTU4 "c_Actinobacteria" "o_Actinomycetales"
#> OTU5 "c_Actinobacteria" "o_Actinomycetales"
#> OTU6 "c_Actinobacteria" "o_Actinomycetales"
#> OTU7 "c_Actinobacteria" "o_Actinomycetales"
#> OTU8 "c_Actinobacteria" "o_Actinomycetales"
#> OTU9 "c_unclassified1_k_Unclassified1" "o_unclassified1_k_Unclassified1"
#> OTU10 "c_Actinobacteria" "o_Actinomycetales"
#> Family
#> OTU1 "f_Propionibacteriaceae"
#> OTU2 "f_unclassified1_o_Actinomycetales"
#> OTU3 "f_Propionibacteriaceae"
#> OTU4 "f_Propionibacteriaceae"
#> OTU5 "f_Propionibacteriaceae"
#> OTU6 "f_1_o_Actinomycetales"
#> OTU7 "f_Nocardioidaceae"
#> OTU8 "f_Nocardioidaceae"
#> OTU9 "f_unclassified2_k_Unclassified1"
#> OTU10 "f_2_o_Actinomycetales"
#> Genus
#> OTU1 "g_Propionibacterium"
#> OTU2 "g_unclassified1_o_Actinomycetales"
#> OTU3 "g_unclassified2_f_Propionibacteriaceae"
#> OTU4 "g_Tessaracoccus"
#> OTU5 "g_Aestuariimicrobium"
#> OTU6 "g_1_o_Actinomycetales"
#> OTU7 "g_2_f_Nocardioidaceae"
#> OTU8 "g_Propionicimonas"
#> OTU9 "g_unclassified3_k_Unclassified1"
#> OTU10 "g_3_o_Actinomycetales"
#> Species
#> OTU1 "s_Propionibacteriumacnes"
#> OTU2 "s_unclassified1_o_Actinomycetales"
#> OTU3 "s_unclassified2_f_Propionibacteriaceae"
#> OTU4 "s_1_g_Tessaracoccus"
#> OTU5 "s_unclassified3_g_Aestuariimicrobium"
#> OTU6 "s_2_o_Actinomycetales"
#> OTU7 "s_3_f_Nocardioidaceae"
#> OTU8 "s_4_g_Propionicimonas"
#> OTU9 "s_unclassified4_k_Unclassified1"
#> OTU10 "s_5_o_Actinomycetales"
#--- Example 2 --------------------------------------------------------------
# - Use phyloseq object (subset of class clostridia to decrease runtime)
global_sub <- subset_taxa(global, Class == "Clostridia")
renamed2 <- renameTaxa(global_sub)
tax_table(renamed2)[1:5, ]
#> Taxonomy Table: [5 taxa by 7 taxonomic ranks]:
#> Kingdom Phylum Class Order
#> 69790 "k_Bacteria" "p_Firmicutes" "c_Clostridia" "o_Halanaerobiales"
#> 201587 "k_Bacteria" "p_Firmicutes" "c_Clostridia" "o_Halanaerobiales"
#> 14244 "k_Bacteria" "p_Firmicutes" "c_Clostridia" "o_Clostridiales"
#> 589048 "k_Bacteria" "p_Firmicutes" "c_Clostridia" "o_Clostridiales"
#> 310026 "k_Bacteria" "p_Firmicutes" "c_Clostridia" "o_Clostridiales"
#> Family Genus
#> 69790 "f_Halobacteroidaceae" "g_1_f_Halobacteroidaceae"
#> 201587 "f_Halanaerobiaceae" "g_2_f_Halanaerobiaceae"
#> 14244 "f_1_o_Clostridiales" "g_3_o_Clostridiales"
#> 589048 "f_2_o_Clostridiales" "g_4_o_Clostridiales"
#> 310026 "f_3_o_Clostridiales" "g_5_o_Clostridiales"
#> Species
#> 69790 "s_1_f_Halobacteroidaceae"
#> 201587 "s_2_f_Halanaerobiaceae"
#> 14244 "s_3_o_Clostridiales"
#> 589048 "s_4_o_Clostridiales"
#> 310026 "s_5_o_Clostridiales"
#--- Example 3 --------------------------------------------------------------
# - Known names remain unchanged
# - Substituted names are indicated by their rank in brackets
# - Pattern for numbering unclassified taxa changed
# - e.g., unknown genus -> "Streptococcaceae (F)"
# - Note: Numbering of unknowns is not shown because "<name>" is not
# included in "substPat"
renamed3 <- renameTaxa(taxtab, numUnclassPat = "<name>_<num>",
pat = "<name>",
substPat = "<subst_name> (<subst_R>)")
renamed3
#> Kingdom Phylum Class
#> OTU1 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU2 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU3 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU4 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU5 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU6 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU7 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU8 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU9 "Unclassified_1" "Unclassified_1 (K)" "Unclassified_1 (K)"
#> OTU10 "Bacteria" "Actinobacteria" "Actinobacteria"
#> Order Family Genus
#> OTU1 "Actinomycetales" "Propionibacteriaceae" "Propionibacterium"
#> OTU2 "Actinomycetales" "Actinomycetales (O)" "Actinomycetales (O)"
#> OTU3 "Actinomycetales" "Propionibacteriaceae" "Propionibacteriaceae (F)"
#> OTU4 "Actinomycetales" "Propionibacteriaceae" "Tessaracoccus"
#> OTU5 "Actinomycetales" "Propionibacteriaceae" "Aestuariimicrobium"
#> OTU6 "Actinomycetales" "Actinomycetales (O)" "Actinomycetales (O)"
#> OTU7 "Actinomycetales" "Nocardioidaceae" "Nocardioidaceae (F)"
#> OTU8 "Actinomycetales" "Nocardioidaceae" "Propionicimonas"
#> OTU9 "Unclassified_1 (K)" "Unclassified_1 (K)" "Unclassified_1 (K)"
#> OTU10 "Actinomycetales" "Actinomycetales (O)" "Actinomycetales (O)"
#> Species
#> OTU1 "Propionibacteriumacnes"
#> OTU2 "Actinomycetales (O)"
#> OTU3 "Propionibacteriaceae (F)"
#> OTU4 "Tessaracoccus (G)"
#> OTU5 "Aestuariimicrobium (G)"
#> OTU6 "Actinomycetales (O)"
#> OTU7 "Nocardioidaceae (F)"
#> OTU8 "Propionicimonas (G)"
#> OTU9 "Unclassified_1 (K)"
#> OTU10 "Actinomycetales (O)"
#--- Example 4 --------------------------------------------------------------
# - Same as before but numbering shown for unknown names
# - e.g., unknown genus -> "1 Streptococcaceae (F)"
renamed4 <- renameTaxa(taxtab, numUnclassPat = "<name>_<num>",
pat = "<name>",
substPat = "<name> <subst_name> (<subst_R>)")
renamed4
#> Kingdom Phylum
#> OTU1 "Bacteria" "Actinobacteria"
#> OTU2 "Bacteria" "Actinobacteria"
#> OTU3 "Bacteria" "Actinobacteria"
#> OTU4 "Bacteria" "Actinobacteria"
#> OTU5 "Bacteria" "Actinobacteria"
#> OTU6 "Bacteria" "Actinobacteria"
#> OTU7 "Bacteria" "Actinobacteria"
#> OTU8 "Bacteria" "Actinobacteria"
#> OTU9 "Unclassified_1" "unclassified_1 Unclassified_1 (K)"
#> OTU10 "Bacteria" "Actinobacteria"
#> Class Order
#> OTU1 "Actinobacteria" "Actinomycetales"
#> OTU2 "Actinobacteria" "Actinomycetales"
#> OTU3 "Actinobacteria" "Actinomycetales"
#> OTU4 "Actinobacteria" "Actinomycetales"
#> OTU5 "Actinobacteria" "Actinomycetales"
#> OTU6 "Actinobacteria" "Actinomycetales"
#> OTU7 "Actinobacteria" "Actinomycetales"
#> OTU8 "Actinobacteria" "Actinomycetales"
#> OTU9 "unclassified_1 Unclassified_1 (K)" "unclassified_1 Unclassified_1 (K)"
#> OTU10 "Actinobacteria" "Actinomycetales"
#> Family
#> OTU1 "Propionibacteriaceae"
#> OTU2 "unclassified_1 Actinomycetales (O)"
#> OTU3 "Propionibacteriaceae"
#> OTU4 "Propionibacteriaceae"
#> OTU5 "Propionibacteriaceae"
#> OTU6 "1 Actinomycetales (O)"
#> OTU7 "Nocardioidaceae"
#> OTU8 "Nocardioidaceae"
#> OTU9 "unclassified_2 Unclassified_1 (K)"
#> OTU10 "2 Actinomycetales (O)"
#> Genus
#> OTU1 "Propionibacterium"
#> OTU2 "unclassified_1 Actinomycetales (O)"
#> OTU3 "unclassified_2 Propionibacteriaceae (F)"
#> OTU4 "Tessaracoccus"
#> OTU5 "Aestuariimicrobium"
#> OTU6 "1 Actinomycetales (O)"
#> OTU7 "2 Nocardioidaceae (F)"
#> OTU8 "Propionicimonas"
#> OTU9 "unclassified_3 Unclassified_1 (K)"
#> OTU10 "3 Actinomycetales (O)"
#> Species
#> OTU1 "Propionibacteriumacnes"
#> OTU2 "unclassified_1 Actinomycetales (O)"
#> OTU3 "unclassified_2 Propionibacteriaceae (F)"
#> OTU4 "1 Tessaracoccus (G)"
#> OTU5 "unclassified_3 Aestuariimicrobium (G)"
#> OTU6 "2 Actinomycetales (O)"
#> OTU7 "3 Nocardioidaceae (F)"
#> OTU8 "4 Propionicimonas (G)"
#> OTU9 "unclassified_4 Unclassified_1 (K)"
#> OTU10 "5 Actinomycetales (O)"
#--- Example 5 --------------------------------------------------------------
# - Same numbering for unkown names and unclassified taxa
# - e.g., unknown genus -> "1_Streptococcaceae(F)"
# - Note: We get a warning here because "Unclassified" (with capital U)
# are not included in "unknown" but occur in the data
renamed5 <- renameTaxa(taxtab, unclass = NULL,
unknown = c(NA, " ", "unclassified"),
pat = "<name>",
substPat = "<name>_<subst_name>(<subst_R>)")
#> Warning: Taxonomic table contains unclassified taxa. Consider adding "Unclassified" to argument "unknown".
renamed5
#> Kingdom Phylum Class
#> OTU1 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU2 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU3 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU4 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU5 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU6 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU7 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU8 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU9 "Unclassified" "1_Unclassified(K)" "1_Unclassified(K)"
#> OTU10 "Bacteria" "Actinobacteria" "Actinobacteria"
#> Order Family Genus
#> OTU1 "Actinomycetales" "Propionibacteriaceae" "Propionibacterium"
#> OTU2 "Actinomycetales" "1_Actinomycetales(O)" "1_Actinomycetales(O)"
#> OTU3 "Actinomycetales" "Propionibacteriaceae" "2_Propionibacteriaceae(F)"
#> OTU4 "Actinomycetales" "Propionibacteriaceae" "Tessaracoccus"
#> OTU5 "Actinomycetales" "Propionibacteriaceae" "Aestuariimicrobium"
#> OTU6 "Actinomycetales" "2_Actinomycetales(O)" "3_Actinomycetales(O)"
#> OTU7 "Actinomycetales" "Nocardioidaceae" "4_Nocardioidaceae(F)"
#> OTU8 "Actinomycetales" "Nocardioidaceae" "Propionicimonas"
#> OTU9 "1_Unclassified(K)" "3_Unclassified(K)" "5_Unclassified(K)"
#> OTU10 "Actinomycetales" "4_Actinomycetales(O)" "6_Actinomycetales(O)"
#> Species
#> OTU1 "Propionibacteriumacnes"
#> OTU2 "1_Actinomycetales(O)"
#> OTU3 "2_Propionibacteriaceae(F)"
#> OTU4 "3_Tessaracoccus(G)"
#> OTU5 "4_Aestuariimicrobium(G)"
#> OTU6 "5_Actinomycetales(O)"
#> OTU7 "6_Nocardioidaceae(F)"
#> OTU8 "7_Propionicimonas(G)"
#> OTU9 "8_Unclassified(K)"
#> OTU10 "9_Actinomycetales(O)"
#--- Example 6 --------------------------------------------------------------
# - Same as before, but OTU9 is now renamed correctly
renamed6 <- renameTaxa(taxtab, unclass = NULL,
unknown = c(NA, " ", "unclassified", "Unclassified"),
pat = "<name>",
substPat = "<name>_<subst_name>(<subst_R>)")
renamed6
#> Kingdom Phylum Class Order
#> OTU1 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU2 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU3 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU4 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU5 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU6 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU7 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU8 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU9 "1" "1_1(K)" "1_1(K)" "1_1(K)"
#> OTU10 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> Family Genus
#> OTU1 "Propionibacteriaceae" "Propionibacterium"
#> OTU2 "1_Actinomycetales(O)" "1_Actinomycetales(O)"
#> OTU3 "Propionibacteriaceae" "2_Propionibacteriaceae(F)"
#> OTU4 "Propionibacteriaceae" "Tessaracoccus"
#> OTU5 "Propionibacteriaceae" "Aestuariimicrobium"
#> OTU6 "2_Actinomycetales(O)" "3_Actinomycetales(O)"
#> OTU7 "Nocardioidaceae" "4_Nocardioidaceae(F)"
#> OTU8 "Nocardioidaceae" "Propionicimonas"
#> OTU9 "3_1(K)" "5_1(K)"
#> OTU10 "4_Actinomycetales(O)" "6_Actinomycetales(O)"
#> Species
#> OTU1 "Propionibacteriumacnes"
#> OTU2 "1_Actinomycetales(O)"
#> OTU3 "2_Propionibacteriaceae(F)"
#> OTU4 "3_Tessaracoccus(G)"
#> OTU5 "4_Aestuariimicrobium(G)"
#> OTU6 "5_Actinomycetales(O)"
#> OTU7 "6_Nocardioidaceae(F)"
#> OTU8 "7_Propionicimonas(G)"
#> OTU9 "8_1(K)"
#> OTU10 "9_Actinomycetales(O)"
#--- Example 7 --------------------------------------------------------------
# - Add "(<Rank>: unknown)" to unknown names
# - e.g., unknown genus -> "1 Streptococcaceae (Genus: unknown)"
renamed7 <- renameTaxa(taxtab, unclass = NULL,
unknown = c(NA, " ", "unclassified", "Unclassified"),
pat = "<name>",
substPat = "<name> <subst_name> (<Rank>: unknown)")
renamed7
#> Kingdom Phylum Class
#> OTU1 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU2 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU3 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU4 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU5 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU6 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU7 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU8 "Bacteria" "Actinobacteria" "Actinobacteria"
#> OTU9 "1" "1 1 (Phylum: unknown)" "1 1 (Class: unknown)"
#> OTU10 "Bacteria" "Actinobacteria" "Actinobacteria"
#> Order Family
#> OTU1 "Actinomycetales" "Propionibacteriaceae"
#> OTU2 "Actinomycetales" "1 Actinomycetales (Family: unknown)"
#> OTU3 "Actinomycetales" "Propionibacteriaceae"
#> OTU4 "Actinomycetales" "Propionibacteriaceae"
#> OTU5 "Actinomycetales" "Propionibacteriaceae"
#> OTU6 "Actinomycetales" "2 Actinomycetales (Family: unknown)"
#> OTU7 "Actinomycetales" "Nocardioidaceae"
#> OTU8 "Actinomycetales" "Nocardioidaceae"
#> OTU9 "1 1 (Order: unknown)" "3 1 (Family: unknown)"
#> OTU10 "Actinomycetales" "4 Actinomycetales (Family: unknown)"
#> Genus
#> OTU1 "Propionibacterium"
#> OTU2 "1 Actinomycetales (Genus: unknown)"
#> OTU3 "2 Propionibacteriaceae (Genus: unknown)"
#> OTU4 "Tessaracoccus"
#> OTU5 "Aestuariimicrobium"
#> OTU6 "3 Actinomycetales (Genus: unknown)"
#> OTU7 "4 Nocardioidaceae (Genus: unknown)"
#> OTU8 "Propionicimonas"
#> OTU9 "5 1 (Genus: unknown)"
#> OTU10 "6 Actinomycetales (Genus: unknown)"
#> Species
#> OTU1 "Propionibacteriumacnes"
#> OTU2 "1 Actinomycetales (Species: unknown)"
#> OTU3 "2 Propionibacteriaceae (Species: unknown)"
#> OTU4 "3 Tessaracoccus (Species: unknown)"
#> OTU5 "4 Aestuariimicrobium (Species: unknown)"
#> OTU6 "5 Actinomycetales (Species: unknown)"
#> OTU7 "6 Nocardioidaceae (Species: unknown)"
#> OTU8 "7 Propionicimonas (Species: unknown)"
#> OTU9 "8 1 (Species: unknown)"
#> OTU10 "9 Actinomycetales (Species: unknown)"
#--- Example 8 --------------------------------------------------------------
# - Do not substitute unknowns and unclassified taxa by higher ranks
# - e.g., unknown genus -> "1"
renamed8 <- renameTaxa(taxtab,
pat = "<name>", substPat = "<name>")
renamed8
#> Kingdom Phylum Class Order
#> OTU1 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU2 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU3 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU4 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU5 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU6 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU7 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU8 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU9 "Unclassified1" "unclassified1" "unclassified1" "unclassified1"
#> OTU10 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> Family Genus Species
#> OTU1 "Propionibacteriaceae" "Propionibacterium" "Propionibacteriumacnes"
#> OTU2 "unclassified1" "unclassified1" "unclassified1"
#> OTU3 "Propionibacteriaceae" "unclassified2" "unclassified2"
#> OTU4 "Propionibacteriaceae" "Tessaracoccus" "1"
#> OTU5 "Propionibacteriaceae" "Aestuariimicrobium" "unclassified3"
#> OTU6 "1" "1" "2"
#> OTU7 "Nocardioidaceae" "2" "3"
#> OTU8 "Nocardioidaceae" "Propionicimonas" "4"
#> OTU9 "unclassified2" "unclassified3" "unclassified4"
#> OTU10 "2" "3" "5"
#--- Example 9 --------------------------------------------------------------
# - Error if ranks cannot be automatically determined
# from column names or taxonomic names
taxtab_noranks <- taxtab
colnames(taxtab_noranks) <- paste0("Rank", 1:ncol(taxtab))
head(taxtab_noranks)
#> Rank1 Rank2 Rank3 Rank4
#> OTU1 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU2 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU3 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU4 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU5 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> OTU6 "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales"
#> Rank5 Rank6 Rank7
#> OTU1 "Propionibacteriaceae" "Propionibacterium" "Propionibacteriumacnes"
#> OTU2 "unclassified" "unclassified" "unclassified"
#> OTU3 "Propionibacteriaceae" "unclassified" "unclassified"
#> OTU4 "Propionibacteriaceae" "Tessaracoccus" NA
#> OTU5 "Propionibacteriaceae" "Aestuariimicrobium" "unclassified"
#> OTU6 NA NA NA
if (FALSE) { # \dontrun{
renamed9 <- renameTaxa(taxtab_noranks,
pat = "<name>",
substPat = "<name>_<subst_name>(<subst_R>)")
} # }
# Ranks can either be given via "ranks" ...
(ranks <- colnames(taxtab))
#> [1] "Kingdom" "Phylum" "Class" "Order" "Family" "Genus" "Species"
renamed9 <- renameTaxa(taxtab_noranks,
pat = "<name>",
substPat = "<name>_<subst_name>(<subst_R>)",
ranks = ranks)
renamed9
#> Rank1 Rank2
#> OTU1 "Bacteria" "Actinobacteria"
#> OTU2 "Bacteria" "Actinobacteria"
#> OTU3 "Bacteria" "Actinobacteria"
#> OTU4 "Bacteria" "Actinobacteria"
#> OTU5 "Bacteria" "Actinobacteria"
#> OTU6 "Bacteria" "Actinobacteria"
#> OTU7 "Bacteria" "Actinobacteria"
#> OTU8 "Bacteria" "Actinobacteria"
#> OTU9 "Unclassified1" "unclassified1_Unclassified1(K)"
#> OTU10 "Bacteria" "Actinobacteria"
#> Rank3 Rank4
#> OTU1 "Actinobacteria" "Actinomycetales"
#> OTU2 "Actinobacteria" "Actinomycetales"
#> OTU3 "Actinobacteria" "Actinomycetales"
#> OTU4 "Actinobacteria" "Actinomycetales"
#> OTU5 "Actinobacteria" "Actinomycetales"
#> OTU6 "Actinobacteria" "Actinomycetales"
#> OTU7 "Actinobacteria" "Actinomycetales"
#> OTU8 "Actinobacteria" "Actinomycetales"
#> OTU9 "unclassified1_Unclassified1(K)" "unclassified1_Unclassified1(K)"
#> OTU10 "Actinobacteria" "Actinomycetales"
#> Rank5
#> OTU1 "Propionibacteriaceae"
#> OTU2 "unclassified1_Actinomycetales(O)"
#> OTU3 "Propionibacteriaceae"
#> OTU4 "Propionibacteriaceae"
#> OTU5 "Propionibacteriaceae"
#> OTU6 "1_Actinomycetales(O)"
#> OTU7 "Nocardioidaceae"
#> OTU8 "Nocardioidaceae"
#> OTU9 "unclassified2_Unclassified1(K)"
#> OTU10 "2_Actinomycetales(O)"
#> Rank6
#> OTU1 "Propionibacterium"
#> OTU2 "unclassified1_Actinomycetales(O)"
#> OTU3 "unclassified2_Propionibacteriaceae(F)"
#> OTU4 "Tessaracoccus"
#> OTU5 "Aestuariimicrobium"
#> OTU6 "1_Actinomycetales(O)"
#> OTU7 "2_Nocardioidaceae(F)"
#> OTU8 "Propionicimonas"
#> OTU9 "unclassified3_Unclassified1(K)"
#> OTU10 "3_Actinomycetales(O)"
#> Rank7
#> OTU1 "Propionibacteriumacnes"
#> OTU2 "unclassified1_Actinomycetales(O)"
#> OTU3 "unclassified2_Propionibacteriaceae(F)"
#> OTU4 "1_Tessaracoccus(G)"
#> OTU5 "unclassified3_Aestuariimicrobium(G)"
#> OTU6 "2_Actinomycetales(O)"
#> OTU7 "3_Nocardioidaceae(F)"
#> OTU8 "4_Propionicimonas(G)"
#> OTU9 "unclassified4_Unclassified1(K)"
#> OTU10 "5_Actinomycetales(O)"
# ... or "ranksAbb" (we now use the lower case within "substPat")
(ranks <- substr(colnames(taxtab), 1, 1))
#> [1] "K" "P" "C" "O" "F" "G" "S"
renamed9 <- renameTaxa(taxtab_noranks,
pat = "<name>",
substPat = "<name>_<subst_name>(<subst_r>)",
ranksAbb = ranks)
renamed9
#> Rank1 Rank2
#> OTU1 "Bacteria" "Actinobacteria"
#> OTU2 "Bacteria" "Actinobacteria"
#> OTU3 "Bacteria" "Actinobacteria"
#> OTU4 "Bacteria" "Actinobacteria"
#> OTU5 "Bacteria" "Actinobacteria"
#> OTU6 "Bacteria" "Actinobacteria"
#> OTU7 "Bacteria" "Actinobacteria"
#> OTU8 "Bacteria" "Actinobacteria"
#> OTU9 "Unclassified1" "unclassified1_Unclassified1(k)"
#> OTU10 "Bacteria" "Actinobacteria"
#> Rank3 Rank4
#> OTU1 "Actinobacteria" "Actinomycetales"
#> OTU2 "Actinobacteria" "Actinomycetales"
#> OTU3 "Actinobacteria" "Actinomycetales"
#> OTU4 "Actinobacteria" "Actinomycetales"
#> OTU5 "Actinobacteria" "Actinomycetales"
#> OTU6 "Actinobacteria" "Actinomycetales"
#> OTU7 "Actinobacteria" "Actinomycetales"
#> OTU8 "Actinobacteria" "Actinomycetales"
#> OTU9 "unclassified1_Unclassified1(k)" "unclassified1_Unclassified1(k)"
#> OTU10 "Actinobacteria" "Actinomycetales"
#> Rank5
#> OTU1 "Propionibacteriaceae"
#> OTU2 "unclassified1_Actinomycetales(o)"
#> OTU3 "Propionibacteriaceae"
#> OTU4 "Propionibacteriaceae"
#> OTU5 "Propionibacteriaceae"
#> OTU6 "1_Actinomycetales(o)"
#> OTU7 "Nocardioidaceae"
#> OTU8 "Nocardioidaceae"
#> OTU9 "unclassified2_Unclassified1(k)"
#> OTU10 "2_Actinomycetales(o)"
#> Rank6
#> OTU1 "Propionibacterium"
#> OTU2 "unclassified1_Actinomycetales(o)"
#> OTU3 "unclassified2_Propionibacteriaceae(f)"
#> OTU4 "Tessaracoccus"
#> OTU5 "Aestuariimicrobium"
#> OTU6 "1_Actinomycetales(o)"
#> OTU7 "2_Nocardioidaceae(f)"
#> OTU8 "Propionicimonas"
#> OTU9 "unclassified3_Unclassified1(k)"
#> OTU10 "3_Actinomycetales(o)"
#> Rank7
#> OTU1 "Propionibacteriumacnes"
#> OTU2 "unclassified1_Actinomycetales(o)"
#> OTU3 "unclassified2_Propionibacteriaceae(f)"
#> OTU4 "1_Tessaracoccus(g)"
#> OTU5 "unclassified3_Aestuariimicrobium(g)"
#> OTU6 "2_Actinomycetales(o)"
#> OTU7 "3_Nocardioidaceae(f)"
#> OTU8 "4_Propionicimonas(g)"
#> OTU9 "unclassified4_Unclassified1(k)"
#> OTU10 "5_Actinomycetales(o)"
#--- Example 10 -------------------------------------------------------------
# - Make names of ranks "Family" and "Order" unique by adding numbers to
# duplicated names
renamed10 <- renameTaxa(taxtab,
pat = "<name>",
substPat = "<name>_<subst_name>(<subst_R>)",
numDupli = c("Family", "Order"))
renamed10
#> Kingdom Phylum
#> OTU1 "Bacteria" "Actinobacteria"
#> OTU2 "Bacteria" "Actinobacteria"
#> OTU3 "Bacteria" "Actinobacteria"
#> OTU4 "Bacteria" "Actinobacteria"
#> OTU5 "Bacteria" "Actinobacteria"
#> OTU6 "Bacteria" "Actinobacteria"
#> OTU7 "Bacteria" "Actinobacteria"
#> OTU8 "Bacteria" "Actinobacteria"
#> OTU9 "Unclassified1" "unclassified1_Unclassified1(K)"
#> OTU10 "Bacteria" "Actinobacteria"
#> Class Order
#> OTU1 "Actinobacteria" "Actinomycetales1"
#> OTU2 "Actinobacteria" "Actinomycetales2"
#> OTU3 "Actinobacteria" "Actinomycetales3"
#> OTU4 "Actinobacteria" "Actinomycetales4"
#> OTU5 "Actinobacteria" "Actinomycetales5"
#> OTU6 "Actinobacteria" "Actinomycetales6"
#> OTU7 "Actinobacteria" "Actinomycetales7"
#> OTU8 "Actinobacteria" "Actinomycetales8"
#> OTU9 "unclassified1_Unclassified1(K)" "unclassified1_Unclassified1(K)"
#> OTU10 "Actinobacteria" "Actinomycetales9"
#> Family
#> OTU1 "Propionibacteriaceae1"
#> OTU2 "unclassified1_Actinomycetales2(O)"
#> OTU3 "Propionibacteriaceae2"
#> OTU4 "Propionibacteriaceae3"
#> OTU5 "Propionibacteriaceae4"
#> OTU6 "1_Actinomycetales6(O)"
#> OTU7 "Nocardioidaceae1"
#> OTU8 "Nocardioidaceae2"
#> OTU9 "unclassified2_Unclassified1(K)"
#> OTU10 "2_Actinomycetales9(O)"
#> Genus
#> OTU1 "Propionibacterium"
#> OTU2 "unclassified1_Actinomycetales2(O)"
#> OTU3 "unclassified2_Propionibacteriaceae2(F)"
#> OTU4 "Tessaracoccus"
#> OTU5 "Aestuariimicrobium"
#> OTU6 "1_Actinomycetales6(O)"
#> OTU7 "2_Nocardioidaceae1(F)"
#> OTU8 "Propionicimonas"
#> OTU9 "unclassified3_Unclassified1(K)"
#> OTU10 "3_Actinomycetales9(O)"
#> Species
#> OTU1 "Propionibacteriumacnes"
#> OTU2 "unclassified1_Actinomycetales2(O)"
#> OTU3 "unclassified2_Propionibacteriaceae2(F)"
#> OTU4 "1_Tessaracoccus(G)"
#> OTU5 "unclassified3_Aestuariimicrobium(G)"
#> OTU6 "2_Actinomycetales6(O)"
#> OTU7 "3_Nocardioidaceae1(F)"
#> OTU8 "4_Propionicimonas(G)"
#> OTU9 "unclassified4_Unclassified1(K)"
#> OTU10 "5_Actinomycetales9(O)"
any(duplicated(renamed10[, "Family"]))
#> [1] FALSE
any(duplicated(renamed10[, "Order"]))
#> [1] FALSE