Identifies phyloseq tax_table values as unknown or uninformative and replaces them with the first informative value from a higher taxonomic rank.
Short values in phyloseq tax_table are typically empty strings or " ", or "g__" etc. so it is helpful to replace them. (If this is unwanted: set
min_length= 0 to avoid filtering on length.)Values in
unknownsare also removed, even if longer thanmin_length. It is up to the user to specify sensible values inunknownsif their dataset has other unwanted values.NA values are also replaced.
See this article for an extended discussion of tax_table fixing. https://david-barnett.github.io/microViz/articles/web-only/tax-fixing.html
Usage
tax_fix(
ps,
min_length = 4,
unknowns = NA,
suffix_rank = "classified",
sep = " ",
anon_unique = TRUE,
verbose = TRUE
)Arguments
- ps
phyloseq or tax_table (taxonomyTable)
- min_length
replace strings shorter than this, must be integer > 0
- unknowns
also replace strings matching any in this vector, NA default vector shown in details!
- suffix_rank
"classified" (default) or "current", when replacing an entry, should the suffix be taken from the lowest classified rank for that taxon, "classified", or the "current" unclassified rank?
- sep
character(s) separating new name and taxonomic rank level suffix (see suffix_rank)
- anon_unique
make anonymous taxa unique by replacing unknowns with taxa_name? otherwise they are replaced with paste("unknown", first_rank_name), which is therefore the same for every anonymous taxon, meaning they will be merged if tax_agg is used. (anonymous taxa are taxa with all unknown values in their tax_table row, i.e. cannot be classified even at highest rank available)
- verbose
emit warnings when cannot replace with informative name?
Details
By default (unknowns = NA), unknowns is set to a vector containing:
's__' 'g__' 'f__' 'o__' 'c__' 'p__' 'k__' 'S__' 'G__' 'F__' 'O__' 'C__' 'P__' 'K__' 'NA' 'NaN' ' ' ” 'unknown' 'Unknown' 's__unknown' 's__Unknown' 's__NA' 'g__unknown' 'g__Unknown' 'g__NA' 'f__unknown' 'f__Unknown' 'f__NA' 'o__unknown' 'o__Unknown' 'o__NA' 'c__unknown' 'c__Unknown' 'c__NA' 'p__unknown' 'p__Unknown' 'p__NA' 'k__unknown' 'k__Unknown' 'k__NA' 'S__unknown' 'S__Unknown' 'S__NA' 'G__unknown' 'G__Unknown' 'G__NA' 'F__unknown' 'F__Unknown' 'F__NA' 'O__unknown' 'O__Unknown' 'O__NA' 'C__unknown' 'C__Unknown' 'C__NA' 'P__unknown' 'P__Unknown' 'P__NA' 'K__unknown' 'K__Unknown' 'K__NA'
See also
tax_fix_interactive for interactive tax_fix help
Examples
library(dplyr)
library(phyloseq)
data(dietswap, package = "microbiome")
ps <- dietswap
# create unknowns to test filling
tt <- tax_table(ps)
ntax <- ntaxa(ps)
set.seed(123)
g <- sample(1:ntax, 30)
f <- sample(g, 10)
p <- sample(f, 3)
tt[g, 3] <- "g__"
tt[f, 2] <- "f__"
tt[p, 1] <- "p__"
tt[sample(1:ntax, 10), 3] <- "unknown"
# create a row with only NAs
tt[1, ] <- NA
tax_table(ps) <- tax_table(tt)
ps
#> phyloseq-class experiment-level object
#> otu_table() OTU Table: [ 130 taxa and 222 samples ]
#> sample_data() Sample Data: [ 222 samples by 8 sample variables ]
#> tax_table() Taxonomy Table: [ 130 taxa by 3 taxonomic ranks ]
# tax_fix with defaults should solve most problems
tax_table(ps) %>% head(50)
#> Taxonomy Table: [50 taxa by 3 taxonomic ranks]:
#> Phylum
#> Actinomycetaceae NA
#> Aerococcus "Firmicutes"
#> Aeromonas "Proteobacteria"
#> Akkermansia "Verrucomicrobia"
#> Alcaligenes faecalis et rel. "Proteobacteria"
#> Allistipes et rel. "Bacteroidetes"
#> Anaerobiospirillum "Proteobacteria"
#> Anaerofustis "Firmicutes"
#> Anaerostipes caccae et rel. "Firmicutes"
#> Anaerotruncus colihominis et rel. "Firmicutes"
#> Anaerovorax odorimutans et rel. "Firmicutes"
#> Aneurinibacillus "Firmicutes"
#> Aquabacterium "Proteobacteria"
#> Asteroleplasma et rel. "Firmicutes"
#> Atopobium "Actinobacteria"
#> Bacillus "Firmicutes"
#> Bacteroides fragilis et rel. "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes"
#> Bacteroides stercoris et rel. "Bacteroidetes"
#> Bacteroides uniformis et rel. "Bacteroidetes"
#> Bacteroides vulgatus et rel. "Bacteroidetes"
#> Bifidobacterium "p__"
#> Bilophila et rel. "Proteobacteria"
#> Brachyspira "Spirochaetes"
#> Bryantella formatexigens et rel. "Firmicutes"
#> Bulleidia moorei et rel. "Firmicutes"
#> Burkholderia "Proteobacteria"
#> Butyrivibrio crossotus et rel. "Firmicutes"
#> Campylobacter "Proteobacteria"
#> Catenibacterium mitsuokai et rel. "Firmicutes"
#> Clostridium (sensu stricto) "Firmicutes"
#> Clostridium cellulosi et rel. "Firmicutes"
#> Clostridium colinum et rel. "p__"
#> Clostridium difficile et rel. "Firmicutes"
#> Clostridium felsineum et rel. "Firmicutes"
#> Clostridium leptum et rel. "Firmicutes"
#> Clostridium nexile et rel. "Firmicutes"
#> Clostridium orbiscindens et rel. "Firmicutes"
#> Clostridium ramosum et rel. "Firmicutes"
#> Clostridium sphenoides et rel. "Firmicutes"
#> Clostridium stercorarium et rel. "Firmicutes"
#> Clostridium symbiosum et rel. "Firmicutes"
#> Clostridium thermocellum et rel. "Firmicutes"
#> Collinsella "Actinobacteria"
#> Coprobacillus catenaformis et rel. "Firmicutes"
#> Coprococcus eutactus et rel. "Firmicutes"
#> Corynebacterium "Actinobacteria"
#> Family
#> Actinomycetaceae NA
#> Aerococcus "Bacilli"
#> Aeromonas "Proteobacteria"
#> Akkermansia "Verrucomicrobia"
#> Alcaligenes faecalis et rel. "Proteobacteria"
#> Allistipes et rel. "Bacteroidetes"
#> Anaerobiospirillum "Proteobacteria"
#> Anaerofustis "Clostridium cluster XV"
#> Anaerostipes caccae et rel. "Clostridium cluster XIVa"
#> Anaerotruncus colihominis et rel. "Clostridium cluster IV"
#> Anaerovorax odorimutans et rel. "Clostridium cluster XI"
#> Aneurinibacillus "Bacilli"
#> Aquabacterium "Proteobacteria"
#> Asteroleplasma et rel. "Asteroleplasma"
#> Atopobium "Actinobacteria"
#> Bacillus "Bacilli"
#> Bacteroides fragilis et rel. "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes"
#> Bacteroides stercoris et rel. "Bacteroidetes"
#> Bacteroides uniformis et rel. "Bacteroidetes"
#> Bacteroides vulgatus et rel. "Bacteroidetes"
#> Bifidobacterium "f__"
#> Bilophila et rel. "f__"
#> Brachyspira "Spirochaetes"
#> Bryantella formatexigens et rel. "Clostridium cluster XIVa"
#> Bulleidia moorei et rel. "Clostridium cluster XVI"
#> Burkholderia "Proteobacteria"
#> Butyrivibrio crossotus et rel. "Clostridium cluster XIVa"
#> Campylobacter "Proteobacteria"
#> Catenibacterium mitsuokai et rel. "Clostridium cluster XVII"
#> Clostridium (sensu stricto) "Clostridium cluster I"
#> Clostridium cellulosi et rel. "Clostridium cluster IV"
#> Clostridium colinum et rel. "f__"
#> Clostridium difficile et rel. "Clostridium cluster XI"
#> Clostridium felsineum et rel. "Clostridium cluster XI"
#> Clostridium leptum et rel. "Clostridium cluster IV"
#> Clostridium nexile et rel. "Clostridium cluster XIVa"
#> Clostridium orbiscindens et rel. "Clostridium cluster IV"
#> Clostridium ramosum et rel. "f__"
#> Clostridium sphenoides et rel. "Clostridium cluster XIVa"
#> Clostridium stercorarium et rel. "Clostridium cluster III"
#> Clostridium symbiosum et rel. "Clostridium cluster XIVa"
#> Clostridium thermocellum et rel. "Clostridium cluster III"
#> Collinsella "Actinobacteria"
#> Coprobacillus catenaformis et rel. "Clostridium cluster XVIII"
#> Coprococcus eutactus et rel. "Clostridium cluster XIVa"
#> Corynebacterium "Actinobacteria"
#> Genus
#> Actinomycetaceae NA
#> Aerococcus "Aerococcus"
#> Aeromonas "Aeromonas"
#> Akkermansia "Akkermansia"
#> Alcaligenes faecalis et rel. "Alcaligenes faecalis et rel."
#> Allistipes et rel. "Allistipes et rel."
#> Anaerobiospirillum "g__"
#> Anaerofustis "Anaerofustis"
#> Anaerostipes caccae et rel. "g__"
#> Anaerotruncus colihominis et rel. "Anaerotruncus colihominis et rel."
#> Anaerovorax odorimutans et rel. "Anaerovorax odorimutans et rel."
#> Aneurinibacillus "Aneurinibacillus"
#> Aquabacterium "unknown"
#> Asteroleplasma et rel. "g__"
#> Atopobium "Atopobium"
#> Bacillus "Bacillus"
#> Bacteroides fragilis et rel. "Bacteroides fragilis et rel."
#> Bacteroides intestinalis et rel. "Bacteroides intestinalis et rel."
#> Bacteroides ovatus et rel. "Bacteroides ovatus et rel."
#> Bacteroides plebeius et rel. "Bacteroides plebeius et rel."
#> Bacteroides splachnicus et rel. "Bacteroides splachnicus et rel."
#> Bacteroides stercoris et rel. "Bacteroides stercoris et rel."
#> Bacteroides uniformis et rel. "Bacteroides uniformis et rel."
#> Bacteroides vulgatus et rel. "Bacteroides vulgatus et rel."
#> Bifidobacterium "g__"
#> Bilophila et rel. "g__"
#> Brachyspira "Brachyspira"
#> Bryantella formatexigens et rel. "Bryantella formatexigens et rel."
#> Bulleidia moorei et rel. "Bulleidia moorei et rel."
#> Burkholderia "Burkholderia"
#> Butyrivibrio crossotus et rel. "Butyrivibrio crossotus et rel."
#> Campylobacter "Campylobacter"
#> Catenibacterium mitsuokai et rel. "Catenibacterium mitsuokai et rel."
#> Clostridium (sensu stricto) "unknown"
#> Clostridium cellulosi et rel. "Clostridium cellulosi et rel."
#> Clostridium colinum et rel. "g__"
#> Clostridium difficile et rel. "Clostridium difficile et rel."
#> Clostridium felsineum et rel. "Clostridium felsineum et rel."
#> Clostridium leptum et rel. "Clostridium leptum et rel."
#> Clostridium nexile et rel. "Clostridium nexile et rel."
#> Clostridium orbiscindens et rel. "Clostridium orbiscindens et rel."
#> Clostridium ramosum et rel. "g__"
#> Clostridium sphenoides et rel. "g__"
#> Clostridium stercorarium et rel. "Clostridium stercorarium et rel."
#> Clostridium symbiosum et rel. "Clostridium symbiosum et rel."
#> Clostridium thermocellum et rel. "Clostridium thermocellum et rel."
#> Collinsella "Collinsella"
#> Coprobacillus catenaformis et rel. "Coprobacillus catenaformis et rel."
#> Coprococcus eutactus et rel. "Coprococcus eutactus et rel."
#> Corynebacterium "g__"
# this will replace "unknown"s as well as short values including "g__" and "f__"
tax_fix(ps) %>%
tax_table() %>%
head(50)
#> Row named: Actinomycetaceae
#> contains no non-unknown values, returning:
#> 'Actinomycetaceae' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Bifidobacterium
#> contains no non-unknown values, returning:
#> 'Bifidobacterium' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Clostridium colinum et rel.
#> contains no non-unknown values, returning:
#> 'Clostridium colinum et rel.' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Escherichia coli et rel.
#> contains no non-unknown values, returning:
#> 'Escherichia coli et rel.' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Taxonomy Table: [50 taxa by 3 taxonomic ranks]:
#> Phylum
#> Actinomycetaceae "Actinomycetaceae"
#> Aerococcus "Firmicutes"
#> Aeromonas "Proteobacteria"
#> Akkermansia "Verrucomicrobia"
#> Alcaligenes faecalis et rel. "Proteobacteria"
#> Allistipes et rel. "Bacteroidetes"
#> Anaerobiospirillum "Proteobacteria"
#> Anaerofustis "Firmicutes"
#> Anaerostipes caccae et rel. "Firmicutes"
#> Anaerotruncus colihominis et rel. "Firmicutes"
#> Anaerovorax odorimutans et rel. "Firmicutes"
#> Aneurinibacillus "Firmicutes"
#> Aquabacterium "Proteobacteria"
#> Asteroleplasma et rel. "Firmicutes"
#> Atopobium "Actinobacteria"
#> Bacillus "Firmicutes"
#> Bacteroides fragilis et rel. "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes"
#> Bacteroides stercoris et rel. "Bacteroidetes"
#> Bacteroides uniformis et rel. "Bacteroidetes"
#> Bacteroides vulgatus et rel. "Bacteroidetes"
#> Bifidobacterium "Bifidobacterium"
#> Bilophila et rel. "Proteobacteria"
#> Brachyspira "Spirochaetes"
#> Bryantella formatexigens et rel. "Firmicutes"
#> Bulleidia moorei et rel. "Firmicutes"
#> Burkholderia "Proteobacteria"
#> Butyrivibrio crossotus et rel. "Firmicutes"
#> Campylobacter "Proteobacteria"
#> Catenibacterium mitsuokai et rel. "Firmicutes"
#> Clostridium (sensu stricto) "Firmicutes"
#> Clostridium cellulosi et rel. "Firmicutes"
#> Clostridium colinum et rel. "Clostridium colinum et rel."
#> Clostridium difficile et rel. "Firmicutes"
#> Clostridium felsineum et rel. "Firmicutes"
#> Clostridium leptum et rel. "Firmicutes"
#> Clostridium nexile et rel. "Firmicutes"
#> Clostridium orbiscindens et rel. "Firmicutes"
#> Clostridium ramosum et rel. "Firmicutes"
#> Clostridium sphenoides et rel. "Firmicutes"
#> Clostridium stercorarium et rel. "Firmicutes"
#> Clostridium symbiosum et rel. "Firmicutes"
#> Clostridium thermocellum et rel. "Firmicutes"
#> Collinsella "Actinobacteria"
#> Coprobacillus catenaformis et rel. "Firmicutes"
#> Coprococcus eutactus et rel. "Firmicutes"
#> Corynebacterium "Actinobacteria"
#> Family
#> Actinomycetaceae "Actinomycetaceae"
#> Aerococcus "Bacilli"
#> Aeromonas "Proteobacteria"
#> Akkermansia "Verrucomicrobia"
#> Alcaligenes faecalis et rel. "Proteobacteria"
#> Allistipes et rel. "Bacteroidetes"
#> Anaerobiospirillum "Proteobacteria"
#> Anaerofustis "Clostridium cluster XV"
#> Anaerostipes caccae et rel. "Clostridium cluster XIVa"
#> Anaerotruncus colihominis et rel. "Clostridium cluster IV"
#> Anaerovorax odorimutans et rel. "Clostridium cluster XI"
#> Aneurinibacillus "Bacilli"
#> Aquabacterium "Proteobacteria"
#> Asteroleplasma et rel. "Asteroleplasma"
#> Atopobium "Actinobacteria"
#> Bacillus "Bacilli"
#> Bacteroides fragilis et rel. "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes"
#> Bacteroides stercoris et rel. "Bacteroidetes"
#> Bacteroides uniformis et rel. "Bacteroidetes"
#> Bacteroides vulgatus et rel. "Bacteroidetes"
#> Bifidobacterium "Bifidobacterium"
#> Bilophila et rel. "Proteobacteria Phylum"
#> Brachyspira "Spirochaetes"
#> Bryantella formatexigens et rel. "Clostridium cluster XIVa"
#> Bulleidia moorei et rel. "Clostridium cluster XVI"
#> Burkholderia "Proteobacteria"
#> Butyrivibrio crossotus et rel. "Clostridium cluster XIVa"
#> Campylobacter "Proteobacteria"
#> Catenibacterium mitsuokai et rel. "Clostridium cluster XVII"
#> Clostridium (sensu stricto) "Clostridium cluster I"
#> Clostridium cellulosi et rel. "Clostridium cluster IV"
#> Clostridium colinum et rel. "Clostridium colinum et rel."
#> Clostridium difficile et rel. "Clostridium cluster XI"
#> Clostridium felsineum et rel. "Clostridium cluster XI"
#> Clostridium leptum et rel. "Clostridium cluster IV"
#> Clostridium nexile et rel. "Clostridium cluster XIVa"
#> Clostridium orbiscindens et rel. "Clostridium cluster IV"
#> Clostridium ramosum et rel. "Firmicutes Phylum"
#> Clostridium sphenoides et rel. "Clostridium cluster XIVa"
#> Clostridium stercorarium et rel. "Clostridium cluster III"
#> Clostridium symbiosum et rel. "Clostridium cluster XIVa"
#> Clostridium thermocellum et rel. "Clostridium cluster III"
#> Collinsella "Actinobacteria"
#> Coprobacillus catenaformis et rel. "Clostridium cluster XVIII"
#> Coprococcus eutactus et rel. "Clostridium cluster XIVa"
#> Corynebacterium "Actinobacteria"
#> Genus
#> Actinomycetaceae "Actinomycetaceae"
#> Aerococcus "Aerococcus"
#> Aeromonas "Aeromonas"
#> Akkermansia "Akkermansia"
#> Alcaligenes faecalis et rel. "Alcaligenes faecalis et rel."
#> Allistipes et rel. "Allistipes et rel."
#> Anaerobiospirillum "Proteobacteria Family"
#> Anaerofustis "Anaerofustis"
#> Anaerostipes caccae et rel. "Clostridium cluster XIVa Family"
#> Anaerotruncus colihominis et rel. "Anaerotruncus colihominis et rel."
#> Anaerovorax odorimutans et rel. "Anaerovorax odorimutans et rel."
#> Aneurinibacillus "Aneurinibacillus"
#> Aquabacterium "Proteobacteria Family"
#> Asteroleplasma et rel. "Asteroleplasma Family"
#> Atopobium "Atopobium"
#> Bacillus "Bacillus"
#> Bacteroides fragilis et rel. "Bacteroides fragilis et rel."
#> Bacteroides intestinalis et rel. "Bacteroides intestinalis et rel."
#> Bacteroides ovatus et rel. "Bacteroides ovatus et rel."
#> Bacteroides plebeius et rel. "Bacteroides plebeius et rel."
#> Bacteroides splachnicus et rel. "Bacteroides splachnicus et rel."
#> Bacteroides stercoris et rel. "Bacteroides stercoris et rel."
#> Bacteroides uniformis et rel. "Bacteroides uniformis et rel."
#> Bacteroides vulgatus et rel. "Bacteroides vulgatus et rel."
#> Bifidobacterium "Bifidobacterium"
#> Bilophila et rel. "Proteobacteria Phylum"
#> Brachyspira "Brachyspira"
#> Bryantella formatexigens et rel. "Bryantella formatexigens et rel."
#> Bulleidia moorei et rel. "Bulleidia moorei et rel."
#> Burkholderia "Burkholderia"
#> Butyrivibrio crossotus et rel. "Butyrivibrio crossotus et rel."
#> Campylobacter "Campylobacter"
#> Catenibacterium mitsuokai et rel. "Catenibacterium mitsuokai et rel."
#> Clostridium (sensu stricto) "Clostridium cluster I Family"
#> Clostridium cellulosi et rel. "Clostridium cellulosi et rel."
#> Clostridium colinum et rel. "Clostridium colinum et rel."
#> Clostridium difficile et rel. "Clostridium difficile et rel."
#> Clostridium felsineum et rel. "Clostridium felsineum et rel."
#> Clostridium leptum et rel. "Clostridium leptum et rel."
#> Clostridium nexile et rel. "Clostridium nexile et rel."
#> Clostridium orbiscindens et rel. "Clostridium orbiscindens et rel."
#> Clostridium ramosum et rel. "Firmicutes Phylum"
#> Clostridium sphenoides et rel. "Clostridium cluster XIVa Family"
#> Clostridium stercorarium et rel. "Clostridium stercorarium et rel."
#> Clostridium symbiosum et rel. "Clostridium symbiosum et rel."
#> Clostridium thermocellum et rel. "Clostridium thermocellum et rel."
#> Collinsella "Collinsella"
#> Coprobacillus catenaformis et rel. "Coprobacillus catenaformis et rel."
#> Coprococcus eutactus et rel. "Coprococcus eutactus et rel."
#> Corynebacterium "Actinobacteria Family"
# This will only replace short entries, and so won't replace literal "unknown" values
ps %>%
tax_fix(unknowns = NULL) %>%
tax_table() %>%
head(50)
#> Row named: Actinomycetaceae
#> contains no non-unknown values, returning:
#> 'Actinomycetaceae' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Bifidobacterium
#> contains no non-unknown values, returning:
#> 'Bifidobacterium' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Clostridium colinum et rel.
#> contains no non-unknown values, returning:
#> 'Clostridium colinum et rel.' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Escherichia coli et rel.
#> contains no non-unknown values, returning:
#> 'Escherichia coli et rel.' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Taxonomy Table: [50 taxa by 3 taxonomic ranks]:
#> Phylum
#> Actinomycetaceae "Actinomycetaceae"
#> Aerococcus "Firmicutes"
#> Aeromonas "Proteobacteria"
#> Akkermansia "Verrucomicrobia"
#> Alcaligenes faecalis et rel. "Proteobacteria"
#> Allistipes et rel. "Bacteroidetes"
#> Anaerobiospirillum "Proteobacteria"
#> Anaerofustis "Firmicutes"
#> Anaerostipes caccae et rel. "Firmicutes"
#> Anaerotruncus colihominis et rel. "Firmicutes"
#> Anaerovorax odorimutans et rel. "Firmicutes"
#> Aneurinibacillus "Firmicutes"
#> Aquabacterium "Proteobacteria"
#> Asteroleplasma et rel. "Firmicutes"
#> Atopobium "Actinobacteria"
#> Bacillus "Firmicutes"
#> Bacteroides fragilis et rel. "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes"
#> Bacteroides stercoris et rel. "Bacteroidetes"
#> Bacteroides uniformis et rel. "Bacteroidetes"
#> Bacteroides vulgatus et rel. "Bacteroidetes"
#> Bifidobacterium "Bifidobacterium"
#> Bilophila et rel. "Proteobacteria"
#> Brachyspira "Spirochaetes"
#> Bryantella formatexigens et rel. "Firmicutes"
#> Bulleidia moorei et rel. "Firmicutes"
#> Burkholderia "Proteobacteria"
#> Butyrivibrio crossotus et rel. "Firmicutes"
#> Campylobacter "Proteobacteria"
#> Catenibacterium mitsuokai et rel. "Firmicutes"
#> Clostridium (sensu stricto) "Firmicutes"
#> Clostridium cellulosi et rel. "Firmicutes"
#> Clostridium colinum et rel. "Clostridium colinum et rel."
#> Clostridium difficile et rel. "Firmicutes"
#> Clostridium felsineum et rel. "Firmicutes"
#> Clostridium leptum et rel. "Firmicutes"
#> Clostridium nexile et rel. "Firmicutes"
#> Clostridium orbiscindens et rel. "Firmicutes"
#> Clostridium ramosum et rel. "Firmicutes"
#> Clostridium sphenoides et rel. "Firmicutes"
#> Clostridium stercorarium et rel. "Firmicutes"
#> Clostridium symbiosum et rel. "Firmicutes"
#> Clostridium thermocellum et rel. "Firmicutes"
#> Collinsella "Actinobacteria"
#> Coprobacillus catenaformis et rel. "Firmicutes"
#> Coprococcus eutactus et rel. "Firmicutes"
#> Corynebacterium "Actinobacteria"
#> Family
#> Actinomycetaceae "Actinomycetaceae"
#> Aerococcus "Bacilli"
#> Aeromonas "Proteobacteria"
#> Akkermansia "Verrucomicrobia"
#> Alcaligenes faecalis et rel. "Proteobacteria"
#> Allistipes et rel. "Bacteroidetes"
#> Anaerobiospirillum "Proteobacteria"
#> Anaerofustis "Clostridium cluster XV"
#> Anaerostipes caccae et rel. "Clostridium cluster XIVa"
#> Anaerotruncus colihominis et rel. "Clostridium cluster IV"
#> Anaerovorax odorimutans et rel. "Clostridium cluster XI"
#> Aneurinibacillus "Bacilli"
#> Aquabacterium "Proteobacteria"
#> Asteroleplasma et rel. "Asteroleplasma"
#> Atopobium "Actinobacteria"
#> Bacillus "Bacilli"
#> Bacteroides fragilis et rel. "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes"
#> Bacteroides stercoris et rel. "Bacteroidetes"
#> Bacteroides uniformis et rel. "Bacteroidetes"
#> Bacteroides vulgatus et rel. "Bacteroidetes"
#> Bifidobacterium "Bifidobacterium"
#> Bilophila et rel. "Proteobacteria Phylum"
#> Brachyspira "Spirochaetes"
#> Bryantella formatexigens et rel. "Clostridium cluster XIVa"
#> Bulleidia moorei et rel. "Clostridium cluster XVI"
#> Burkholderia "Proteobacteria"
#> Butyrivibrio crossotus et rel. "Clostridium cluster XIVa"
#> Campylobacter "Proteobacteria"
#> Catenibacterium mitsuokai et rel. "Clostridium cluster XVII"
#> Clostridium (sensu stricto) "Clostridium cluster I"
#> Clostridium cellulosi et rel. "Clostridium cluster IV"
#> Clostridium colinum et rel. "Clostridium colinum et rel."
#> Clostridium difficile et rel. "Clostridium cluster XI"
#> Clostridium felsineum et rel. "Clostridium cluster XI"
#> Clostridium leptum et rel. "Clostridium cluster IV"
#> Clostridium nexile et rel. "Clostridium cluster XIVa"
#> Clostridium orbiscindens et rel. "Clostridium cluster IV"
#> Clostridium ramosum et rel. "Firmicutes Phylum"
#> Clostridium sphenoides et rel. "Clostridium cluster XIVa"
#> Clostridium stercorarium et rel. "Clostridium cluster III"
#> Clostridium symbiosum et rel. "Clostridium cluster XIVa"
#> Clostridium thermocellum et rel. "Clostridium cluster III"
#> Collinsella "Actinobacteria"
#> Coprobacillus catenaformis et rel. "Clostridium cluster XVIII"
#> Coprococcus eutactus et rel. "Clostridium cluster XIVa"
#> Corynebacterium "Actinobacteria"
#> Genus
#> Actinomycetaceae "Actinomycetaceae"
#> Aerococcus "Aerococcus"
#> Aeromonas "Aeromonas"
#> Akkermansia "Akkermansia"
#> Alcaligenes faecalis et rel. "Alcaligenes faecalis et rel."
#> Allistipes et rel. "Allistipes et rel."
#> Anaerobiospirillum "Proteobacteria Family"
#> Anaerofustis "Anaerofustis"
#> Anaerostipes caccae et rel. "Clostridium cluster XIVa Family"
#> Anaerotruncus colihominis et rel. "Anaerotruncus colihominis et rel."
#> Anaerovorax odorimutans et rel. "Anaerovorax odorimutans et rel."
#> Aneurinibacillus "Aneurinibacillus"
#> Aquabacterium "unknown"
#> Asteroleplasma et rel. "Asteroleplasma Family"
#> Atopobium "Atopobium"
#> Bacillus "Bacillus"
#> Bacteroides fragilis et rel. "Bacteroides fragilis et rel."
#> Bacteroides intestinalis et rel. "Bacteroides intestinalis et rel."
#> Bacteroides ovatus et rel. "Bacteroides ovatus et rel."
#> Bacteroides plebeius et rel. "Bacteroides plebeius et rel."
#> Bacteroides splachnicus et rel. "Bacteroides splachnicus et rel."
#> Bacteroides stercoris et rel. "Bacteroides stercoris et rel."
#> Bacteroides uniformis et rel. "Bacteroides uniformis et rel."
#> Bacteroides vulgatus et rel. "Bacteroides vulgatus et rel."
#> Bifidobacterium "Bifidobacterium"
#> Bilophila et rel. "Proteobacteria Phylum"
#> Brachyspira "Brachyspira"
#> Bryantella formatexigens et rel. "Bryantella formatexigens et rel."
#> Bulleidia moorei et rel. "Bulleidia moorei et rel."
#> Burkholderia "Burkholderia"
#> Butyrivibrio crossotus et rel. "Butyrivibrio crossotus et rel."
#> Campylobacter "Campylobacter"
#> Catenibacterium mitsuokai et rel. "Catenibacterium mitsuokai et rel."
#> Clostridium (sensu stricto) "unknown"
#> Clostridium cellulosi et rel. "Clostridium cellulosi et rel."
#> Clostridium colinum et rel. "Clostridium colinum et rel."
#> Clostridium difficile et rel. "Clostridium difficile et rel."
#> Clostridium felsineum et rel. "Clostridium felsineum et rel."
#> Clostridium leptum et rel. "Clostridium leptum et rel."
#> Clostridium nexile et rel. "Clostridium nexile et rel."
#> Clostridium orbiscindens et rel. "Clostridium orbiscindens et rel."
#> Clostridium ramosum et rel. "Firmicutes Phylum"
#> Clostridium sphenoides et rel. "Clostridium cluster XIVa Family"
#> Clostridium stercorarium et rel. "Clostridium stercorarium et rel."
#> Clostridium symbiosum et rel. "Clostridium symbiosum et rel."
#> Clostridium thermocellum et rel. "Clostridium thermocellum et rel."
#> Collinsella "Collinsella"
#> Coprobacillus catenaformis et rel. "Coprobacillus catenaformis et rel."
#> Coprococcus eutactus et rel. "Coprococcus eutactus et rel."
#> Corynebacterium "Actinobacteria Family"
# Change rank suffix and separator settings
tax_fix(ps, suffix_rank = "current", sep = " - ") %>%
tax_table() %>%
head(50)
#> Row named: Actinomycetaceae
#> contains no non-unknown values, returning:
#> 'Actinomycetaceae' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Bifidobacterium
#> contains no non-unknown values, returning:
#> 'Bifidobacterium' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Clostridium colinum et rel.
#> contains no non-unknown values, returning:
#> 'Clostridium colinum et rel.' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Escherichia coli et rel.
#> contains no non-unknown values, returning:
#> 'Escherichia coli et rel.' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Taxonomy Table: [50 taxa by 3 taxonomic ranks]:
#> Phylum
#> Actinomycetaceae "Actinomycetaceae"
#> Aerococcus "Firmicutes"
#> Aeromonas "Proteobacteria"
#> Akkermansia "Verrucomicrobia"
#> Alcaligenes faecalis et rel. "Proteobacteria"
#> Allistipes et rel. "Bacteroidetes"
#> Anaerobiospirillum "Proteobacteria"
#> Anaerofustis "Firmicutes"
#> Anaerostipes caccae et rel. "Firmicutes"
#> Anaerotruncus colihominis et rel. "Firmicutes"
#> Anaerovorax odorimutans et rel. "Firmicutes"
#> Aneurinibacillus "Firmicutes"
#> Aquabacterium "Proteobacteria"
#> Asteroleplasma et rel. "Firmicutes"
#> Atopobium "Actinobacteria"
#> Bacillus "Firmicutes"
#> Bacteroides fragilis et rel. "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes"
#> Bacteroides stercoris et rel. "Bacteroidetes"
#> Bacteroides uniformis et rel. "Bacteroidetes"
#> Bacteroides vulgatus et rel. "Bacteroidetes"
#> Bifidobacterium "Bifidobacterium"
#> Bilophila et rel. "Proteobacteria"
#> Brachyspira "Spirochaetes"
#> Bryantella formatexigens et rel. "Firmicutes"
#> Bulleidia moorei et rel. "Firmicutes"
#> Burkholderia "Proteobacteria"
#> Butyrivibrio crossotus et rel. "Firmicutes"
#> Campylobacter "Proteobacteria"
#> Catenibacterium mitsuokai et rel. "Firmicutes"
#> Clostridium (sensu stricto) "Firmicutes"
#> Clostridium cellulosi et rel. "Firmicutes"
#> Clostridium colinum et rel. "Clostridium colinum et rel."
#> Clostridium difficile et rel. "Firmicutes"
#> Clostridium felsineum et rel. "Firmicutes"
#> Clostridium leptum et rel. "Firmicutes"
#> Clostridium nexile et rel. "Firmicutes"
#> Clostridium orbiscindens et rel. "Firmicutes"
#> Clostridium ramosum et rel. "Firmicutes"
#> Clostridium sphenoides et rel. "Firmicutes"
#> Clostridium stercorarium et rel. "Firmicutes"
#> Clostridium symbiosum et rel. "Firmicutes"
#> Clostridium thermocellum et rel. "Firmicutes"
#> Collinsella "Actinobacteria"
#> Coprobacillus catenaformis et rel. "Firmicutes"
#> Coprococcus eutactus et rel. "Firmicutes"
#> Corynebacterium "Actinobacteria"
#> Family
#> Actinomycetaceae "Actinomycetaceae"
#> Aerococcus "Bacilli"
#> Aeromonas "Proteobacteria"
#> Akkermansia "Verrucomicrobia"
#> Alcaligenes faecalis et rel. "Proteobacteria"
#> Allistipes et rel. "Bacteroidetes"
#> Anaerobiospirillum "Proteobacteria"
#> Anaerofustis "Clostridium cluster XV"
#> Anaerostipes caccae et rel. "Clostridium cluster XIVa"
#> Anaerotruncus colihominis et rel. "Clostridium cluster IV"
#> Anaerovorax odorimutans et rel. "Clostridium cluster XI"
#> Aneurinibacillus "Bacilli"
#> Aquabacterium "Proteobacteria"
#> Asteroleplasma et rel. "Asteroleplasma"
#> Atopobium "Actinobacteria"
#> Bacillus "Bacilli"
#> Bacteroides fragilis et rel. "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes"
#> Bacteroides stercoris et rel. "Bacteroidetes"
#> Bacteroides uniformis et rel. "Bacteroidetes"
#> Bacteroides vulgatus et rel. "Bacteroidetes"
#> Bifidobacterium "Bifidobacterium"
#> Bilophila et rel. "Proteobacteria - Family"
#> Brachyspira "Spirochaetes"
#> Bryantella formatexigens et rel. "Clostridium cluster XIVa"
#> Bulleidia moorei et rel. "Clostridium cluster XVI"
#> Burkholderia "Proteobacteria"
#> Butyrivibrio crossotus et rel. "Clostridium cluster XIVa"
#> Campylobacter "Proteobacteria"
#> Catenibacterium mitsuokai et rel. "Clostridium cluster XVII"
#> Clostridium (sensu stricto) "Clostridium cluster I"
#> Clostridium cellulosi et rel. "Clostridium cluster IV"
#> Clostridium colinum et rel. "Clostridium colinum et rel."
#> Clostridium difficile et rel. "Clostridium cluster XI"
#> Clostridium felsineum et rel. "Clostridium cluster XI"
#> Clostridium leptum et rel. "Clostridium cluster IV"
#> Clostridium nexile et rel. "Clostridium cluster XIVa"
#> Clostridium orbiscindens et rel. "Clostridium cluster IV"
#> Clostridium ramosum et rel. "Firmicutes - Family"
#> Clostridium sphenoides et rel. "Clostridium cluster XIVa"
#> Clostridium stercorarium et rel. "Clostridium cluster III"
#> Clostridium symbiosum et rel. "Clostridium cluster XIVa"
#> Clostridium thermocellum et rel. "Clostridium cluster III"
#> Collinsella "Actinobacteria"
#> Coprobacillus catenaformis et rel. "Clostridium cluster XVIII"
#> Coprococcus eutactus et rel. "Clostridium cluster XIVa"
#> Corynebacterium "Actinobacteria"
#> Genus
#> Actinomycetaceae "Actinomycetaceae"
#> Aerococcus "Aerococcus"
#> Aeromonas "Aeromonas"
#> Akkermansia "Akkermansia"
#> Alcaligenes faecalis et rel. "Alcaligenes faecalis et rel."
#> Allistipes et rel. "Allistipes et rel."
#> Anaerobiospirillum "Proteobacteria - Genus"
#> Anaerofustis "Anaerofustis"
#> Anaerostipes caccae et rel. "Clostridium cluster XIVa - Genus"
#> Anaerotruncus colihominis et rel. "Anaerotruncus colihominis et rel."
#> Anaerovorax odorimutans et rel. "Anaerovorax odorimutans et rel."
#> Aneurinibacillus "Aneurinibacillus"
#> Aquabacterium "Proteobacteria - Genus"
#> Asteroleplasma et rel. "Asteroleplasma - Genus"
#> Atopobium "Atopobium"
#> Bacillus "Bacillus"
#> Bacteroides fragilis et rel. "Bacteroides fragilis et rel."
#> Bacteroides intestinalis et rel. "Bacteroides intestinalis et rel."
#> Bacteroides ovatus et rel. "Bacteroides ovatus et rel."
#> Bacteroides plebeius et rel. "Bacteroides plebeius et rel."
#> Bacteroides splachnicus et rel. "Bacteroides splachnicus et rel."
#> Bacteroides stercoris et rel. "Bacteroides stercoris et rel."
#> Bacteroides uniformis et rel. "Bacteroides uniformis et rel."
#> Bacteroides vulgatus et rel. "Bacteroides vulgatus et rel."
#> Bifidobacterium "Bifidobacterium"
#> Bilophila et rel. "Proteobacteria - Genus"
#> Brachyspira "Brachyspira"
#> Bryantella formatexigens et rel. "Bryantella formatexigens et rel."
#> Bulleidia moorei et rel. "Bulleidia moorei et rel."
#> Burkholderia "Burkholderia"
#> Butyrivibrio crossotus et rel. "Butyrivibrio crossotus et rel."
#> Campylobacter "Campylobacter"
#> Catenibacterium mitsuokai et rel. "Catenibacterium mitsuokai et rel."
#> Clostridium (sensu stricto) "Clostridium cluster I - Genus"
#> Clostridium cellulosi et rel. "Clostridium cellulosi et rel."
#> Clostridium colinum et rel. "Clostridium colinum et rel."
#> Clostridium difficile et rel. "Clostridium difficile et rel."
#> Clostridium felsineum et rel. "Clostridium felsineum et rel."
#> Clostridium leptum et rel. "Clostridium leptum et rel."
#> Clostridium nexile et rel. "Clostridium nexile et rel."
#> Clostridium orbiscindens et rel. "Clostridium orbiscindens et rel."
#> Clostridium ramosum et rel. "Firmicutes - Genus"
#> Clostridium sphenoides et rel. "Clostridium cluster XIVa - Genus"
#> Clostridium stercorarium et rel. "Clostridium stercorarium et rel."
#> Clostridium symbiosum et rel. "Clostridium symbiosum et rel."
#> Clostridium thermocellum et rel. "Clostridium thermocellum et rel."
#> Collinsella "Collinsella"
#> Coprobacillus catenaformis et rel. "Coprobacillus catenaformis et rel."
#> Coprococcus eutactus et rel. "Coprococcus eutactus et rel."
#> Corynebacterium "Actinobacteria - Genus"
# by default, completely unclassified (anonymous) taxa are named by their
# taxa_names / rownames at all ranks.
# This makes anonymous taxa distinct from each other,
# and so they won't be merged on aggregation with tax_agg.
# If you think your anonymous taxa should merge on tax_agg,
# or you just want them to be named the all same for another reason,
# set anon_unique = FALSE (compare the warning messages)
tax_fix(ps, anon_unique = FALSE)
#> Row named: Actinomycetaceae
#> contains no non-unknown values, returning:
#> 'unclassified Phylum' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Bifidobacterium
#> contains no non-unknown values, returning:
#> 'unclassified Phylum' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Clostridium colinum et rel.
#> contains no non-unknown values, returning:
#> 'unclassified Phylum' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Escherichia coli et rel.
#> contains no non-unknown values, returning:
#> 'unclassified Phylum' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> phyloseq-class experiment-level object
#> otu_table() OTU Table: [ 130 taxa and 222 samples ]
#> sample_data() Sample Data: [ 222 samples by 8 sample variables ]
#> tax_table() Taxonomy Table: [ 130 taxa by 3 taxonomic ranks ]
tax_fix(ps, anon_unique = TRUE)
#> Row named: Actinomycetaceae
#> contains no non-unknown values, returning:
#> 'Actinomycetaceae' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Bifidobacterium
#> contains no non-unknown values, returning:
#> 'Bifidobacterium' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Clostridium colinum et rel.
#> contains no non-unknown values, returning:
#> 'Clostridium colinum et rel.' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> Row named: Escherichia coli et rel.
#> contains no non-unknown values, returning:
#> 'Escherichia coli et rel.' for all replaced levels.
#> Consider editing this tax_table entry manually.
#> phyloseq-class experiment-level object
#> otu_table() OTU Table: [ 130 taxa and 222 samples ]
#> sample_data() Sample Data: [ 222 samples by 8 sample variables ]
#> tax_table() Taxonomy Table: [ 130 taxa by 3 taxonomic ranks ]
# here's a larger example tax_table shows its still fast with 1000s rows,
# from microbiomeutilities package
# library(microbiomeutilities)
# data("hmp2")
# system.time(tax_fix(hmp2, min_length = 1))