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 unknowns are also removed, even if longer than min_length.
It is up to the user to specify sensible values in unknowns if 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
tax_fix(
ps,
min_length = 4,
unknowns = NA,
suffix_rank = "classified",
sep = " ",
anon_unique = TRUE,
verbose = TRUE
)phyloseq or tax_table (taxonomyTable)
replace strings shorter than this, must be integer > 0
also replace strings matching any in this vector, NA default vector shown in details!
"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?
character(s) separating new name and taxonomic rank level suffix (see suffix_rank)
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)
emit warnings when cannot replace with informative name?
object same class as ps
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'
tax_fix_interactive for interactive tax_fix help
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))