Multiple ways of sorting taxa are possible and determined by the by argument.
The by argument must be one of:
'rev' to reverse the current order
'name' (sort alphabetically by at)
'asis' to keep current order as is
a sample name (descending abundance sorting within that sample)
summary stat. function e.g. sum or mean
The at argument must be "names" for sorting unique taxa,
or a rank name, for sorting at that rank.
at is ignored when by is "rev".
tax_sort(
data,
by = "name",
at = "names",
...,
tree_warn = TRUE,
verbose = TRUE,
trans = "identity",
use_counts = TRUE,
counts_warn = TRUE
)psExtra or phyloseq
how to sort, see description
"names" or a taxonomic rank to apply sorting method to, as specified in by.
used if summary function given, or pass undetected arg
for tax_transform("binary") if by = "prev" or "prevalence"
If phylogenetic tree is present in phyloseq phy_tree slot, taxa cannot be reordered. Default behaviour of tax_sort is to remove the phylogenetic tree and warn about this. tree_warn = FALSE will suppress the warning message, but still remove the tree!
passed to phyloseq_validate verbose (if TRUE: message about suspicious values in tax_table, and how to fix)
name of transformation to apply to taxa before sorting (taxa are returned un-transformed)
use count data if available, instead of transformed data
warn if count data are not available?
sorted phyloseq or psExtra
Don't forget to pass na.rm = TRUE to ...
if using a summary stat function in by
library(phyloseq)
data("dietswap", package = "microbiome")
dietswap
#> 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 ]
# reverse current order
dietswap %>%
tax_sort("rev") %>%
tax_table() %>%
head(30)
#> Taxonomy Table: [30 taxa by 3 taxonomic ranks]:
#> Phylum Family
#> Yersinia et rel. "Proteobacteria" "Proteobacteria"
#> Xanthomonadaceae "Proteobacteria" "Proteobacteria"
#> Wissella et rel. "Firmicutes" "Bacilli"
#> Weissella et rel. "Firmicutes" "Bacilli"
#> Vibrio "Proteobacteria" "Proteobacteria"
#> Veillonella "Firmicutes" "Clostridium cluster IX"
#> Uncultured Selenomonadaceae "Firmicutes" "Clostridium cluster IX"
#> Uncultured Mollicutes "Firmicutes" "Uncultured Mollicutes"
#> Uncultured Clostridiales II "Firmicutes" "Uncultured Clostridiales"
#> Uncultured Clostridiales I "Firmicutes" "Uncultured Clostridiales"
#> Uncultured Chroococcales "Cyanobacteria" "Cyanobacteria"
#> Uncultured Bacteroidetes "Bacteroidetes" "Bacteroidetes"
#> Tannerella et rel. "Bacteroidetes" "Bacteroidetes"
#> Sutterella wadsworthia et rel. "Proteobacteria" "Proteobacteria"
#> Subdoligranulum variable at rel. "Firmicutes" "Clostridium cluster IV"
#> Streptococcus mitis et rel. "Firmicutes" "Bacilli"
#> Streptococcus intermedius et rel. "Firmicutes" "Bacilli"
#> Streptococcus bovis et rel. "Firmicutes" "Bacilli"
#> Staphylococcus "Firmicutes" "Bacilli"
#> Sporobacter termitidis et rel. "Firmicutes" "Clostridium cluster IV"
#> Serratia "Proteobacteria" "Proteobacteria"
#> Ruminococcus obeum et rel. "Firmicutes" "Clostridium cluster XIVa"
#> Ruminococcus lactaris et rel. "Firmicutes" "Clostridium cluster XIVa"
#> Ruminococcus gnavus et rel. "Firmicutes" "Clostridium cluster XIVa"
#> Ruminococcus callidus et rel. "Firmicutes" "Clostridium cluster IV"
#> Ruminococcus bromii et rel. "Firmicutes" "Clostridium cluster IV"
#> Roseburia intestinalis et rel. "Firmicutes" "Clostridium cluster XIVa"
#> Pseudomonas "Proteobacteria" "Proteobacteria"
#> Proteus et rel. "Proteobacteria" "Proteobacteria"
#> Propionibacterium "Actinobacteria" "Actinobacteria"
#> Genus
#> Yersinia et rel. "Yersinia et rel."
#> Xanthomonadaceae "Xanthomonadaceae"
#> Wissella et rel. "Wissella et rel."
#> Weissella et rel. "Weissella et rel."
#> Vibrio "Vibrio"
#> Veillonella "Veillonella"
#> Uncultured Selenomonadaceae "Uncultured Selenomonadaceae"
#> Uncultured Mollicutes "Uncultured Mollicutes"
#> Uncultured Clostridiales II "Uncultured Clostridiales II"
#> Uncultured Clostridiales I "Uncultured Clostridiales I"
#> Uncultured Chroococcales "Uncultured Chroococcales"
#> Uncultured Bacteroidetes "Uncultured Bacteroidetes"
#> Tannerella et rel. "Tannerella et rel."
#> Sutterella wadsworthia et rel. "Sutterella wadsworthia et rel."
#> Subdoligranulum variable at rel. "Subdoligranulum variable at rel."
#> Streptococcus mitis et rel. "Streptococcus mitis et rel."
#> Streptococcus intermedius et rel. "Streptococcus intermedius et rel."
#> Streptococcus bovis et rel. "Streptococcus bovis et rel."
#> Staphylococcus "Staphylococcus"
#> Sporobacter termitidis et rel. "Sporobacter termitidis et rel."
#> Serratia "Serratia"
#> Ruminococcus obeum et rel. "Ruminococcus obeum et rel."
#> Ruminococcus lactaris et rel. "Ruminococcus lactaris et rel."
#> Ruminococcus gnavus et rel. "Ruminococcus gnavus et rel."
#> Ruminococcus callidus et rel. "Ruminococcus callidus et rel."
#> Ruminococcus bromii et rel. "Ruminococcus bromii et rel."
#> Roseburia intestinalis et rel. "Roseburia intestinalis et rel."
#> Pseudomonas "Pseudomonas"
#> Proteus et rel. "Proteus et rel."
#> Propionibacterium "Propionibacterium"
# sort alphabetically by a taxonomic rank (or "names" for taxa_names)
dietswap %>%
tax_sort(by = "name", at = "Phylum") %>%
tax_table() %>%
head(30)
#> Taxonomy Table: [30 taxa by 3 taxonomic ranks]:
#> Phylum Family
#> Actinomycetaceae "Actinobacteria" "Actinobacteria"
#> Atopobium "Actinobacteria" "Actinobacteria"
#> Bifidobacterium "Actinobacteria" "Actinobacteria"
#> Collinsella "Actinobacteria" "Actinobacteria"
#> Corynebacterium "Actinobacteria" "Actinobacteria"
#> Eggerthella lenta et rel. "Actinobacteria" "Actinobacteria"
#> Micrococcaceae "Actinobacteria" "Actinobacteria"
#> Propionibacterium "Actinobacteria" "Actinobacteria"
#> Allistipes et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides fragilis et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides stercoris et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides uniformis et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides vulgatus et rel. "Bacteroidetes" "Bacteroidetes"
#> Parabacteroides distasonis et rel. "Bacteroidetes" "Bacteroidetes"
#> Prevotella melaninogenica et rel. "Bacteroidetes" "Bacteroidetes"
#> Prevotella oralis et rel. "Bacteroidetes" "Bacteroidetes"
#> Prevotella ruminicola et rel. "Bacteroidetes" "Bacteroidetes"
#> Prevotella tannerae et rel. "Bacteroidetes" "Bacteroidetes"
#> Tannerella et rel. "Bacteroidetes" "Bacteroidetes"
#> Uncultured Bacteroidetes "Bacteroidetes" "Bacteroidetes"
#> Uncultured Chroococcales "Cyanobacteria" "Cyanobacteria"
#> Aerococcus "Firmicutes" "Bacilli"
#> Anaerofustis "Firmicutes" "Clostridium cluster XV"
#> Anaerostipes caccae et rel. "Firmicutes" "Clostridium cluster XIVa"
#> Anaerotruncus colihominis et rel. "Firmicutes" "Clostridium cluster IV"
#> Anaerovorax odorimutans et rel. "Firmicutes" "Clostridium cluster XI"
#> Genus
#> Actinomycetaceae "Actinomycetaceae"
#> Atopobium "Atopobium"
#> Bifidobacterium "Bifidobacterium"
#> Collinsella "Collinsella"
#> Corynebacterium "Corynebacterium"
#> Eggerthella lenta et rel. "Eggerthella lenta et rel."
#> Micrococcaceae "Micrococcaceae"
#> Propionibacterium "Propionibacterium"
#> Allistipes et rel. "Allistipes et rel."
#> 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."
#> Parabacteroides distasonis et rel. "Parabacteroides distasonis et rel."
#> Prevotella melaninogenica et rel. "Prevotella melaninogenica et rel."
#> Prevotella oralis et rel. "Prevotella oralis et rel."
#> Prevotella ruminicola et rel. "Prevotella ruminicola et rel."
#> Prevotella tannerae et rel. "Prevotella tannerae et rel."
#> Tannerella et rel. "Tannerella et rel."
#> Uncultured Bacteroidetes "Uncultured Bacteroidetes"
#> Uncultured Chroococcales "Uncultured Chroococcales"
#> Aerococcus "Aerococcus"
#> Anaerofustis "Anaerofustis"
#> Anaerostipes caccae et rel. "Anaerostipes caccae et rel."
#> Anaerotruncus colihominis et rel. "Anaerotruncus colihominis et rel."
#> Anaerovorax odorimutans et rel. "Anaerovorax odorimutans et rel."
# sequentially sorting by higher ranks
# sets tax_table in nested alphabetical order
dietswap %>%
tax_sort(at = "names") %>%
tax_sort(at = "Genus") %>%
tax_sort(at = "Family") %>%
tax_sort(at = "Phylum") %>%
tax_table() %>%
head(30)
#> Taxonomy Table: [30 taxa by 3 taxonomic ranks]:
#> Phylum Family
#> Actinomycetaceae "Actinobacteria" "Actinobacteria"
#> Atopobium "Actinobacteria" "Actinobacteria"
#> Bifidobacterium "Actinobacteria" "Actinobacteria"
#> Collinsella "Actinobacteria" "Actinobacteria"
#> Corynebacterium "Actinobacteria" "Actinobacteria"
#> Eggerthella lenta et rel. "Actinobacteria" "Actinobacteria"
#> Micrococcaceae "Actinobacteria" "Actinobacteria"
#> Propionibacterium "Actinobacteria" "Actinobacteria"
#> Allistipes et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides fragilis et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides stercoris et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides uniformis et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides vulgatus et rel. "Bacteroidetes" "Bacteroidetes"
#> Parabacteroides distasonis et rel. "Bacteroidetes" "Bacteroidetes"
#> Prevotella melaninogenica et rel. "Bacteroidetes" "Bacteroidetes"
#> Prevotella oralis et rel. "Bacteroidetes" "Bacteroidetes"
#> Prevotella ruminicola et rel. "Bacteroidetes" "Bacteroidetes"
#> Prevotella tannerae et rel. "Bacteroidetes" "Bacteroidetes"
#> Tannerella et rel. "Bacteroidetes" "Bacteroidetes"
#> Uncultured Bacteroidetes "Bacteroidetes" "Bacteroidetes"
#> Uncultured Chroococcales "Cyanobacteria" "Cyanobacteria"
#> Asteroleplasma et rel. "Firmicutes" "Asteroleplasma"
#> Aerococcus "Firmicutes" "Bacilli"
#> Aneurinibacillus "Firmicutes" "Bacilli"
#> Bacillus "Firmicutes" "Bacilli"
#> Enterococcus "Firmicutes" "Bacilli"
#> Genus
#> Actinomycetaceae "Actinomycetaceae"
#> Atopobium "Atopobium"
#> Bifidobacterium "Bifidobacterium"
#> Collinsella "Collinsella"
#> Corynebacterium "Corynebacterium"
#> Eggerthella lenta et rel. "Eggerthella lenta et rel."
#> Micrococcaceae "Micrococcaceae"
#> Propionibacterium "Propionibacterium"
#> Allistipes et rel. "Allistipes et rel."
#> 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."
#> Parabacteroides distasonis et rel. "Parabacteroides distasonis et rel."
#> Prevotella melaninogenica et rel. "Prevotella melaninogenica et rel."
#> Prevotella oralis et rel. "Prevotella oralis et rel."
#> Prevotella ruminicola et rel. "Prevotella ruminicola et rel."
#> Prevotella tannerae et rel. "Prevotella tannerae et rel."
#> Tannerella et rel. "Tannerella et rel."
#> Uncultured Bacteroidetes "Uncultured Bacteroidetes"
#> Uncultured Chroococcales "Uncultured Chroococcales"
#> Asteroleplasma et rel. "Asteroleplasma et rel."
#> Aerococcus "Aerococcus"
#> Aneurinibacillus "Aneurinibacillus"
#> Bacillus "Bacillus"
#> Enterococcus "Enterococcus"
# sort by function e.g. total sum or median abundance
dietswap %>%
tax_sort(by = sum) %>%
taxa_names() %>%
head(20)
#> [1] "Prevotella melaninogenica et rel."
#> [2] "Oscillospira guillermondii et rel."
#> [3] "Bacteroides vulgatus et rel."
#> [4] "Clostridium cellulosi et rel."
#> [5] "Prevotella oralis et rel."
#> [6] "Faecalibacterium prausnitzii et rel."
#> [7] "Sporobacter termitidis et rel."
#> [8] "Clostridium symbiosum et rel."
#> [9] "Allistipes et rel."
#> [10] "Clostridium orbiscindens et rel."
#> [11] "Subdoligranulum variable at rel."
#> [12] "Ruminococcus obeum et rel."
#> [13] "Butyrivibrio crossotus et rel."
#> [14] "Bacteroides fragilis et rel."
#> [15] "Akkermansia"
#> [16] "Bacteroides ovatus et rel."
#> [17] "Parabacteroides distasonis et rel."
#> [18] "Dorea formicigenerans et rel."
#> [19] "Bacteroides uniformis et rel."
#> [20] "Dialister"
# transform to compositional data (proportions) before sorting
# note that abundances are returned untransformed
dietswap %>%
tax_sort(by = sum, trans = "compositional") %>%
taxa_names() %>%
head(20)
#> [1] "Prevotella melaninogenica et rel."
#> [2] "Oscillospira guillermondii et rel."
#> [3] "Bacteroides vulgatus et rel."
#> [4] "Clostridium cellulosi et rel."
#> [5] "Prevotella oralis et rel."
#> [6] "Faecalibacterium prausnitzii et rel."
#> [7] "Sporobacter termitidis et rel."
#> [8] "Allistipes et rel."
#> [9] "Clostridium symbiosum et rel."
#> [10] "Clostridium orbiscindens et rel."
#> [11] "Ruminococcus obeum et rel."
#> [12] "Subdoligranulum variable at rel."
#> [13] "Bacteroides fragilis et rel."
#> [14] "Butyrivibrio crossotus et rel."
#> [15] "Akkermansia"
#> [16] "Parabacteroides distasonis et rel."
#> [17] "Bacteroides ovatus et rel."
#> [18] "Bacteroides uniformis et rel."
#> [19] "Dialister"
#> [20] "Dorea formicigenerans et rel."
# order by descending abundance in a single named sample
dietswap %>%
tax_sort(by = "Sample-1") %>%
otu_table() %>%
.[1:8, 1:4]
#> OTU Table: [4 taxa and 8 samples]
#> taxa are columns
#> Bacteroides vulgatus et rel. Oscillospira guillermondii et rel.
#> Sample-1 2774 861
#> Sample-2 48 4697
#> Sample-3 455 2915
#> Sample-4 469 4279
#> Sample-5 167 392
#> Sample-6 75 200
#> Sample-7 33 2201
#> Sample-8 85 1123
#> Bacteroides fragilis et rel. Bacteroides ovatus et rel.
#> Sample-1 443 427
#> Sample-2 21 15
#> Sample-3 73 31
#> Sample-4 29 46
#> Sample-5 33 29
#> Sample-6 14 13
#> Sample-7 22 15
#> Sample-8 560 19
# sum order should always equal mean order if non-negative abundances
# don't forget to add na.rm = TRUE if you expect NAs in otu_table somehow
dietswap %>%
tax_sort(by = sum, na.rm = TRUE) %>%
taxa_names() %>%
head(20)
#> [1] "Prevotella melaninogenica et rel."
#> [2] "Oscillospira guillermondii et rel."
#> [3] "Bacteroides vulgatus et rel."
#> [4] "Clostridium cellulosi et rel."
#> [5] "Prevotella oralis et rel."
#> [6] "Faecalibacterium prausnitzii et rel."
#> [7] "Sporobacter termitidis et rel."
#> [8] "Clostridium symbiosum et rel."
#> [9] "Allistipes et rel."
#> [10] "Clostridium orbiscindens et rel."
#> [11] "Subdoligranulum variable at rel."
#> [12] "Ruminococcus obeum et rel."
#> [13] "Butyrivibrio crossotus et rel."
#> [14] "Bacteroides fragilis et rel."
#> [15] "Akkermansia"
#> [16] "Bacteroides ovatus et rel."
#> [17] "Parabacteroides distasonis et rel."
#> [18] "Dorea formicigenerans et rel."
#> [19] "Bacteroides uniformis et rel."
#> [20] "Dialister"
# if your phyloseq object has a phylogenetic tree,
# tax_sort will remove the tree, and warn you about this
# unless you disable that warning with tree_warn = FALSE
# You can sort by abundance at higher taxonomic ranks,
# without losing lower rank info
# e.g. sort (descending) by phyla abundances
dietswap %>%
tax_sort(by = sum, at = "Phylum") %>%
tax_table() %>%
head()
#> Taxonomy Table: [6 taxa by 3 taxonomic ranks]:
#> Phylum Family
#> Allistipes et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides fragilis et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides intestinalis et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides ovatus et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides plebeius et rel. "Bacteroidetes" "Bacteroidetes"
#> Bacteroides splachnicus et rel. "Bacteroidetes" "Bacteroidetes"
#> Genus
#> Allistipes et rel. "Allistipes et rel."
#> 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."
# You can sort by ascending abundance (or prevalence etc) by reversing after
dietswap %>%
tax_sort(by = "prev", at = "Phylum") %>%
tax_sort(by = "rev") %>%
tax_table() %>%
head()
#> Taxonomy Table: [6 taxa by 3 taxonomic ranks]:
#> Phylum Family
#> Uncultured Chroococcales "Cyanobacteria" "Cyanobacteria"
#> Brachyspira "Spirochaetes" "Spirochaetes"
#> Fusobacteria "Fusobacteria" "Fusobacteria"
#> Uncultured Bacteroidetes "Bacteroidetes" "Bacteroidetes"
#> Tannerella et rel. "Bacteroidetes" "Bacteroidetes"
#> Prevotella tannerae et rel. "Bacteroidetes" "Bacteroidetes"
#> Genus
#> Uncultured Chroococcales "Uncultured Chroococcales"
#> Brachyspira "Brachyspira"
#> Fusobacteria "Fusobacteria"
#> Uncultured Bacteroidetes "Uncultured Bacteroidetes"
#> Tannerella et rel. "Tannerella et rel."
#> Prevotella tannerae et rel. "Prevotella tannerae et rel."