Get summary taxa abundances.
Usage
taxa_sums(
biom,
rank = -1,
sort = NULL,
lineage = FALSE,
unc = "singly",
transform = "none"
)
taxa_means(
biom,
rank = -1,
sort = NULL,
lineage = FALSE,
unc = "singly",
transform = "none"
)
taxa_apply(
biom,
FUN,
rank = -1,
sort = NULL,
lineage = FALSE,
unc = "singly",
transform = "none",
...
)Arguments
- biom
An rbiom object, or any value accepted by
as_rbiom().- rank
What rank(s) of taxa to display. E.g.
"Phylum","Genus",".otu", etc. An integer vector can also be given, where1is the highest rank,2is the second highest,-1is the lowest rank,-2is the second lowest, and0is the OTU "rank". Runbiom$ranksto see all options for a given rbiom object. Default:-1.- sort
Sort the result. Options:
NULL,"asc", or"desc", whereNULLwill not sort the result."asc"will sort in ascending order (smallest to largest), and"desc"in descending order (largest to smallest). Ignored when the result is not a simple numeric vector. Default:NULL- lineage
Include all ranks in the name of the taxa. For instance, setting to
TRUEwill produceBacteria; Actinobacteria; Coriobacteriia; Coriobacteriales. Otherwise the taxa name will simply beCoriobacteriales. You want to set this to TRUE whenunc = "asis"and you have taxa names (such as Incertae_Sedis) that map to multiple higher level ranks. Default:FALSE- unc
How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are:
"singly"-Replaces them with the OTU name.
"grouped"-Replaces them with a higher rank's name.
"drop"-Excludes them from the result.
"asis"-To not check/modify any taxa names.
Abbreviations are allowed. Default:
"singly"- transform
Transformation to apply. Options are:
c("none", "rank", "log", "log1p", "sqrt", "percent")."rank"is useful for correcting for non-normally distributions before applying regression statistics. Default:"none"- FUN
The function to apply to each row of the
taxa_matrix().- ...
Optional arguments to
FUN.
Value
For taxa_sums and taxa_means, a named numeric vector.
For taxa_apply, a named vector or list with the results of FUN.
The names are the taxa IDs.
See also
Other taxa_abundance:
sample_sums(),
taxa_boxplot(),
taxa_clusters(),
taxa_corrplot(),
taxa_heatmap(),
taxa_stacked(),
taxa_stats(),
taxa_table()
Examples
library(rbiom)
taxa_sums(hmp50) %>% head(4)
#> Abiotrophia Acidaminococcus Acinetobacter Actinobacillus
#> 135 62 44 242
taxa_means(hmp50, 'Family') %>% head(5)
#> Acidaminococcaceae Actinomycetaceae Aerococcaceae Alcaligenaceae
#> 14.58 16.92 2.86 11.28
#> Alicyclobacillaceae
#> 0.12
taxa_apply(hmp50, max) %>% head(5)
#> Abiotrophia Acidaminococcus Acinetobacter Actinobacillus Actinomyces
#> 78 59 42 100 105
taxa_apply(hmp50, fivenum) %>% head(5)
#> Abiotrophia Acidaminococcus Acinetobacter Actinobacillus Actinomyces
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 1
#> [4,] 1 0 0 2 21
#> [5,] 78 59 42 100 105
#> Actinotignum Aerococcus Akkermansia Alistipes Alloprevotella Alloscardovia
#> [1,] 0 0 0 0 0.0 0
#> [2,] 0 0 0 0 0.0 0
#> [3,] 0 0 0 0 0.5 0
#> [4,] 0 0 0 3 12.0 0
#> [5,] 1 2 107 583 135.0 1
#> Anaerococcus Anaeroglobus Anaerostipes Anaerotruncus Atopobium Bacteroides
#> [1,] 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 2
#> [4,] 0 0 0 0 2 7
#> [5,] 488 1 14 28 107 5786
#> Barnesiella Bergeyella Bifidobacterium Bilophila Blautia Bosea
#> [1,] 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0
#> [4,] 0 10 0 0 0 0
#> [5,] 59 114 3 2 67 2
#> Bradyrhizobium Brevundimonas Brochothrix Burkholderia Butyricimonas
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 4 16 11 15 77
#> Butyrivibrio Butyrivibrio 2 Campylobacter Candidatus Saccharimonas
#> [1,] 0 0 0 0
#> [2,] 0 0 0 0
#> [3,] 0 0 0 0
#> [4,] 0 0 2 0
#> [5,] 382 5 69 4
#> Candidatus Stoquefichus Capnocytophaga Cardiobacterium Catenibacterium
#> [1,] 0 0 0 0
#> [2,] 0 0 0 0
#> [3,] 0 0 0 0
#> [4,] 0 15 0 0
#> [5,] 7 235 9 2
#> Catonella Christensenellaceae R_7 Clostridiales XIII_AD3011
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 1 0 0
#> [5,] 27 62 2
#> Clostridiales XIII_UCG_001 Clostridium sensu_stricto_1 Collinsella
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 0 0
#> [5,] 4 1 8
#> Comamonas Conchiformibius Coprobacter Coprococcus 1 Coprococcus 2
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 4 2 1 6 10
#> Corynebacterium Corynebacterium 1 Defluviitaleaceae UCG_011 Deinococcus
#> [1,] 0 0 0 0
#> [2,] 0 0 0 0
#> [3,] 0 0 0 0
#> [4,] 1 1 0 0
#> [5,] 32 4644 12 3
#> Dermabacter Desulfovibrio Dialister Dolosigranulum Dorea Eikenella
#> [1,] 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0
#> [4,] 0 0 2 0 1 0
#> [5,] 1 3 32 707 59 22
#> Elizabethkingia Enterococcus Erysipelatoclostridium
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 0 0
#> [5,] 12 1 26
#> Erysipelotrichaceae UCG_003 Escherichia Shigella Eubacterium brachy
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 0 0
#> [5,] 13 65 3
#> Eubacterium coprostanoligenes Eubacterium nodatum Eubacterium ruminantium
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 1 0
#> [5,] 55 8 3
#> Eubacterium ventriosum Ezakiella Facklamia Faecalibacterium Faecalitalea
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 2 0
#> [5,] 21 11 3 933 14
#> Fastidiosipila Filifactor Finegoldia Flavobacterium Flavonifractor
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 1 0 0
#> [5,] 731 9 79 2 51
#> Fretibacterium Fusicatenibacter Fusobacterium Gallicola Gardnerella
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 6 0 0
#> [5,] 3 60 482 3 4
#> Gemella Gordonia Granulicatella Haemophilus Herbaspirillum Holdemania
#> [1,] 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0
#> [3,] 1 0 2 3 0 0
#> [4,] 25 0 24 92 0 0
#> [5,] 391 3 141 922 38 4
#> Howardella Hydrogenoanaerobacterium Intestinibacter Intestinimonas
#> [1,] 0 0 0 0
#> [2,] 0 0 0 0
#> [3,] 0 0 0 0
#> [4,] 0 0 0 0
#> [5,] 1 1 9 2
#> Janibacter Jeotgalicoccus Johnsonella Kingella Lachnoanaerobaculum
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 5
#> [5,] 2 1 46 17 45
#> Lachnoclostridium Lachnospira Lachnospiraceae FCS020
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 0 0
#> [5,] 142 67 2
#> Lachnospiraceae NC2004 Lachnospiraceae ND3007 Lachnospiraceae NK4A136
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 0 0
#> [5,] 5 9 44
#> Lachnospiraceae NK4B4 Lachnospiraceae UCG_003 Lachnospiraceae UCG_004
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 0 0
#> [5,] 2 105 6
#> Lachnospiraceae UCG_008 Lactobacillus Lactococcus Lautropia Leptotrichia
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 1 1 0 9 13
#> [5,] 50 16220 19 171 72
#> Luteibacter Megasphaera Methylobacterium Methyloversatilis Micrococcus
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 2 0 0 0
#> [5,] 2 217 3 2 8
#> Mitsuokella Mobiluncus Mogibacterium Moraxella Moryella Mycobacterium
#> [1,] 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0
#> [5,] 2 7 6 4 2 6
#> Mycoplasma Negativicoccus Neisseria Nevskia Odoribacter Oribacterium
#> [1,] 0 0 0.0 0 0 0
#> [2,] 0 0 0.0 0 0 0
#> [3,] 0 0 1.5 0 0 0
#> [4,] 0 0 57.0 0 0 9
#> [5,] 9 6 623.0 1 114 258
#> Oscillospira Oxalobacter Parabacteroides Paracocccus Paraprevotella
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 2 0 0
#> [5,] 3 5 403 9 7
#> Parasutterella Parvimonas Pelomonas Peptoclostridium Peptococcus
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 360 52 2 43 6
#> Peptoniphilus Peptostreptococcus Phascolarctobacterium Porphyromonas
#> [1,] 0 0 0 0
#> [2,] 0 0 0 0
#> [3,] 0 0 0 0
#> [4,] 1 1 0 6
#> [5,] 165 23 290 63
#> Prevotella Prevotella 1 Prevotella 2 Prevotella 6 Prevotella 7
#> [1,] 0.0 0 0 0 0
#> [2,] 0.0 0 0 0 0
#> [3,] 3.5 0 0 0 0
#> [4,] 37.0 0 1 3 42
#> [5,] 290.0 13 28 36 393
#> Prevotella 9 Prevotellaceae NK3B31 Propionibacterium Propionivibrio
#> [1,] 0 0 0 0
#> [2,] 0 0 0 0
#> [3,] 0 0 0 0
#> [4,] 0 0 2 0
#> [5,] 2 80 4468 1
#> Providencia Pseudobutyrivibrio Pseudomonas Ralstonia Rhodobacter
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 1 0 0 0
#> [5,] 1 346 18 4 1
#> Rikenellaceae RC9_gut Roseburia Rothia Ruminiclostridium
#> [1,] 0 0 0 0
#> [2,] 0 0 0 0
#> [3,] 0 0 0 0
#> [4,] 0 0 6 0
#> [5,] 49 2 107 3
#> Ruminiclostridium 1 Ruminiclostridium 5 Ruminiclostridium 6
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 0 0
#> [5,] 1 37 13
#> Ruminiclostridium 9 Ruminococcaceae NK4A214 Ruminococcaceae UCG_002
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 0 0
#> [5,] 30 4 132
#> Ruminococcaceae UCG_003 Ruminococcaceae UCG_005 Ruminococcaceae UCG_010
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 0 0
#> [5,] 69 9 35
#> Ruminococcaceae UCG_013 Ruminococcaceae UCG_014 Ruminococcus 1
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 5 0
#> [5,] 34 193 186
#> Ruminococcus 2 Scardovia Selenomonas Selenomonas 3 Selenomonas 4
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 2 0
#> [5,] 47 2 3 123 6
#> Senegalimassilia Shuttleworthia Sneathia Solobacterium Sphingobium
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 100 1654 90 2 3
#> Sphingomonas Sphingopyxis Sporolactobacillus Staphylococcus
#> [1,] 0 0 0 0
#> [2,] 0 0 0 0
#> [3,] 0 0 0 0
#> [4,] 0 0 0 1
#> [5,] 4 7 3 9581
#> Stenotrophomonas Stomatobaculum Streptobacillus Streptococcus
#> [1,] 0 0 0 0
#> [2,] 0 0 0 0
#> [3,] 0 0 0 27
#> [4,] 0 1 0 411
#> [5,] 2 54 2 6308
#> Subdoligranulum Sutterella Tannerella Thalassospira Treponema 2
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 1 0 0 0 0
#> [5,] 40 27 18 170 49
#> Tumebacillus Turicibacter Tyzzerella Unc. BactOral Unc. FctCyli5
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 3 2 4 6 3
#> Unc. FirmOra2 Unc. GcbBacte Unc. Hu4Lup30 Unc. HunGu114 Unc. PinJeffr
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 6 14 93 5 11
#> Unc. Unc006vd Unc. Unc00a1s Unc. Unc00g7e Unc. Unc00lvf Unc. Unc00zke
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 24 4 1 898 1
#> Unc. Unc0168y Unc. Unc01skg Unc. Unc021pc Unc. Unc0266w Unc. Unc029kz
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 2 1 3 2992 7
#> Unc. Unc02cxe Unc. Unc02jgy Unc. Unc02oth Unc. Unc02vkz Unc. Unc037e3
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 2 1 15 9 2
#> Unc. Unc038h1 Unc. Unc038t2 Unc. Unc0397y Unc. Unc039sp Unc. Unc03dfb
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 11 16 93 120 1
#> Unc. Unc03f4o Unc. Unc03iw8 Unc. Unc03j4k Unc. Unc03m1r Unc. Unc03php
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 3 5 5 4 15
#> Unc. Unc03tng Unc. Unc03to4 Unc. Unc0406b Unc. Unc0434x Unc. Unc04cb2
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 3 1 4 26 9
#> Unc. Unc13404 Unc. Unc23927 Unc. Unc28979 Unc. Unc29437 Unc. Unc48787
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 2 2 34 1 1
#> Unc. Unc58411 Unc. Unc61746 Unc. Unc66966 Unc. Unc71514 Unc. Unc72229
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 2 923 12 4 1
#> Unc. Unc75035 Unc. Unc79323 Unc. Unc82785 Unc. Unc89065 Unc. Unc90828
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 2 1 2 3 71
#> Unc. UncO2854 Veillonella
#> [1,] 0 0.0
#> [2,] 0 0.0
#> [3,] 0 1.5
#> [4,] 0 90.0
#> [5,] 66 1223.0