taxa_matrix()
-Accepts a single
rank
and returns a matrix.taxa_table()
-Can accept more than one
rank
and returns a tibble data.frame.
Usage
taxa_table(
biom,
rank = -1,
taxa = 6,
lineage = FALSE,
md = ".all",
unc = "singly",
other = FALSE,
transform = "none",
ties = "random",
seed = 0
)
taxa_matrix(
biom,
rank = -1,
taxa = NULL,
lineage = FALSE,
sparse = FALSE,
unc = "singly",
other = FALSE,
transform = "none",
ties = "random",
seed = 0
)
Arguments
- biom
An rbiom object, such as from
as_rbiom()
. Any value accepted byas_rbiom()
can also be given here.- rank
What rank(s) of taxa to display. E.g.
"Phylum"
,"Genus"
,".otu"
, etc. An integer vector can also be given, where1
is the highest rank,2
is the second highest,-1
is the lowest rank,-2
is the second lowest, and0
is the OTU "rank". Runbiom$ranks
to see all options for a given rbiom object. Default:-1
.- taxa
Which taxa to display. An integer value will show the top n most abundant taxa. A value 0 <= n < 1 will show any taxa with that mean abundance or greater (e.g.
0.1
implies >= 10%). A character vector of taxa names will show only those named taxa. Default:6
.- lineage
Include all ranks in the name of the taxa. For instance, setting to
TRUE
will 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
- md
Dataset field(s) to include in the output data frame, or
'.all'
to include all metadata fields. Default:'.all'
- 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.
Default:
"singly"
Abbreviations are allowed.- other
Sum all non-itemized taxa into an "Other" taxa. When
FALSE
, only returns taxa matched by thetaxa
argument. SpecifyingTRUE
adds "Other" to the returned set. A string can also be given to implyTRUE
, but with that value as the name to use instead of "Other". Default:FALSE
- 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"
- ties
When
transform="rank"
, how to rank identical values. Options are:c("average", "first", "last", "random", "max", "min")
. Seerank()
for details. Default:"random"
- seed
Random seed for permutations. Default:
0
- sparse
If
TRUE
, returns asimple_triplet_matrix::simple_triplet_matrix()
, otherwise returns a normal R matrix object. Default:FALSE
Value
taxa_matrix()
-A numeric matrix with taxa as rows, and samples as columns.
taxa_table()
-A tibble data frame with column names .sample, .taxa, .abundance, and any requested by
md
.
See also
Other taxa_abundance:
sample_sums()
,
taxa_boxplot()
,
taxa_clusters()
,
taxa_corrplot()
,
taxa_heatmap()
,
taxa_stacked()
,
taxa_stats()
,
taxa_sums()
Examples
library(rbiom)
hmp50$ranks
#> [1] ".otu" "Kingdom" "Phylum" "Class" "Order" "Family" "Genus"
taxa_matrix(hmp50, 'Phylum')[1:4,1:6]
#> HMP01 HMP02 HMP03 HMP04 HMP05 HMP06
#> Actinobacteria 18 60 126 120 30 71
#> Bacteroidetes 276 221 313 218 144 880
#> Cyanobacteria 0 0 0 0 0 0
#> Deinococcus Thermus 0 0 0 0 0 0
taxa_table(hmp50, 'Phylum')
#> # A tibble: 300 × 8
#> .rank .sample .taxa .abundance Age BMI `Body Site` Sex
#> <fct> <chr> <fct> <dbl> <dbl> <dbl> <fct> <fct>
#> 1 Phylum HMP01 Firmicutes 1208 22 20 Buccal mucosa Female
#> 2 Phylum HMP01 Bacteroidetes 276 22 20 Buccal mucosa Female
#> 3 Phylum HMP01 Actinobacteria 18 22 20 Buccal mucosa Female
#> 4 Phylum HMP01 Proteobacteria 103 22 20 Buccal mucosa Female
#> 5 Phylum HMP01 Fusobacteria 41 22 20 Buccal mucosa Female
#> 6 Phylum HMP01 Tenericutes 0 22 20 Buccal mucosa Female
#> 7 Phylum HMP02 Firmicutes 931 24 23 Buccal mucosa Male
#> 8 Phylum HMP02 Bacteroidetes 221 24 23 Buccal mucosa Male
#> 9 Phylum HMP02 Actinobacteria 60 24 23 Buccal mucosa Male
#> 10 Phylum HMP02 Proteobacteria 112 24 23 Buccal mucosa Male
#> # ℹ 290 more rows