taxa_table | R Documentation |
taxa_matrix()
- Accepts a single rank
and returns a matrix.
taxa_table()
- Can accept more than one rank
and returns a tibble data.frame.
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
)
biom |
An rbiom object, such as from |
rank |
What rank(s) of taxa to display. E.g. |
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. |
lineage |
Include all ranks in the name of the taxa. For instance,
setting to |
md |
Dataset field(s) to include in the output data frame, or |
unc |
How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are:
Abbreviations are allowed. Default: |
other |
Sum all non-itemized taxa into an "Other" taxa. When
|
transform |
Transformation to apply. Options are:
|
ties |
When |
seed |
Random seed for permutations. Must be a non-negative integer.
Default: |
sparse |
If |
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
.
Other taxa_abundance:
sample_sums()
,
taxa_boxplot()
,
taxa_clusters()
,
taxa_corrplot()
,
taxa_heatmap()
,
taxa_stacked()
,
taxa_stats()
,
taxa_sums()
library(rbiom)
hmp50$ranks
taxa_matrix(hmp50, 'Phylum')[1:4,1:6]
taxa_table(hmp50, 'Phylum')
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