bdiv_ord_table | R Documentation |
The biplot parameters (taxa
, unc
, p.top
, and
p.adj
) only only have an effect when rank
is not NULL
.
bdiv_ord_table(
biom,
bdiv = "Bray-Curtis",
ord = "PCoA",
weighted = TRUE,
md = NULL,
k = 2,
stat.by = NULL,
split.by = NULL,
tree = NULL,
test = "adonis2",
seed = 0,
permutations = 999,
rank = NULL,
taxa = 6,
p.top = Inf,
p.adj = "fdr",
unc = "singly",
underscores = FALSE,
...
)
biom |
An rbiom object, such as from |
bdiv |
Beta diversity distance algorithm(s) to use. Options are:
|
ord |
Method for reducing dimensionality. Options are:
Multiple/abbreviated values allowed. Default: |
weighted |
Take relative abundances into account. When
|
md |
Dataset field(s) to include in the output data frame, or |
k |
Number of ordination dimensions to return. Either |
stat.by |
The categorical or numeric metadata field over which statistics should be calculated. Required. |
split.by |
Dataset field(s) that the data should be split by prior to
any calculations. Must be categorical. Default: |
tree |
A |
test |
Permutational test for accessing significance. Options are:
Abbreviations are allowed. Default: |
seed |
Random seed for permutations. Must be a non-negative integer.
Default: |
permutations |
Number of random permutations to use.
Default: |
rank |
What rank(s) of taxa to compute biplot coordinates and
statistics for, or |
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. |
p.top |
Only display taxa with the most significant differences in
abundance. If |
p.adj |
Method to use for multiple comparisons adjustment of
p-values. Run |
unc |
How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are:
Abbreviations are allowed. Default: |
underscores |
When parsing the tree, should underscores be kept as
is? By default they will be converted to spaces (unless the entire ID
is quoted). Default |
... |
Additional arguments to pass on to |
A data.frame with columns .sample
, .weighted
,
.bdiv
, .ord
, .x
, .y
, and (optionally)
.z
. Any columns given by md
, split.by
, and
stat.by
are included as well.
If stat.by
is given, then $stats
and
$stats$code)
are set.
If rank
is given, then $taxa_coords
,
$taxa_stats
, and $taxa_stats$code
are set.
Other beta_diversity:
bdiv_boxplot()
,
bdiv_clusters()
,
bdiv_corrplot()
,
bdiv_heatmap()
,
bdiv_ord_plot()
,
bdiv_stats()
,
bdiv_table()
,
distmat_stats()
Other ordination:
bdiv_ord_plot()
,
distmat_ord_table()
library(rbiom)
ord <- bdiv_ord_table(hmp50, "bray", "pcoa", stat.by="Body Site", rank="g")
head(ord)
ord$stats
ord$taxa_stats
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