Run ordinations on a distance matrix.
Arguments
- dm
A
dist
-class distance matrix, as returned frombdiv_distmat()
orstats::dist()
. Required.- ord
Method for reducing dimensionality. Options are:
"PCoA"
-Principal coordinate analysis;
ape::pcoa()
."UMAP"
-Uniform manifold approximation and projection;
uwot::umap()
."NMDS"
-Nonmetric multidimensional scaling;
vegan::metaMDS()
."tSNE"
-t-distributed stochastic neighbor embedding;
tsne::tsne()
.
Default:
"PCoA"
Multiple/abbreviated values allowed.- k
Number of ordination dimensions to return. Either
2L
or3L
. Default:2L
- ...
Additional arguments for
ord
.
See also
Other ordination:
bdiv_ord_plot()
,
bdiv_ord_table()
Examples
library(rbiom)
dm <- bdiv_distmat(hmp50, "bray")
ord <- distmat_ord_table(dm, "PCoA")
head(ord)
#> # Ordination: ape::pcoa(D = dm)
#> # A tibble: 6 × 4
#> .ord .sample .x .y
#> <fct> <chr> <dbl> <dbl>
#> 1 PCoA HMP01 -0.358 0.00236
#> 2 PCoA HMP02 -0.420 0.0104
#> 3 PCoA HMP03 -0.382 0.0135
#> 4 PCoA HMP04 -0.388 0.00485
#> 5 PCoA HMP05 -0.415 -0.0115
#> 6 PCoA HMP06 -0.414 -0.00703