capscale.phyloseq {phyloseq} | R Documentation

## Constrained Analysis of Principal Coordinates, `capscale`.

### Description

See `capscale` for details. A formula is main input.

### Usage

    capscale.phyloseq(physeq, formula, distance, ...)

    ## S4 method for signature 'phyloseq,formula,dist'
    capscale.phyloseq(physeq, formula,
      distance, ...)

    ## S4 method for signature 'phyloseq,formula,character'
    capscale.phyloseq(physeq, formula,
      distance, ...)

### Arguments

`physeq` | (Required). Phylogenetic sequencing data (`phyloseq-class`). The data on which you want to perform the ordination.
`formula` | (Required). A `formula`, specifying the input. No need to directly access components. `capscale.phyloseq` understands where to find the abundance table (LHS) and `sample_data` (RHS) from within the phyloseq object.
`distance` | (Required). A `character` string, specifying the name of the dissimilarity (or distance) method supported by the phyloseq `distance` function. Alternatively, a pre-computed `dist`-object can be provided here, in which case it supersedes any use of the `otu_table` in your phyloseq object. Note that `capscale` with Euclidean distances will be identical to `rda` in eigenvalues and in site, species, and biplot scores (except for possible sign reversal). However, it makes no sense to use `capscale` with Euclidean distances, since direct use of `rda` is much more efficient (and supported in the `ordinate` function with `method=="RDA"`) Even with non-Euclidean dissimilarities, the rest of the analysis will be metric and linear.
`...` | (Optional). Additional named arguments passed to `capscale`.

### Value

Ordination object defined by `capscale`.

### See Also

`plot_ordination`

`rda`

`capscale`

### Examples

    # See other examples at
    # http://joey711.github.io/phyloseq/plot_ordination-examples
    data(GlobalPatterns)
    GP = prune_taxa(names(sort(taxa_sums(GlobalPatterns), TRUE)[1:50]), GlobalPatterns)
    ordcap = ordinate(GP, "CAP", "bray", ~SampleType)
    plot_ordination(GP, ordcap, "samples", color="SampleType")

[Package phyloseq version 1.28.0 Index]