phyloseq (version 1.16.2)

distance: Calculate distance, dissimilarity

Description

Takes a phyloseq-class object and method option, and returns a distance object suitable for certain ordination methods and other distance-based analyses. Only sample-wise distances are currently supported (the type argument), but eventually species-wise (OTU-wise) distances may be supported as well.

Usage

distance(physeq, method, type = "samples", ...)
## S3 method for class 'phyloseq,ANY':
distance(physeq, method)
## S3 method for class 'otu_table,character':
distance(physeq, method, type = "samples",
  ...)
## S3 method for class 'phyloseq,character':
distance(physeq, method, type = "samples", ...)

Arguments

physeq

(Required). A phyloseq-class or an otu_table-class object. The latter is only appropriate for methods that do not require any additional data (one-table). For example, the ``wunifrac'' option (UniFrac) requires phyloseq-class that contains both an otu_table and a phylogenetic tree (phylo).

method

(Required). A character string. Provide one of the currently supported options. See distanceMethodList for a detailed list of the supported options here, and links to accompanying documentation. Note that for the common definition of Jaccard distance using the vegan-package implementation, an additional argument is needed, with the full call having the form: distance(physeq, method = "jaccard", binary = TRUE) The following methods are implemented explicitly within the phyloseq-package, and accessed by the following method options: [object Object],[object Object],[object Object],[object Object]

Alternatively, you can provide a character string that defines a custom distance method, if it has the form described in designdist.

type

(Optional). A character string. The type of pairwise comparisons being calculated: sample-wise or taxa-wise. The default is c("samples").

...

Additional arguments passed on to the appropriate distance function, determined by the method argument.

Value

• An object of class ``dist'' suitable for certain ordination methods and other distance-based analyses.

Details

Depending on the method argument, distance() wraps one of UniFrac, DPCoA, JSD, vegdist, betadiver, designdist, or dist.

See Also

plot_ordination, UniFrac, DPCoA, JSD, vegdist, betadiver, designdist, dist.

Examples

data(esophagus)
distance(esophagus, "uunifrac") # Unweighted UniFrac
distance(esophagus, "wunifrac") # weighted UniFrac
distance(esophagus, "jaccard", binary = TRUE) # vegdist jaccard
distance(esophagus, "gower") # vegdist option "gower"
distance(esophagus, "g") # designdist method option "g"
distance(esophagus, "minkowski") # invokes a method from the base dist() function.
distance(esophagus, "(A+B-2*J)/(A+B)") # designdist custom distance
distanceMethodList
help("distance")