distance {phyloseq} | R Documentation

## Calculate distance, dissimilarity

### Description

Takes a `phyloseq-class` object and method option, and returns a `dist`ance 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", ...)

    ## S4 method for signature 'phyloseq,ANY'
    distance(physeq, method)

    ## S4 method for signature 'otu_table,character'
    distance(physeq, method, type = "samples",
      ...)

    ## S4 method for signature '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: `"unifrac"` Original (unweighted) UniFrac distance, `UniFrac` `"wunifrac"` weighted-UniFrac distance, `UniFrac` `"dpcoa"` sample-wise distance used in Double Principle Coordinate Analysis, `DPCoA` `"jsd"` Jensen-Shannon Divergence, `JSD` 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.

### Details

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

### Value

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

### 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")

[Package phyloseq version 1.26.1 Index]