distance

distance()

distance(physeq, method="unifrac", type="samples", ...)

The distance function takes a data object (phyloseq-class) and method option (character string), and returns a distance object (dist-class) suitable for certain ordination methods and other distance-based analyses. There are currently 44 explicitly supported method options, as well as user-provided arbitrary methods via an interface to designdist. For the complete list of currently supported options/arguments to the method parameter, type distance("list") at the command-line. Only sample-wise distances are currently supported (the type argument), but eventually species-wise (OTU-wise) distances will be supported as well.

Example: "Enterotypes" dataset using many different methods

Because the distance() function organizes distance calculations into one function, it is relatively straightforward to calculate all supported distance methods and investigate the results. The following code will perform such a loop on the "Enterotypes" dataset, perform multi-dimensional scaling (a.k.a. principle coordinates analysis), and plot the first two axes, shading and shaping the points in each plot according to sequencing technology and assigned "Enterotype" label.

Note that we have omitted the options that require a phylogenetic tree because the "enterotype" example dataset currently included in the phyloseq-package does not have one.