This function wraps several commonly-used ordination methods. The type of
ordination depends upon the argument to method. Try
ordinate("help") or ordinate("list") for the currently
supported method options.
(Required). Phylogenetic sequencing data
(phyloseq-class). The data on which you want to perform
the ordination. In general, these methods will be based in some fashion on
the abundance table ultimately stored as a contingency matrix
(otu_table-class). If you're able to import data into
phyloseq-class format, than you don't need to worry, as an
otu_table is a required component of this class. In addition, some
ordination methods require additional data, like a constraining variable
or phylogenetic tree. If that is the case, the relevant data should be
included in physeq prior to running. Integrating the data in this way
also results in these different data components being checked for validity
and completeness by the method.
Performs correspondence analysis,
or optionally, constrained correspondence analysis
(a.k.a. canonical correspondence analysis),
via cca
RDA
Performs redundancy analysis, or optionally
principal components analysis, via rda
CAP
[Partial] Constrained Analysis of Principal Coordinates
or distance-based RDA, via capscale.
See capscale.phyloseq for more details.
In particular, a formula argument must be provided.
DPCoA
Performs Double Principle Coordinate Analysis using a
(corrected, if necessary) phylogenetic/patristic distance
between species. The calculation is performed by
DPCoA(), which ultimately uses
dpcoa after making the appropriate
accessions/corrections of the data.
NMDS
Performs Non-metric MultiDimenstional Scaling of a sample-wise
ecological distance matrix onto a user-specified number of axes, k.
By default, k=2, but this can be modified as a supplementary argument.
This method is ultimately carried out by metaMDS after the
appropriate accessions and distance calculations.
Because metaMDS includes its own distance
calculation wrappers to vegdist, and these provide
additional functionality in the form of species scores,
ordinate will pass-on the distance
argument to metaMDS if it is among the
supported vegdist methods. However, all distance methods
supported by distance are supported here,
including "unifrac" (the default) and "DPCoA".
MDS/PCoA
Performs principal coordinate analysis
(also called principle coordinate decomposition,
multidimensional scaling (MDS), or classical scaling)
of a distance matrix (Gower 1966),
including two correction methods for negative eigenvalues.
See
pcoa for further details.
distance
(Optional). A character string. Default is "bray".
The name of a supported distance method;
or, alternatively,
a pre-computed dist-class object.
This argument is only utilized
if a distance matrix is required by the ordination method specified by the
method argument (above).
Any supported distance methods
are supported arguments to distance here.
See distance for more details, examples.
formula
(Optional). A model formula.
Only relevant for certain ordination methods.
The left hand side is ignored, defined by
the physeq and distance arguemnts.
The right hand side gives the constraining variables,
and conditioning variables can be given
within a special function Condition.
See cca or capscale
for examples/details.
...
(Optional). Additional arguments to supporting functions. For
example, the additional argument weighted=TRUE would be passed on
to UniFrac if "unifrac" were chosen as the
distance option and "MDS" as the ordination method
option. Alternatively, if "DCA" were chosen as the
ordination method option, additional arguments would be passed on
to the relevant ordination function, decorana, for example.
Value
An ordination object. The specific class of the returned object depends upon the
ordination method, as well as the function/package that is called internally
to perform it.
As a general rule, any of the ordination classes
returned by this function will be recognized by downstream tools in the
phyloseq package, for example the ordination plotting
function, plot_ordination.
NMDS and MDS/PCoA both operate on distance matrices, typically based on some
pairwise comparison of the microbiomes in an experiment/project. There are
a number of common methods to use to calculate these pairwise distances, and
the most convenient function (from a phyloseq point of view) for calculating
these distance matrices is the
function. It can be
thought of as a distance / dissimilarity-index companion function for
ordinate, and indeed the distance options provided to ordinate
are often simply passed on to distance.
A good quick summary of ordination is provided in the introductory vignette
for vegan:
# See http://joey711.github.io/phyloseq/plot_ordination-examples# for many more examples.# plot_ordination(GP, ordinate(GP, "DCA"), "samples", color="SampleType")
