get_pcoa {MicrobiotaProcess} | R Documentation

## performs principal coordinate analysis (PCoA)

### Description

performs principal coordinate analysis (PCoA)

### Usage

    get_pcoa(obj, ...)

    ## S3 method for class 'data.frame'
    get_pcoa(
      obj,
      distmethod = "euclidean",
      taxa_are_rows = FALSE,
      sampleda = NULL,
      tree = NULL,
      method = "hellinger",
      ...
    )

    ## S3 method for class 'dist'
    get_pcoa(
      obj,
      distmethod,
      data = NULL,
      sampleda = NULL,
      method = "hellinger",
      ...
    )

    ## S3 method for class 'phyloseq'
    get_pcoa(obj, distmethod = "euclidean", ...)

### Arguments

`obj` | phyloseq, the phyloseq class or dist class.
`...,` | additional parameter, see also `get_dist`.
`distmethod` | character, the method of distance, see also `distance`
`taxa_are_rows` | logical, if feature of data is column, it should be set FALSE.
`sampleda` | data.frame, nrow sample * ncol factor, default is NULL.
`tree` | phylo, the phylo class, default is NULL, when use unifrac method, it should be required.
`method` | character, the standardization method for community ecologists, default is hellinger, if the data has be normlized, it shound be set NULL.
`data` | data.frame, numeric data.frame nrow sample * ncol features.

### Value

pcasample object, contained prcomp or pcoa and sampleda (data.frame).

### Author(s)

Shuangbin Xu

### Examples

    ## Not run:
        library(phyloseq)
        data(GlobalPatterns)
        subGlobal <- subset_samples(GlobalPatterns,
                      SampleType %in% c("Feces", "Mock", "Ocean", "Skin"))
        pcoares <- get_pcoa(subGlobal,
                           distmethod="euclidean",
                           method="hellinger")
        pcoaplot <- ggordpoint(pcoares, biplot=FALSE,
                                speciesannot=FALSE,
                                factorNames=c("SampleType"),
                                ellipse=FALSE)

    ## End(Not run)

[Package MicrobiotaProcess version 1.4.4 Index]