get_clust {MicrobiotaProcess} | R Documentation

## Hierarchical cluster analysis for the samples

### Description

Hierarchical cluster analysis for the samples

### Usage

    get_clust(obj, ...)

    ## S3 method for class 'dist'
    get_clust(obj, distmethod, sampleda = NULL, hclustmethod = "average", ...)

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

    ## S3 method for class 'phyloseq'
    get_clust(
      obj,
      distmethod = "euclidean",
      method = "hellinger",
      hclustmethod = "average",
      ...
    )

### Arguments

`obj` | phyloseq, phyloseq class or dist class, or data.frame, data.frame, default is nrow samples * ncol features.
`...,` | additional parameters.
`distmethod` | character, the method of dist, when the obj is data.frame or phyloseq default is "euclidean". see also `get_dist`.
`sampleda` | data.frame, nrow sample * ncol factor. default is NULL.
`hclustmethod` | character, the method of hierarchical cluster, default is average.
`taxa_are_rows` | logical, if the features of data.frame(obj) is in column, it should set FALSE.
`tree` | phylo, the phylo class, see also `as.phylo`.
`method` | character, the standardization methods for community ecologists, see also `decostand`

### Value

treedata object.

### Author(s)

Shuangbin Xu

### Examples

    ## Not run:
    library(phyloseq)
    data(GlobalPatterns)
    subGlobal <- subset_samples(GlobalPatterns,
             SampleType %in% c("Feces", "Mock", "Ocean", "Skin"))
    hcsample <- get_clust(subGlobal, distmethod="jaccard",
                      method="hellinger", hclustmethod="average")

    ## End(Not run)

[Package MicrobiotaProcess version 1.4.4 Index]