get_clust: Hierarchical cluster analysis for the samples

In xiangpin/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

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)

xiangpin/MicrobiotaProcess documentation built on Nov. 12, 2024, 2:05 p.m.