get_clust {MicrobiotaProcess} | R Documentation |
Hierarchical cluster analysis for the samples
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", ... )
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
|
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 |
method |
character, the standardization methods for community
ecologists, see also |
clustplotClass object.
Shuangbin Xu
#don't run in examples #library(phyloseq) #data(GlobalPatterns) #subGlobal <- subset_samples(GlobalPatterns, # SampleType %in% c("Feces", "Mock", "Ocean", "Skin")) # don't run in examples #hcsample <- get_clust(subGlobal, distmethod="jaccard", # method="hellinger", hclustmethod="average")