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Cluster samples by taxa abundances k-means.

Source: R/clustering.r
taxa_clusters.Rd

Cluster samples by taxa abundances k-means.

Usage

taxa_clusters(biom, rank = ".otu", k = 5, ...)

Arguments

biom

An rbiom object, such as from as_rbiom(). Any value accepted by as_rbiom() can also be given here.

rank

Which taxa rank to use. E.g. "Phylum", "Genus", ".otu", etc. An integer can also be given, where 1 is the highest rank, 2 is the second highest, -1 is the lowest rank, -2 is the second lowest, and 0 is the OTU "rank". Run biom$ranks to see all options for a given rbiom object. Default: .otu.

k

Number of clusters. Default: 5L

...

Passed on to stats::kmeans().

Value

A numeric factor assigning samples to clusters.

See also

Other taxa_abundance: sample_sums(), taxa_boxplot(), taxa_corrplot(), taxa_heatmap(), taxa_stacked(), taxa_stats(), taxa_sums(), taxa_table()

Other clustering: bdiv_clusters()

Examples

    library(rbiom)
    
    biom <- rarefy(hmp50)
    biom$metadata$otu_cluster <- taxa_clusters(biom)
    
    pull(biom, 'otu_cluster')[1:10]
#> HMP01 HMP02 HMP03 HMP04 HMP05 HMP06 HMP07 HMP08 HMP09 HMP10 
#>     5     2     2     2     5     2     5     2     2     1 
#> Levels: 1 2 3 4 5
    
    bdiv_ord_plot(biom, layers = "p", stat.by = "otu_cluster")