net_cls,matrix,ANY-method {mina}R Documentation

Network clustering based on the sparsed adjacacency matrix.

Description

Network clustering based on the sparsed adjacacency matrix.

Usage

## S4 method for signature 'matrix,ANY'
net_cls(x, method, cutoff = 0.4, neg = FALSE, ...)

## S4 method for signature 'matrix,character'
net_cls(x, method, cutoff = 0.4, neg = FALSE, ...)

Arguments

x

Adjacency matrix used for clustering.

method

The clustering method used.

cutoff

The cutoff for the sparsed adjacacency matrix, default 0.4.

neg

Whether to keep the negative edges, cannot be TRUE when using 'mcl' for clustering. Default FALSE.

...

Additional parameters.

Value

y The cluster table.

Examples

asv_norm <- norm_tab(maize_asv2, method = "raref", depth = 1000)
asv_adj <- adj(asv_norm, method = "spearman")
asv_cls <- net_cls(asv_adj, method = "mcl")

[Package mina version 1.2.0 Index]