net_cls,mina,ANY-method {mina} | R Documentation |
Network clustering based on the sparsed adjacacency matrix.
## S4 method for signature 'mina,ANY' net_cls(x, method, cutoff = 0.4, neg = FALSE, ...) ## S4 method for signature 'mina,character' net_cls(x, method, cutoff = 0.4, neg = FALSE, ...)
x |
An object of class 'mina' with 'adj' defined. |
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. |
x The same 'mina' class with @cls added.
maize <- new("mina", tab = maize_asv2, des = maize_des2) maize <- norm_tab(maize, method = "raref", depth = 1000) maize <- fit_tabs(maize) maize <- adj(maize, method = "spearman") maize <- net_cls(maize, method = "mcl", cutoff = 0.4, neg = FALSE) maize <- net_cls(maize, method = "ap", cutoff = 0.4, neg = FALSE)