get_net_cls_tab-matrix-data.frame-method: Get the cluster table 'cls_tab' from quantitative table...
In Guan06/mina: Microbial community dIversity and Network Analysis

Description Usage Arguments Value Examples

Get the cluster table 'cls_tab' from quantitative table 'norm' and network clustering results 'cls'.

1 2	## S4 method for signature 'matrix,data.frame' get_net_cls_tab(x_norm, x_cls, uw = FALSE)

`x_norm`	The normalized quantitative table used for netowrk inference and clustering.
`x_cls`	The network clustering table.
`uw`	By summing up the number of present components of each cluster instead of relative abundance, default is FALSE.

x_cls The quantitative table with clusters in rows.

maize <- new("mina", tab = maize_asv2, des = maize_des2)
maize <- norm_tab(maize, method = "raref", depth = 1000)
maize <- fit_tabs(maize)
maize_norm <- norm(maize)
maize_adj <- adj(maize_norm, method = "spearman")
maize_cls <- net_cls(maize_adj, method = "ap", cutoff = 0.5)
maize_cls_tab <- get_net_cls_tab(maize_norm, maize_cls)