get_net_cls_tab,matrix,data.frame-method {mina} | R Documentation |
Get the cluster table 'cls_tab' from quantitative table 'norm' and network clustering results 'cls'.
## 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)