R/net_cls_tab.R

In Guan06/mina: Microbial community dIversity and Network Analysis

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#' Get the cluster table `cls_tab` from quantitative table `norm` and network
#' clustering results `cls`.
#'
#' @include all_classes.R all_generics.R
#' @param x An object of class `mina` with `norm` and `cls` defined.
#' @param uw By summing up the number of present components of each cluster
#' instead of relative abundance, default is FALSE.
#' @return x The same `mina` object with `cls_tab` added.
#' @examples
#' 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 = 0.5)
#' maize <- net_cls_tab(maize)
#' @exportMethod net_cls_tab

setMethod("net_cls_tab", signature("mina", "ANY"),
          function(x, uw = FALSE) {
              stopifnot(is.logical(uw))
              cls_tab(x) <- get_net_cls_tab(norm(x), cls(x), uw)
              return(x)
          }
)
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#' Get the cluster table `cls_tab` from quantitative table `norm` and network
#' clustering results `cls`.
#'
#' @include all_classes.R all_generics.R
#' @param x_norm The normalized quantitative table used for netowrk inference
#' and clustering.
#' @param x_cls The network clustering table.
#' @param uw By summing up the number of present components of each cluster
#' instead of relative abundance, default is FALSE.
#' @return x_cls The quantitative table with clusters in rows.
#' @examples
#' 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)
#' @exportMethod get_net_cls_tab

setMethod("get_net_cls_tab", signature("matrix", "data.frame", "ANY"),
          function(x_norm, x_cls, uw = FALSE) {
              stopifnot(is.logical(uw))
              tab <- x_norm
              cls <- x_cls

              if (nrow(tab) != nrow(cls)) {
                  message("Different number of components!")
                  message("Filtering...")
                  tab <- tab[rownames(tab) %in% cls$ID, ]
              }

              if (uw) {
                  tab[tab > 0] <- 1
              }
              group <- cls$Cluster
              tab <- tab[match(cls$ID, rownames(tab)), ]
              cls_tab <- apply(tab, 2, function(x) rowsum(x, group))
              rownames(cls_tab) <- paste0("Cluster_", unique(group))
              return(cls_tab)
          }
)