R/enrich_dend_.R

In nicohuttmann/pOmics: Framework for proteomics data analysis

#' Calculates enrichment for each cluster level
#'
#' @param cor_list cor_list object
#' @param proteins annotated proteins or protein score vector
#' @param n max number of clusters
#' @param inverse inverse enrichment (works for both Fisher and KS test)
#' @param name name
#' @param plot.lines Plot lines plot
#' @param plot.matrix Plot correlation matrix
#' @param cut cut dendrogram
#' @param fun.enrich Do functional enrichment
#' @param labels proteins to label on y-axis
#' @param database databases to use for functional enrichment
#' @param algorithm algorithm to use ("classic", "elim", "weight", "weight01")
#' @param add.info adds protein information to fun enrich tables
#'
#' @return
#' @export
#'
#' @importFrom magrittr %>%
#'
#'
enrich_dend_ <- function(cor_list,
                         proteins,
                         n = 10,
                         inverse = F,
                         name,
                         cut = T,
                         plot.lines = F,
                         plot.matrix = T,
                         labels,
                         fun.enrich = F,
                         database = "GO",
                         algorithm = "weight01",
                         add.info = F) {

  # Check input
  if(!hasArg(cor_list) || !hasArg(proteins)) stop("Missing input.")

  # name
  name <- ask_name(name = name, message = "Name for enrichment type: ")

  # Test anotation input; if numeric -> ks test
  if (is.numeric(proteins) && length(names(proteins)) > 0) {
    cor_list[[paste0("dend.enrich_", name)]] <- enrich_dend_ks(dend.table = cor_list[["dend.table"]],
                                                               protein.scores = proteins,
                                                               n = n,
                                                               inverse = inverse) %>%
                                                eval_dend_enrich(cut = cut)
  # Test anotation input; if protein vector -> fisher test
  } else if(is.character(proteins)) {
    cor_list[[paste0("dend.enrich_", name)]] <- enrich_dend_fisher(dend.table = cor_list[["dend.table"]],
                                                                   annotated.proteins = proteins,
                                                                   n = n,
                                                                   inverse = inverse) %>%
                                                eval_dend_enrich(cut = cut)
  # Incorrect input
  } else {
    stop("Incorrect input.")
  }


  # Plot lines
  cor_list <- plot_dend_enrich_lines_(cor_list = cor_list, name = name, print = plot.lines)


  # plot cormat
  if (!hasArg(labels)) {
    cor_list <- plot_cormat_enrichment_(cor_list = cor_list, name = name, print = plot.matrix)
  } else {
    cor_list <- plot_cormat_enrichment_labels(cor_list = cor_list, name = name, labels = labels, print = plot.matrix)
  }



  # Functional enrichment
  if (fun.enrich) cor_list <- fun_enrich_(cor_list = cor_list,
                                          name = name,
                                          inverse = F,
                                          database = database,
                                          algorithm = algorithm,
                                          add.info = add.info)

  # Return
  return(invisible(cor_list))

}