R/clust_group_terms.R

In GSEAmining: Make Biological Sense of Gene Set Enrichment Analysis Outputs

#' @title clust_group_terms
#'
#' @description Takes the output of clust_groups, a data frame , and process
#' it to obtain the enrichment of terms in gene sets names within each cluster.
#' The output is used in the functions gm_enrichterms and gm_enrichreport.
#'
#' @param cg A data frame output from the GSEAmining cluster_groups function.
#'
#' @return  A tibble with four variables (Cluster, Enrichment, monogram, n).
#'
#' @export
#'
#' @examples
#' data(genesets_sel)
#' gs.cl <- gm_clust(genesets_sel)
#' clust.groups <- clust_groups(genesets_sel, gs.cl)
#' clust.groups.wordcloud <- clust_group_terms(clust.groups)
#'
clust_group_terms <- function(cg) {
  # Obtain the terms of each gene set -----------------------------------------
  stop.words <- stop_words()

  clust_groups_wordcloud <- cg %>%
    mutate(Enrichment = ifelse(test = .data$NES > 0,
                               yes= 'Pos',
                               no = 'Neg')) %>%
    # separate the words of the geneset
    mutate(ID2 = str_replace_all(.data$ID,
                                 pattern='_',
                                 replacement = ' ')) %>%
    # eliminate the first word of the geneset
    mutate(ID2 = word(.data$ID2,
                      start = 2,
                      end = -1)) %>%
    # create word tokens (one row per word)
    tidytext::unnest_tokens(.data$monogram,
                            .data$ID2,
                            token = 'ngrams',
                            n = 1,
                            to_lower = FALSE) %>%
    # eliminate words like UP, DW, BY ...
    filter(!.data$monogram %in% stop.words$word) %>%
    # eliminate words that are just numbers
    filter(!grepl('^\\d', .data$monogram)) %>%
    # group by cluster and count how many words
    group_by(.data$Cluster, .data$Enrichment) %>%
    count(.data$monogram, sort = TRUE)

}