Fix R CMD check warnings, documentation links, and reduce package size

DESCRIPTION

@@ -16,7 +16,7 @@ Authors@R: c(
 Description: This package contains functions that help in manipulating tables and generating plots for multi-omics analysis including genomics, transcriptomics, proteomics, methylomics and immunoinformatics.
 License: CC BY-NC-SA 4.0
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Imports:
     dplyr,
     ggplot2,
@@ -30,7 +30,10 @@ Imports:
     grid,
     utils,
     patchwork,
-    cowplot
+    cowplot,
+    igraph,
+    visNetwork,
+    cluster
 Suggests: 
     biomaRt,
     dbscan,

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(add_annotations)
+export(build_net)
 export(detect_filter)
 export(get_annotations)
 export(get_stars)
@@ -17,9 +18,29 @@ export(power_analysis)
 export(save_results)
 export(split_cases)
 export(tpm)
+export(view_net)
 import(ggplot2)
+importFrom(cluster,silhouette)
 importFrom(cowplot,get_legend)
+importFrom(dplyr,distinct)
+importFrom(dplyr,filter)
+importFrom(dplyr,left_join)
+importFrom(dplyr,pull)
+importFrom(dplyr,rename)
+importFrom(igraph,E)
+importFrom(igraph,V)
+importFrom(igraph,as_data_frame)
+importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(magrittr,"%>%")
 importFrom(patchwork,plot_layout)
 importFrom(rlang,.data)
+importFrom(stats,cutree)
+importFrom(stats,dist)
+importFrom(stats,hclust)
+importFrom(tibble,tibble)
 importFrom(utils,modifyList)
+importFrom(utils,read.delim)
+importFrom(visNetwork,visLayout)
+importFrom(visNetwork,visNetwork)
+importFrom(visNetwork,visOptions)
+importFrom(visNetwork,visSave)

R/build_net.R

@@ -0,0 +1,238 @@
+###############################
+# Build enrichment clustering #
+###############################
+
+#' Calculate gene set clusters from GMT files and enrichment results
+#'
+#' This function parses one or more GMT files, filters an enrichment results
+#' data frame by an FDR column, computes a Jaccard similarity matrix between
+#' selected gene sets, performs hierarchical clustering, and determines the
+#' optimal number of clusters using the silhouette index.
+#'
+#' @param results_df A \code{data.frame} or \code{tibble} containing enrichment
+#'   results. Must contain at least the columns specified by \code{fdr_col} and
+#'   \code{pathway_col}.
+#' @param gmt_path A character scalar. Path to a directory containing one or
+#'   more \code{.gmt} files.
+#' @param fdr_threshold A numeric scalar specifying the FDR cutoff used to
+#'   filter \code{results_df}. Only pathways with FDR values less than this
+#'   threshold will be considered. Default is \code{0.25}.
+#' @param fdr_col A character scalar specifying the column name in
+#'   \code{results_df} that contains FDR values.
+#' @param pathway_col A character scalar specifying the column name in
+#'   \code{results_df} that contains pathway identifiers (names matching the
+#'   GMT gene set names).
+#' @param max_k_ratio A numeric scalar used to determine the maximum number of
+#'   clusters to evaluate with the silhouette index. The maximum k is computed
+#'   as \code{max(2, floor(n / max_k_ratio))}, where \code{n} is the number of
+#'   selected gene sets. Default is \code{2.5}.
+#'
+#' @details
+#' GMT files are expected to be tab-delimited, with the first column being the
+#' gene set name, the second column a description (which is ignored), and the
+#' remaining columns listing gene identifiers.
+#'
+#' Jaccard similarity between gene sets \eqn{A} and \eqn{B} is defined as:
+#' \deqn{J(A,B) = |A \cap B| / |A \cup B|}.
+#'
+#' Hierarchical clustering is performed using Euclidean distances derived from
+#' \code{1 - Jaccard_similarity} and the \code{"ward.D2"} linkage method.
+#' The optimal number of clusters is chosen as the \code{k} that maximizes the
+#' mean silhouette width for \code{k} in \code{2:max_k}.
+#'
+#' This function does not perform any file I/O beyond reading GMT files; it is
+#' intended to be used inside packages and downstream plotting functions.
+#'
+#' @return A named list with the following elements:
+#' \itemize{
+#'   \item \code{clusters}: A \code{tibble} with columns \code{pathway} and
+#'     \code{cluster} (integer cluster memberships).
+#'   \item \code{jaccard_matrix}: A symmetric numeric matrix of Jaccard
+#'     similarities between gene sets (rows and columns named by pathways).
+#'   \item \code{hclust_obj}: An \code{\link[stats]{hclust}} object containing
+#'     the hierarchical clustering result.
+#'   \item \code{optimal_k}: An integer giving the selected number of clusters.
+#'   \item \code{silhouette_data}: A \code{tibble} with columns \code{k} and
+#'     \code{silhouette}, suitable for plotting the silhouette index as a
+#'     function of \code{k}.
+#' }
+#'
+#' @examples
+#' \dontrun{
+#' res <- read.csv("pathway_results.csv")
+#' clustering <- build_net(
+#'   results_df   = res,
+#'   gmt_path     = "gmt_dir/",
+#'   fdr_threshold = 0.25,
+#'   fdr_col       = "FDR_gsea",
+#'   pathway_col   = "Pathway",
+#'   max_k_ratio   = 2.5
+#' )
+#' }
+#'
+#' @importFrom stats hclust dist cutree
+#' @importFrom utils read.delim
+#' @importFrom cluster silhouette
+#' @importFrom dplyr filter pull distinct
+#' @importFrom rlang .data
+#' @importFrom tibble tibble
+#' @export
+
+build_net <- function(results_df,
+                                       gmt_path,
+                                       fdr_threshold = 0.25,
+                                       fdr_col,
+                                       pathway_col,
+                                       max_k_ratio = 2.5) {
+  # Basic input checks
+  if (!dir.exists(gmt_path)) {
+    stop("The provided 'gmt_path' does not exist: ", gmt_path)
+  }
+  if (!is.data.frame(results_df)) {
+    stop("'results_df' must be a data.frame or tibble.")
+  }
+  if (!is.character(fdr_col) || length(fdr_col) != 1L) {
+    stop("'fdr_col' must be a single character string.")
+  }
+  if (!is.character(pathway_col) || length(pathway_col) != 1L) {
+    stop("'pathway_col' must be a single character string.")
+  }
+  if (!fdr_col %in% colnames(results_df)) {
+    stop("Column '", fdr_col, "' not found in 'results_df'.")
+  }
+  if (!pathway_col %in% colnames(results_df)) {
+    stop("Column '", pathway_col, "' not found in 'results_df'.")
+  }
+  if (!is.numeric(fdr_threshold) || length(fdr_threshold) != 1L || is.na(fdr_threshold)) {
+    stop("'fdr_threshold' must be a single numeric value.")
+  }
+  if (!is.numeric(max_k_ratio) || length(max_k_ratio) != 1L || is.na(max_k_ratio) || max_k_ratio <= 0) {
+    stop("'max_k_ratio' must be a single positive numeric value.")
+  }
+
+  # Find GMT files
+  gmt_files <- list.files(gmt_path, pattern = "\\.gmt$", full.names = TRUE)
+  if (length(gmt_files) == 0L) {
+    stop("No .gmt files found in directory: ", gmt_path)
+  }
+
+  # Read GMT files into a named list of gene vectors
+  geneset_list <- list()
+  for (f in gmt_files) {
+    gmt <- utils::read.delim(f,
+                             header = FALSE,
+                             stringsAsFactors = FALSE,
+                             sep = "\t",
+                             quote = "",
+                             comment.char = "")
+    if (ncol(gmt) < 3L) {
+      next
+    }
+    for (i in seq_len(nrow(gmt))) {
+      name <- as.character(gmt[i, 1])
+      genes <- as.character(gmt[i, 3:ncol(gmt)])
+      genes <- genes[genes != "" & !is.na(genes)]
+      geneset_list[[name]] <- unique(genes)
+    }
+  }
+
+  if (length(geneset_list) == 0L) {
+    stop("No gene sets could be parsed from the GMT files in '", gmt_path, "'.")
+  }
+
+  # Filter enrichment results by FDR and select pathways
+  results_tbl <- if (inherits(results_df, "tbl_df")) results_df else tibble::as_tibble(results_df)
+
+  results_filtered <- dplyr::filter(
+    results_tbl,
+    .data[[fdr_col]] < fdr_threshold
+  )
+
+  if (nrow(results_filtered) == 0L) {
+    stop("No pathways passed the FDR threshold (", fdr_threshold, ").")
+  }
+
+  selected_sets <- dplyr::pull(results_filtered, .data[[pathway_col]])
+  selected_sets <- unique(as.character(selected_sets))
+
+  # Intersect with gene sets available in GMTs
+  selected_sets <- intersect(selected_sets, names(geneset_list))
+  if (length(selected_sets) == 0L) {
+    stop(
+      "No overlap between pathways in 'results_df' and gene set names in GMT files. ",
+      "Check that '", pathway_col, "' matches the GMT gene set names."
+    )
+  }
+
+  geneset_list <- geneset_list[selected_sets]
+
+  # Build Jaccard similarity matrix
+  n <- length(geneset_list)
+  jaccard_sim <- matrix(
+    0,
+    nrow = n,
+    ncol  = n,
+    dimnames = list(names(geneset_list), names(geneset_list))
+  )
+
+  for (i in seq_along(geneset_list)) {
+    for (j in seq_along(geneset_list)) {
+      a <- geneset_list[[i]]
+      b <- geneset_list[[j]]
+      inter <- length(intersect(a, b))
+      union <- length(unique(c(a, b)))
+      if (union == 0) {
+        jaccard_sim[i, j] <- 0
+      } else {
+        jaccard_sim[i, j] <- inter / union
+      }
+    }
+  }
+
+  # Distance matrix for hierarchical clustering
+  dist_mat <- stats::as.dist(1 - jaccard_sim)
+
+  # Hierarchical clustering using Ward.D2
+  hc <- stats::hclust(dist_mat, method = "ward.D2")
+
+  # Determine maximum k for silhouette evaluation
+  max_k <- max(2L, floor(n / max_k_ratio))
+  max_k <- min(max_k, n - 1L) # cannot have k >= n for silhouette
+
+  if (max_k < 2L) {
+    stop("Not enough gene sets to form at least two clusters.")
+  }
+
+  ks <- 2:max_k
+  sil_scores <- numeric(length(ks))
+
+  for (idx in seq_along(ks)) {
+    k <- ks[idx]
+    cl <- stats::cutree(hc, k = k)
+    sil <- cluster::silhouette(cl, dist_mat)
+    sil_scores[idx] <- mean(sil[, "sil_width"])
+  }
+
+  optimal_k <- ks[which.max(sil_scores)]
+
+  silhouette_data <- tibble::tibble(
+    k = ks,
+    silhouette = sil_scores
+  )
+
+  # Cluster membership at optimal k
+  cluster_assignments <- stats::cutree(hc, k = optimal_k)
+  clusters_tbl <- tibble::tibble(
+    pathway = names(cluster_assignments),
+    cluster = as.integer(cluster_assignments)
+  )
+
+  # Return structured output
+  list(
+    clusters        = clusters_tbl,
+    jaccard_matrix  = jaccard_sim,
+    hclust_obj      = hc,
+    optimal_k       = optimal_k,
+    silhouette_data = silhouette_data
+  )
+}