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+#' Adjust and Export Pathway Analysis Results
+#'
+#' This function processes a dataframe containing fgsea results. It adjusts pathway names
+#' by removing underscores, converting to lowercase, then capitalizing the first letter,
+#' and joining the components with spaces. It selects and merges the top upregulated
+#' and downregulated pathways based on enrichment score (ES) and p-value.
+#'
+#' @param fgseaRes Dataframe containing fgsea results with columns 'pathway', 'ES', and 'pval'.
+#' @param nTop Integer, number of top pathways to select based on the p-value.
+#' @return A vector containing combined top upregulated and downregulated pathways.
+#' @importFrom Hmisc capitalize
+#' @export
+#' @examples
+#' # Create a synthetic fgseaRes dataframe
+#'fgseaRes <- data.frame(
+#'  pathway = c("KEGG_APOPTOSIS",
+#'              "GO_CELL_CYCLE",
+#'              "REACTOME_DNA_REPAIR",
+#'              "KEGG_METABOLISM",
+#'              "GO_TRANSPORT"),
+#'  ES = c(0.45, -0.22, 0.56, -0.35, 0.33),
+#'  pval = c(0.001, 0.02, 0.0003, 0.05, 0.01)
+#')
+#'
+#' # Run the function to get top pathways
+#'result <- adjust_export_pathway(fgseaRes = fgseaRes, nTop = 2)
+#'
+adjust_export_pathway <- function(fgseaRes, nTop = 10) {
+  # Adjust pathway names
+  fgseaRes$pathway <- as.character(fgseaRes$pathway)
+  for(i in 1:nrow(fgseaRes)){
+    message("Processing row ", i)
+    term = fgseaRes$pathway[i]
+    ### 1. Split the string
+    term = unlist(strsplit(term, split="_", fixed=TRUE))[-1]
+    ### 2. Convert to lowercase, then capitalize the first letter
+    term = Hmisc::capitalize(tolower(term))
+    ### 3. Concatenate with spaces
+    term = paste(term, collapse=" ")
+    ### 4. Data export
+    fgseaRes$pathway[i] = term
+  }
+
+  # Select top upregulated pathways
+  topPathwaysUp <- fgseaRes[fgseaRes$ES > 0,][order(fgseaRes$pval[fgseaRes$ES > 0]), 'pathway'][1:nTop]
+
+  # Select top downregulated pathways
+  topPathwaysDown <- fgseaRes[fgseaRes$ES < 0,][order(fgseaRes$pval[fgseaRes$ES < 0]), 'pathway'][1:nTop]
+
+  # Combine top pathways and convert any potential list to a vector
+  combinedPathways <- unlist(c(topPathwaysUp, rev(topPathwaysDown)), use.names = FALSE)
+
+  return(list(combinedPathways = combinedPathways, fgseaRes = fgseaRes))
+}
+
+
+
+
+
+
+#' Randomly Select Pathways with Limited Word Count
+#'
+#' This function randomly selects a specified number of pathways from a given list, ensuring that each selected pathway name does not exceed a specified number of words. It filters out pathways with names longer than the specified word limit before making the selection.
+#'
+#' @param pathways Character vector of pathways.
+#' @param max_words Integer, maximum number of words allowed in the pathway name.
+#' @param num_select Integer, number of pathways to randomly select.
+#' @return A character vector of selected pathways.
+#' @export
+#' @examples
+#' pathway_list <- c("pathway_one response to stimulus",
+#'                   "pathway_two cell growth and death",
+#'                   "pathway_three regulation of cellular process",
+#'                   "pathway_four metabolic process")
+#' selected_pathways <- selectPathways(pathway_list, max_words = 5, num_select = 2)
+#'
+selectPathways <- function(pathways, max_words = 10, num_select = 10) {
+  # Check input
+  if (!is.character(pathways)) {
+    stop("Please provide a character vector of pathways.")
+  }
+
+  # Filter pathways with word count not exceeding max_words
+  filtered_pathways <- pathways[sapply(pathways, function(x) length(strsplit(x, " ")[[1]]) <= max_words)]
+
+  # Randomly select num_select pathways from the filtered list
+  if (length(filtered_pathways) >= num_select) {
+    selected_pathways <- sample(filtered_pathways, num_select)
+  } else {
+    warning("Not enough pathways with <= ", max_words, " words. Returning as many as possible.")
+    selected_pathways <- sample(filtered_pathways, length(filtered_pathways))
+  }
+
+  return(selected_pathways)
+}
+
+
+
+
+#' Draw Dual-Sided Legends on a Plot
+#'
+#' This function creates two sets of legends, one on the left and one on the right side of a plot.
+#' It displays color-coded legends with labels corresponding to different data categories.
+#' Each legend entry consists of a colored rectangle and a text label. The left side legend has
+#' text aligned to the right of the color block, while the right side legend has text aligned
+#' to the left of the color block.
+#'
+#' @param labels Vector of labels for the legends.
+#' @param colors Vector of colors corresponding to the labels.
+#' @param legend_width The width of each legend viewport expressed in grid units.
+#' @param x_positions Numeric vector of length 2 specifying the x-positions of the left and right legends.
+#' @param y_position The y-position common for both legends, expressed as a fraction of the plot height.
+#' @param just_positions List of two vectors, each specifying the horizontal and vertical justification for the legends.
+#' @param text_alignments List of two character strings specifying text alignments for the legends ('left' or 'right').
+#' @param font_size Numeric value specifying the font size for the legend labels.
+#' @return Invisible. This function is called for its side effects of drawing legends on a plot.
+#' @importFrom grid pushViewport viewport grid.roundrect grid.text upViewport unit
+#' @export
+#' @examples
+#' labels <- c("Label1", "Label2", "Label3", "Label4", "Label5", "Label6")
+#' colors <- c("#ff0000", "#00ff00", "#0000ff", "#ffff00", "#ff00ff", "#00ffff")
+#'
+#' # Convert to 'unit' objects for grid
+#' grid::grid.roundrect(
+#'   x = grid::unit(0.5, "npc"),  # "npc" stands for normalized parent coordinates
+#'   y = grid::unit(0.5, "npc"),
+#'   width = grid::unit(0.1, "npc"),
+#'   height = grid::unit(0.05, "npc"),
+#'   gp = grid::gpar(fill = "red"),
+#'   r = grid::unit(0.1, "npc")  # rounding radius
+#' )
+#'
+#' # Example of drawing legends with specific labels and colors
+#' drawLegends(labels, colors, grid::unit(2, "cm"), c(0.225, 0.75), 0.5,
+#'             list(c("left", "center"), c("right", "center")),
+#'             list("right", "left"), 10)
+#'
+drawLegends <- function(labels, colors, legend_width, x_positions, y_position, just_positions, text_alignments, font_size) {
+  half_length <- length(labels) / 2
+  legend_height <- grid::unit(1, "lines") * half_length
+
+  # Draw left-side legend
+  grid::pushViewport(grid::viewport(
+    width = legend_width,
+    height = legend_height,
+    x = x_positions[1],
+    y = y_position,
+    just = just_positions[[1]]
+  ))
+  for (i in seq_len(half_length)) {
+    grid::grid.roundrect(
+      x = grid::unit(1, "npc") - grid::unit(0.5, "cm"),
+      y = grid::unit(1, "npc") - grid::unit(i / half_length, "npc") + grid::unit(0.5 / half_length, "npc"),
+      width = grid::unit(0.7, "cm"),
+      height = grid::unit(0.9 / half_length, "npc"),
+      gp = grid::gpar(fill = colors[i], col = NA),
+      r = grid::unit(0.3, "snpc")
+    )
+    grid::grid.text(
+      labels[i],
+      x = grid::unit(1, "npc") - grid::unit(1, "cm"),
+      y = grid::unit(1, "npc") - grid::unit(i / half_length, "npc") + grid::unit(0.5 / half_length, "npc"),
+      gp = grid::gpar(col = colors[i], fontsize = font_size),
+      just = text_alignments[[1]]
+    )
+  }
+  grid::upViewport()
+
+  # Draw right-side legend
+  grid::pushViewport(grid::viewport(
+    width = legend_width,
+    height = legend_height,
+    x = x_positions[2],
+    y = y_position,
+    just = just_positions[[2]]
+  ))
+  for (i in (half_length + 1):length(labels)) {
+    grid::grid.roundrect(
+      x = grid::unit(1, "npc") - grid::unit(0.6, "cm"),
+      y = grid::unit(1, "npc") - grid::unit((i - half_length) / half_length, "npc") + grid::unit(0.5 / half_length, "npc"),
+      width = grid::unit(0.7, "cm"),
+      height = grid::unit(0.9 / half_length, "npc"),
+      gp = grid::gpar(fill = colors[i], col = NA),
+      r = grid::unit(0.3, "snpc")
+    )
+    grid::grid.text(
+      labels[i],
+      x = grid::unit(1, "npc") - grid::unit(0.1, "cm"),
+      y = grid::unit(1, "npc") - grid::unit((i - half_length) / half_length, "npc") + grid::unit(0.5 / half_length, "npc"),
+      gp = grid::gpar(col = colors[i], fontsize = font_size),
+      just = text_alignments[[2]]
+    )
+  }
+  grid::upViewport()
+}
+
+
+#' Draw Chord Diagram with Legends
+#'
+#' This function creates a chord diagram from a specified dataframe and draws two sets of legends for it.
+#' It adjusts the track height of the chord diagram to optimize space and uses specified colors for the grid.
+#' Legends are drawn at specified positions with configurable text alignments and font sizes.
+#'
+#' @param all_combined_df A dataframe containing the matrix for the chord diagram.
+#' @param original_colors A vector of colors for the grid columns of the chord diagram.
+#' @param labels A vector of labels for the first legend.
+#' @param colors A vector of colors corresponding to the first legend's labels.
+#' @param labels2 A vector of labels for the second legend.
+#' @param colors2 A vector of colors corresponding to the second legend's labels.
+#' @param font_size The font size used for legend texts, defaults to 10.
+#' @return Invisible, primarily used for its side effects of drawing on a graphics device.
+#' @importFrom circlize chordDiagram
+#' @importFrom grid unit
+#' @importFrom graphics strwidth
+#' @export
+#' @examples
+#' # Sample Chord Diagram Matrix
+#' all_combined_df <- data.frame(
+#'   A = c(10, 20, 30),
+#'   B = c(15, 25, 35),
+#'   C = c(5, 10, 15)
+#' )
+#' rownames(all_combined_df) <- c("A", "B", "C")
+#'
+#' # Colors for the grid of the chord diagram (corresponding to columns of the matrix)
+#' original_colors <- c("red", "green", "blue")
+#'
+#' # Name the colors according to the sectors (A, B, C)
+#' names(original_colors) <- colnames(all_combined_df)
+#'
+#' # Labels and Colors for the First Legend
+#' labels <- c("Label 1", "Label 2", "Label 3")
+#' colors <- c("yellow", "purple", "cyan")
+#'
+#' # Labels and Colors for the Second Legend
+#' labels2 <- c("Label A", "Label B", "Label C")
+#' colors2 <- c("orange", "pink", "brown")
+#'
+#' # Font size for the legend texts (optional, default is 10)
+#' font_size <- 10
+#'
+#' # Call the enrichment_circlize function with the sample data
+#' # This is just an example; the plot will be rendered in an appropriate graphics context
+#' # such as RStudio's plot pane or an external plotting window.
+#' plot1 <- enrichment_circlize(all_combined_df,
+#'                              original_colors,
+#'                              labels,
+#'                              colors,
+#'                              labels2,
+#'                              colors2,
+#'                              font_size
+#'                              )
+#'
+enrichment_circlize <- function(all_combined_df, original_colors, labels, colors,
+                                       labels2, colors2, font_size = 10) {
+
+  # Calculate adjusted height for the chord diagram
+  max_height <- max(graphics::strwidth(unlist(dimnames(all_combined_df)), "inches")) * 1.2
+
+  # Draw the chord diagram
+  circlize::chordDiagram(all_combined_df, grid.col = original_colors, annotationTrack = "grid",
+                         directional = -1, direction.type = c("diffHeight", "arrows"),
+                         link.arr.type = "big.arrow", preAllocateTracks = list(track.height = max_height))
+
+  # Draw the first set of legends
+  legend_width <- grid::unit(2, "cm")
+  x_positions <- c(0.225, 0.75)
+  y_position <- 0.5
+  just_positions <- list(c("left", "center"), c("right", "center"))
+  text_alignments <- list("right", "left")
+
+  drawLegends(labels, colors, legend_width, x_positions, y_position, just_positions, text_alignments, font_size)
+
+  # Draw the second set of legends
+  x_positions2 <- c(0.3, 0.68)
+  y_position2 <- 0.7
+
+  drawLegends(labels2, colors2, legend_width, x_positions2, y_position2, just_positions, text_alignments, font_size)
+}