diff --git a/R/cytoscapeNetwork.R b/R/cytoscapeNetwork.R
index d804854..9a0a86a 100644
--- a/R/cytoscapeNetwork.R
+++ b/R/cytoscapeNetwork.R
@@ -1,370 +1,3 @@
-# R/cytoscapeNetwork.R
-#
-# htmlwidgets binding for the Cytoscape network visualisation.
-# The heavy-lifting JS lives in inst/htmlwidgets/cytoscapeNetwork.js.
-# This file is responsible for:
-#   1. Pre-processing nodes / edges in R (colour mapping, element serialisation)
-#   2. Calling htmlwidgets::createWidget() to hand everything to the JS side.
-
-# ── Internal helpers (not exported) ────────────────────────────────────────
-
-#' Map logFC values to a blue-grey-red colour palette
-#' @keywords internal
-#' @noRd
-.mapLogFCToColor <- function(logFC_values) {
-  colors <- c("#ADD8E6", "#ADD8E6", "#D3D3D3", "#FFA590", "#FFA590")
-
-  if (all(is.na(logFC_values)) ||
-      length(unique(logFC_values[!is.na(logFC_values)])) <= 1) {
-    return(rep("#D3D3D3", length(logFC_values)))
-  }
-
-  default_max     <- 2
-  max_logFC       <- max(c(abs(logFC_values), default_max), na.rm = TRUE)
-  min_logFC       <- -max_logFC
-  color_map       <- grDevices::colorRamp(colors)
-  normalized      <- (logFC_values - min_logFC) / (max_logFC - min_logFC)
-  normalized[is.na(normalized)] <- 0.5
-  rgb_colors      <- color_map(normalized)
-  grDevices::rgb(rgb_colors[, 1], rgb_colors[, 2], rgb_colors[, 3],
-                 maxColorValue = 255)
-}
-
-#' Safely escape a string for embedding in a JS single-quoted literal
-#' @keywords internal
-#' @noRd
-.escJS <- function(x) {
-  if (is.null(x)) return("")
-  x <- as.character(x)
-  x <- gsub("\\\\", "\\\\\\\\", x)
-  x <- gsub("'",    "\\\\'",    x)
-  x <- gsub("\r",   "\\\\r",    x)
-  x <- gsub("\n",   "\\\\n",    x)
-  x
-}
-
-#' Relationship properties lookup
-#' @keywords internal
-#' @noRd
-.relProps <- function() {
-  list(
-    complex = list(
-      types       = "Complex",
-      color       = "#8B4513",
-      style       = "solid",
-      arrow       = "none",
-      width       = 4,
-      consolidate = "undirected"
-    ),
-    regulatory = list(
-      types       = c("Inhibition", "Activation", "IncreaseAmount", "DecreaseAmount"),
-      colors      = list(Inhibition     = "#FF4444",
-                         Activation     = "#44AA44",
-                         IncreaseAmount = "#4488FF",
-                         DecreaseAmount = "#FF8844"),
-      style       = "solid",
-      arrow       = "triangle",
-      width       = 3,
-      consolidate = "bidirectional"
-    ),
-    phosphorylation = list(
-      types       = "Phosphorylation",
-      color       = "#9932CC",
-      style       = "dashed",
-      arrow       = "triangle",
-      width       = 2,
-      consolidate = "directed"
-    ),
-    other = list(
-      color       = "#666666",
-      style       = "dotted",
-      arrow       = "triangle",
-      width       = 2,
-      consolidate = "directed"
-    )
-  )
-}
-
-#' Classify an interaction string into a relationship category
-#' @keywords internal
-#' @noRd
-.classify <- function(interaction) {
-  if (is.null(interaction) || is.na(interaction) || !nzchar(trimws(as.character(interaction)))) {
-    return("other")
-  }
-  interaction <- as.character(interaction)
-  props <- .relProps()
-  for (cat_name in names(props)) {
-    if (!is.null(props[[cat_name]]$types) &&
-        interaction %in% props[[cat_name]]$types) {
-      return(cat_name)
-    }
-  }
-  "other"
-}
-
-#' Retrieve edge colour / style / arrow / width
-#' @keywords internal
-#' @noRd
-.edgeStyle <- function(interaction, category, edge_type) {
-  props <- .relProps()
-  p     <- if (category %in% names(props)) props[[category]] else props$other
-
-  color <- if (category == "regulatory" && !is.null(p$colors)) {
-    base <- sub(" \\(bidirectional\\)", "", interaction)
-    if (base %in% names(p$colors)) p$colors[[base]] else "#666666"
-  } else {
-    p$color
-  }
-
-  arrow <- switch(edge_type,
-    undirected   = "none",
-    bidirectional = "triangle",
-    p$arrow
-  )
-
-  list(color = color, style = p$style, arrow = arrow, width = p$width)
-}
-
-#' Aggregate PTM overlap between edge targets and node Site columns
-#' @keywords internal
-#' @noRd
-.ptmOverlap <- function(edges, nodes) {
-  if (nrow(edges) == 0 || is.null(nodes)) return(setNames(character(0), character(0)))
-
-  edges$edge_key <- paste(edges$source, edges$target, edges$interaction, sep = "-")
-  unique_keys    <- unique(edges$edge_key)
-  result         <- setNames(character(length(unique_keys)), unique_keys)
-
-  for (key in unique_keys) {
-    sub_edges <- edges[edges$edge_key == key, ]
-    all_sites <- c()
-
-    for (i in seq_len(nrow(sub_edges))) {
-      e <- sub_edges[i, ]
-      if (!is.na(e$target) && "site" %in% names(e) && !is.na(e$site)) {
-        tnodes <- nodes[nodes$id == e$target, ]
-        if (nrow(tnodes) > 0 && "Site" %in% names(tnodes)) {
-          edge_sites <- trimws(unlist(strsplit(as.character(e$site), "[,;|]")))
-          for (j in seq_len(nrow(tnodes))) {
-            if (!is.na(tnodes$Site[j])) {
-              node_sites   <- trimws(unlist(strsplit(as.character(tnodes$Site[j]), "_")))
-              overlap      <- intersect(edge_sites, node_sites)
-              overlap      <- overlap[overlap != "" & !is.na(overlap)]
-              all_sites    <- c(all_sites, overlap)
-            }
-          }
-        }
-      }
-    }
-
-    u <- unique(all_sites[all_sites != "" & !is.na(all_sites)])
-    result[key] <- if (length(u) == 0) {
-      ""
-    } else if (length(u) == 1) {
-      paste0("Overlapping PTM site: ",  u)
-    } else {
-      paste0("Overlapping PTM sites: ", paste(u, collapse = ", "))
-    }
-  }
-  result
-}
-
-#' Consolidate bidirectional / undirected edges
-#' @keywords internal
-#' @noRd
-.consolidateEdges <- function(edges, nodes = NULL) {
-  if (nrow(edges) == 0) return(edges)
-
-  ptm_map      <- .ptmOverlap(edges, nodes)
-  props        <- .relProps()
-  consolidated <- list()
-  processed    <- c()
-
-  for (i in seq_len(nrow(edges))) {
-    e        <- edges[i, ]
-    pair_key <- paste(sort(c(e$source, e$target)), e$interaction, collapse = "-")
-    if (pair_key %in% processed) next
-
-    cat        <- .classify(e$interaction)
-    rev_edges  <- edges[edges$source == e$target &
-                        edges$target == e$source &
-                        edges$interaction == e$interaction, ]
-    con_type   <- props[[cat]]$consolidate
-    edge_key   <- paste(e$source, e$target, e$interaction, sep = "-")
-    ptm_txt    <- if (edge_key %in% names(ptm_map)) ptm_map[[edge_key]] else ""
-
-    if (nrow(rev_edges) > 0 && con_type %in% c("undirected", "bidirectional")) {
-      new_interaction <- if (con_type == "undirected") e$interaction else
-        paste(e$interaction, "(bidirectional)")
-      new_edge <- data.frame(source      = e$source,
-                             target      = e$target,
-                             interaction = new_interaction,
-                             edge_type   = if (con_type == "undirected") "undirected" else "bidirectional",
-                             category    = cat,
-                             ptm_overlap = ptm_txt,
-                             stringsAsFactors = FALSE)
-      for (col in setdiff(names(e), c("source", "target", "interaction"))) {
-        new_edge[[col]] <- e[[col]]
-      }
-      key <- paste(e$source, e$target, new_interaction, sep = "-")
-      consolidated[[key]] <- new_edge
-      processed <- c(processed, pair_key)
-    } else {
-      de            <- e
-      de$edge_type  <- "directed"
-      de$category   <- cat
-      de$ptm_overlap <- ptm_txt
-      key           <- paste(e$source, e$target, e$interaction, sep = "-")
-      consolidated[[key]] <- de
-    }
-  }
-
-  if (length(consolidated) > 0) {
-    result           <- do.call(rbind, consolidated)
-    rownames(result) <- NULL
-    result
-  } else {
-    edges[0, ]
-  }
-}
-
-#' Build the list of Cytoscape element objects (nodes + edges)
-#'
-#' Returns a list of named lists — jsonlite will serialise them cleanly.
-#' @keywords internal
-#' @noRd
-.buildElements <- function(nodes, edges, display_label_type = "id") {
-  # ── node colours ──────────────────────────────────────────────────────
-  node_colors <- if ("logFC" %in% names(nodes)) {
-    .mapLogFCToColor(nodes$logFC)
-  } else {
-    rep("#D3D3D3", nrow(nodes))
-  }
-
-  label_col <- if (display_label_type == "hgncName" &&
-                   "hgncName" %in% names(nodes)) "hgncName" else "id"
-
-  has_ptm_sites <- if ("Site" %in% names(nodes)) {
-    unique(nodes$id[!is.na(nodes$Site) & trimws(nodes$Site) != ""])
-  } else {
-    character(0)
-  }
-
-  elements        <- list()
-  emitted_prots   <- character(0)
-  emitted_cpds    <- character(0)
-  emitted_ptm_n   <- character(0)
-  emitted_ptm_e   <- character(0)
-
-  for (i in seq_len(nrow(nodes))) {
-    row       <- nodes[i, , drop = FALSE]
-    color     <- node_colors[i]
-    has_site  <- "Site" %in% names(nodes) &&
-                 !is.na(row$Site) && trimws(row$Site) != ""
-
-    display_label <- if (label_col == "hgncName" &&
-                         !is.na(row$hgncName) && row$hgncName != "")
-      row$hgncName else row$id
-
-    needs_compound <- row$id %in% has_ptm_sites
-    compound_id    <- paste0(row$id, "__compound__")
-
-    # Compound container
-    if (needs_compound && !(compound_id %in% emitted_cpds)) {
-      elements <- c(elements, list(
-        list(data = list(id        = compound_id,
-                         node_type = "compound"))
-      ))
-      emitted_cpds <- c(emitted_cpds, compound_id)
-    }
-
-    # Protein node
-    if (!(row$id %in% emitted_prots)) {
-      nd <- list(id        = row$id,
-                 label     = display_label,
-                 color     = color,
-                 node_type = "protein",
-                 width     = max(60, min(nchar(display_label) * 8 + 20, 150)),
-                 height    = max(40, min(nchar(display_label) * 2 + 30, 60)))
-      if (needs_compound) nd$parent <- compound_id
-      elements <- c(elements, list(list(data = nd)))
-      emitted_prots <- c(emitted_prots, row$id)
-    }
-
-    # PTM child nodes + attachment edges
-    if (has_site) {
-      sites <- unique(trimws(unlist(strsplit(as.character(row$Site), "[_,;|]"))))
-      sites <- sites[sites != ""]
-
-      for (site in sites) {
-        ptm_nid <- paste0(row$id, "__ptm__", site)
-        if (!(ptm_nid %in% emitted_ptm_n)) {
-          elements <- c(elements, list(list(data = list(
-            id             = ptm_nid,
-            label          = site,
-            color          = color,
-            parent_protein = row$id,
-            parent         = compound_id,
-            node_type      = "ptm"
-          ))))
-          emitted_ptm_n <- c(emitted_ptm_n, ptm_nid)
-        }
-
-        ptm_eid <- paste0(row$id, "__ptm_edge__", site)
-        if (!(ptm_eid %in% emitted_ptm_e)) {
-          elements <- c(elements, list(list(data = list(
-            id          = ptm_eid,
-            source      = row$id,
-            target      = ptm_nid,
-            edge_type   = "ptm_attachment",
-            category    = "ptm_attachment",
-            interaction = "",
-            color       = color,
-            line_style  = "dotted",
-            arrow_shape = "none",
-            width       = 1.5,
-            tooltip     = ""
-          ))))
-          emitted_ptm_e <- c(emitted_ptm_e, ptm_eid)
-        }
-      }
-    }
-  }
-
-  # ── edges ─────────────────────────────────────────────────────────────
-  if (!is.null(edges) && nrow(edges) > 0) {
-    con <- .consolidateEdges(edges, nodes)
-
-    for (i in seq_len(nrow(con))) {
-      row  <- con[i, ]
-      sty  <- .edgeStyle(row$interaction, row$category, row$edge_type)
-      eid  <- paste(row$source, row$target, row$interaction, sep = "-")
-      elink <- if ("evidenceLink" %in% names(row)) {
-        ev <- row$evidenceLink
-        if (is.na(ev) || ev == "NA") "" else as.character(ev)
-      } else ""
-
-      elements <- c(elements, list(list(data = list(
-        id          = eid,
-        source      = row$source,
-        target      = row$target,
-        interaction = row$interaction,
-        edge_type   = row$edge_type,
-        category    = row$category,
-        evidenceLink = elink,
-        color       = sty$color,
-        line_style  = sty$style,
-        arrow_shape = sty$arrow,
-        width       = sty$width,
-        tooltip     = if (!is.null(row$ptm_overlap)) row$ptm_overlap else ""
-      ))))
-    }
-  }
-
-  elements
-}
-
 #' Render a Cytoscape network visualisation
 #'
 #' Creates an interactive network diagram powered by Cytoscape.js and the dagre
diff --git a/R/utils_cytoscapeNetwork.R b/R/utils_cytoscapeNetwork.R
index a7e2726..f15418f 100644
--- a/R/utils_cytoscapeNetwork.R
+++ b/R/utils_cytoscapeNetwork.R
@@ -64,7 +64,7 @@
             style       = "solid",
             arrow       = "triangle",
             width       = 3,
-            consolidate = "bidirectional"
+            consolidate = "directed"
         ),
         phosphorylation = list(
             types       = "Phosphorylation",
@@ -110,15 +110,13 @@
     p     <- if (category %in% names(props)) props[[category]] else props$other
     
     color <- if (category == "regulatory" && !is.null(p$colors)) {
-        base <- sub(" \\(bidirectional\\)", "", interaction)
-        if (base %in% names(p$colors)) p$colors[[base]] else "#666666"
+        if (interaction %in% names(p$colors)) p$colors[[interaction]] else "#666666"
     } else {
         p$color
     }
-    
+
     arrow <- switch(edge_type,
-                    undirected   = "none",
-                    bidirectional = "triangle",
+                    undirected = "none",
                     p$arrow
     )
     
@@ -170,7 +168,7 @@
     result
 }
 
-#' Consolidate bidirectional / undirected edges
+#' Consolidate undirected edges
 #' @keywords internal
 #' @noRd
 .consolidateEdges <- function(edges, nodes = NULL) {
@@ -194,20 +192,18 @@
         edge_key   <- paste(e$source, e$target, e$interaction, sep = "-")
         ptm_txt    <- if (edge_key %in% names(ptm_map)) ptm_map[[edge_key]] else ""
         
-        if (nrow(rev_edges) > 0 && con_type %in% c("undirected", "bidirectional")) {
-            new_interaction <- if (con_type == "undirected") e$interaction else
-                paste(e$interaction, "(bidirectional)")
+        if (nrow(rev_edges) > 0 && con_type == "undirected") {
             new_edge <- data.frame(source      = e$source,
                                    target      = e$target,
-                                   interaction = new_interaction,
-                                   edge_type   = if (con_type == "undirected") "undirected" else "bidirectional",
+                                   interaction = e$interaction,
+                                   edge_type   = "undirected",
                                    category    = cat,
                                    ptm_overlap = ptm_txt,
                                    stringsAsFactors = FALSE)
             for (col in setdiff(names(e), c("source", "target", "interaction"))) {
                 new_edge[[col]] <- e[[col]]
             }
-            key <- paste(e$source, e$target, new_interaction, sep = "-")
+            key <- paste(e$source, e$target, e$interaction, sep = "-")
             consolidated[[key]] <- new_edge
             processed <- c(processed, pair_key)
         } else {
diff --git a/inst/htmlwidgets/cytoscapeNetwork.js b/inst/htmlwidgets/cytoscapeNetwork.js
index 5dfc3ac..50a4f36 100644
--- a/inst/htmlwidgets/cytoscapeNetwork.js
+++ b/inst/htmlwidgets/cytoscapeNetwork.js
@@ -122,14 +122,6 @@ HTMLWidgets.widget({
             "text-background-padding": "2px"
           }
         },
-        /* ── bidirectional edges – source arrow too ──────────────────── */
-        {
-          selector: "edge[edge_type = 'bidirectional']",
-          style: {
-            "source-arrow-shape": "triangle",
-            "target-arrow-shape": "triangle"
-          }
-        },
         /* ── undirected (complex) edges ──────────────────────────────── */
         {
           selector: "edge[category = 'complex']",
@@ -221,7 +213,7 @@ HTMLWidgets.widget({
       var existingTypes = {};
       cyInstance.edges().forEach(function (e) {
         var raw = e.data("interaction") || "";
-        existingTypes[raw.replace(" (bidirectional)", "")] = true;
+        existingTypes[raw] = true;
       });
 
       var edgeItems = edgeTypeConfigs
diff --git a/tests/testthat/test-utils_cytoscapeNetwork.R b/tests/testthat/test-utils_cytoscapeNetwork.R
index b36eecb..780c611 100644
--- a/tests/testthat/test-utils_cytoscapeNetwork.R
+++ b/tests/testthat/test-utils_cytoscapeNetwork.R
@@ -86,7 +86,7 @@ test_that(".relProps returns correct structure", {
     expect_true(all(c("complex", "regulatory", "phosphorylation", "other") %in% names(props)))
     
     expect_equal(props$complex$consolidate, "undirected")
-    expect_equal(props$regulatory$consolidate, "bidirectional")
+    expect_equal(props$regulatory$consolidate, "directed")
     expect_equal(props$phosphorylation$consolidate, "directed")
     
     expect_true("Inhibition" %in% names(props$regulatory$colors))
@@ -124,11 +124,6 @@ test_that(".edgeStyle returns no arrow for undirected complex edges", {
     expect_equal(style$color, "#8B4513")
 })
 
-test_that(".edgeStyle returns triangle arrows for bidirectional edges", {
-    style <- MSstatsBioNet:::.edgeStyle("Inhibition (bidirectional)", "regulatory", "bidirectional")
-    expect_equal(style$arrow, "triangle")
-})
-
 test_that(".edgeStyle falls back to grey for unknown category", {
     style <- MSstatsBioNet:::.edgeStyle("Unknown", "other", "directed")
     expect_equal(style$color, "#666666")
@@ -138,17 +133,17 @@ test_that(".edgeStyle falls back to grey for unknown category", {
 # .consolidateEdges
 # =============================================================================
 
-test_that(".consolidateEdges consolidates bidirectional inhibition into one edge", {
+test_that(".consolidateEdges keeps opposite regulatory edges as separate directed edges", {
     edges <- create_mock_edges()
     result <- MSstatsBioNet:::.consolidateEdges(edges)
-    
+
     expect_s3_class(result, "data.frame")
     expect_true(all(c("edge_type", "category", "ptm_overlap") %in% names(result)))
-    
-    # Two Inhibition edges in opposite directions → one bidirectional edge
+
+    # Two Inhibition edges in opposite directions → both kept as directed
     inhibition <- result[grepl("Inhibition", result$interaction), ]
-    expect_equal(nrow(inhibition), 1)
-    expect_equal(inhibition$edge_type, "bidirectional")
+    expect_equal(nrow(inhibition), 2)
+    expect_true(all(inhibition$edge_type == "directed"))
 })
 
 test_that(".consolidateEdges marks phosphorylation as directed", {