@@ -67,9 +67,12 @@ function(pathwayid, cell_line = NA,

     if(!isS4(KGML)){

         return()

     }

-    KEGG_mappings <- 

-        expand_KEGG_mappings(KGML,convert_KEGG_IDs = convert_KEGG_IDs)

+    if (!refine_by_cell_line){

+        KEGG_mappings <- expand_KEGG_mappings(KGML,convert_KEGG_IDs = convert_KEGG_IDs)

+    }

+        

     if (refine_by_cell_line) {

+        KEGG_mappings <- expand_KEGG_mappings(KGML,convert_KEGG_IDs = convert_KEGG_IDs)

         full_mappings <- KEGG_mappings

         KEGG_mappings <- refine_mappings(KEGG_mappings, cell_line)

         for (i in 1:nrow(full_mappings)){

@@ -156,7 +156,7 @@ function(expanded_edges, data_added = FALSE, significance_markup = FALSE,

     if (tidy_edge == TRUE) {

       edge_IDs <- seq(min(expanded_edges$edgeID), max(expanded_edges$edgeID))

-      for (i in edge_IDs){

+      for (i in edge_IDs[edge_IDs %in% expanded_edges$edgeID]){

         if(data_added == TRUE){

           expanded_edges <- tidy_edge(edges = expanded_edges,

                                       edge_id = edge_IDs[i],