@@ -19,6 +19,7 @@

 #' with 'stacked' nodes that the user can manipulate when multiple nodes are 

 #' mapped to one location

 #' @param graph_title An optional user-specified graph title

+#' @param tidy_edge A logical indicator; must be set to FALSE for expanded edges

 #' @param get_data A logical indicator; if set to true, will return the 

 #' 'expanded' edge information for the specified pathway

 #' @param convert_KEGG_IDs A logical indicator; if set to TRUE KEGG 

@@ -43,7 +44,7 @@ KL_compare <-

              get_data = FALSE,

              convert_KEGG_IDs = TRUE,

              graph_title = "default",

-             tidy_edges = TRUE,

+             tidy_edge = TRUE,

              layered_nodes = FALSE){

         cell_lines <- c("A375","A549","ASC","HA1E","HCC515","HEK293T","HEKTE",

                         "HEPG2","HT29","MCF7","NCIH716","NPC","PC3","SHSY5Y",

@@ -95,7 +96,8 @@ KL_compare <-

         if(expanded_edges$type[1] == "dummy"){

             graph_title <- paste0("Pathway = ", pathwayid, ":", 

                                   KGML@pathwayInfo@title,

-                                  "Cell-Line: ", cell_line, 

+                                  "Cell-Lines: ", 

+                                  paste0(cell_line1,",", cell_line2), 

                                   "  *No Edges in Pathway")

         }

@@ -104,8 +106,9 @@ KL_compare <-

             edge_map <- edge_mapping_info(expanded_edges)

             if (graph_title == "default"){

                 graph_title <- paste0("Pathway = ", pathwayid, ":", 

-                                      KGML@pathwayInfo@title, "Cell-Line: ", 

-                                      cell_line,  "  *No Edges in Data")

+                                      KGML@pathwayInfo@title, "Cell-Lines: ", 

+                                      paste0(cell_line1,",", cell_line2), 

+                                       "  *No Edges in Data")

             }

             warning("All documented edges are of type 'maplink'; 

                     Overlap data cannot be mapped to selected pathway")

@@ -157,7 +160,8 @@ KL_compare <-

                     edges_compare$summary_score[i] <- exp(abs(edges_compare$test[i]))

-                    if (edges_compare$test[i] <= qnorm(0.1) | edges_compare$test[i] >= qnorm(0.9)){

+                    if (edges_compare$test[i] <= stats::qnorm(0.1) | 

+                        edges_compare$test[i] >= stats::qnorm(0.9)){

                         edges_compare$significant[i] <- 1

                     }

                     else {

@@ -205,7 +209,7 @@ KL_compare <-

                     }

                 }

             }

-            if (tidy_edges == TRUE) {

+            if (tidy_edge == TRUE) {

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

                 for (i in edge_IDs){

                     edge_map <- tidy_edge(edges = edge_map, 

@@ -8,7 +8,7 @@ KL_compare(pathwayid, cell_line1 = NA, cell_line2 = NA,

   refine_by_cell_line = TRUE, add_L1000_edge_data = TRUE,

   significance_markup = TRUE, data_type = "100_full", pert_time = 96,

   only_mapped = TRUE, get_data = FALSE, convert_KEGG_IDs = TRUE,

-  graph_title = "default", tidy_edges = TRUE, layered_nodes = FALSE)

+  graph_title = "default", tidy_edge = TRUE, layered_nodes = FALSE)

 }

 \arguments{

 \item{pathwayid}{A KEGG pathway ID of the form "hsa12345" 

@@ -43,6 +43,8 @@ compounds will remain labeled via KEGG codes (do not need KEGGREST)}

 \item{graph_title}{An optional user-specified graph title}

+\item{tidy_edge}{A logical indicator; must be set to FALSE for expanded edges}

+

 \item{layered_nodes}{A logical indicator; if set to TRUE will create a graph 

 with 'stacked' nodes that the user can manipulate when multiple nodes are 

 mapped to one location}