@@ -117,7 +117,8 @@ function(pathwayid, cell_line = NA,

                                 data_type = data_type, pert_time = pert_time)

         if (!is.na(user_data)[1,1]) {

             edges_plus_data <- add_edge_data(expanded_edges, KEGG_mappings, 

-                                            user_data, c(11,13), 

+                                            user_data, c(11,13),

+                                            map_type = "SYMBOL", 

                                             only_mapped = only_mapped)

             edge_map <- edge_mapping_info(edges_plus_data, data_added = TRUE, 

                                     significance_markup = significance_markup,

@@ -7,14 +7,10 @@

 #' SHSY5Y,SKL,SW480,VCAP)

 #' @param cell_line2 A cell line such that cell_line1 != cell_line2

 #' @param refine_by_cell_line A logical indicator

-#' @param add_L1000_edge_data A logical indicator 

 #' @param data_type Choose from data types: (100_full, 100_bing, 50_lm)

 #' @param pert_time Choose from (6,24,48,96,120,144,168)

 #' @param only_mapped A logical indicator; if set to FALSE will return 'de-novo'

 #' edges that 'exist' in data but are not documented in KEGG

-#' @param significance_markup A logical indicator; if set to TRUE will color

-#'  edges based on direction and significance of correlation (as determined by 

-#'  user-data-analysis)

 #' @param 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

@@ -36,8 +32,6 @@

 KL_compare <-

     function(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,

@@ -144,18 +138,29 @@ KL_compare <-

         if (!is.na(cell_data1)[1,1] & !is.na(cell_data2)[1,1]) {

             edges_plus_data1 <- add_edge_data(expanded_edges, KEGG_mappings, 

                                               cell_data1, c(15,16), 

+                                              map_type = "SYMBOL",

                                               only_mapped = only_mapped)

             edges_plus_data2 <- add_edge_data(expanded_edges, KEGG_mappings, 

                                               cell_data2, c(15,16), 

+                                              map_type = "SYMBOL",

                                               only_mapped = only_mapped)

-            edges_plus_data1$unique_ID <- paste0(edges_plus_data1$entry1symbol, ":", edges_plus_data1$entry2symbol, ":", edges_plus_data1$edgeID)

-            edges_plus_data2$unique_ID <- paste0(edges_plus_data2$entry1symbol, ":", edges_plus_data2$entry2symbol, ":", edges_plus_data2$edgeID)

+            names(edges_plus_data1)[18] <- "SE_1"

+            names(edges_plus_data2)[18] <- "SE_2"

+            edges_plus_data1$unique_ID <- paste0(edges_plus_data1$entry1symbol, 

+                                                 ":", edges_plus_data1$entry2symbol, 

+                                                 ":", edges_plus_data1$edgeID)

+            edges_plus_data2$unique_ID <- paste0(edges_plus_data2$entry1symbol, 

+                                                 ":", edges_plus_data2$entry2symbol, 

+                                                 ":", edges_plus_data2$edgeID)

-            edges_compare <- merge(edges_plus_data1, edges_plus_data2[,c(18,19,21)], by = "unique_ID")

+            edges_compare <- merge(edges_plus_data1, edges_plus_data2[,c(18,19,21)], 

+                                    by = "unique_ID")

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

-                if (!is.na(edges_compare$log_OR_1[i]) & !is.na(edges_compare$log_OR_2[i])){

-                    edges_compare$test[i] <- (edges_compare$log_OR_1[i] - edges_compare$log_OR_2[i])/

+                if (!is.na(edges_compare$log_OR_1[i]) & 

+                    !is.na(edges_compare$log_OR_2[i])){

+                    edges_compare$test[i] <- (edges_compare$log_OR_1[i] - 

+                                                  edges_compare$log_OR_2[i])/

                         sqrt(edges_compare$SE_1[i]^2 + edges_compare$SE_2[i]^2)

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

@@ -5,8 +5,7 @@

 \title{Combines all other package functions for one-step cell line comparison}

 \usage{

 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,

+  refine_by_cell_line = TRUE, data_type = "100_full", pert_time = 96,

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

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

 }

@@ -22,12 +21,6 @@ SHSY5Y,SKL,SW480,VCAP)}

 \item{refine_by_cell_line}{A logical indicator}

-\item{add_L1000_edge_data}{A logical indicator}

-

-\item{significance_markup}{A logical indicator; if set to TRUE will color

-edges based on direction and significance of correlation (as determined by 

-user-data-analysis)}

-

 \item{data_type}{Choose from data types: (100_full, 100_bing, 50_lm)}

 \item{pert_time}{Choose from (6,24,48,96,120,144,168)}