@@ -19,5 +19,5 @@ biocViews: NetworkInference, GeneExpression, DataRepresentation,

         ThirdPartyClient,CellBiology,GraphAndNetwork,Pathways,KEGG,Network

 Imports:

         AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST,

-        methods,graphics,stats,utils, XML

+        methods,graphics,stats,utils, XML, grDevices

 VignetteBuilder: knitr

@@ -27,6 +27,8 @@ import(hgu133a.db)

 import(httr)

 import(methods)

 import(org.Hs.eg.db)

+importFrom(grDevices,col2rgb)

+importFrom(grDevices,rgb)

 importFrom(graphics,barplot)

 importFrom(graphics,legend)

 importFrom(graphics,par)

@@ -24,6 +24,7 @@

 #' 'expanded' edge information for the specified pathway

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

 #' compounds will remain labeled via KEGG codes (do not need KEGGREST)

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

 #' @return  A dynamic map in Cytoscape automatically formatted for convenient 

 #' viewing and, if idicated by user, a data.frame object with detailed 

 #' information for 'expanded' KEGG edges

@@ -51,7 +52,8 @@ function(pathwayid, cell_line = NA,

                             only_mapped = TRUE,

                             layered_nodes = FALSE, graph_title = "default",

                             get_data = FALSE,

-                            convert_KEGG_IDs = TRUE){

+                            convert_KEGG_IDs = TRUE, 

+                            tidy_edge = FALSE){

     if (is.na(refine_by_cell_line)){

         if (is.na(cell_line)){

             refine_by_cell_line <- FALSE

@@ -85,14 +87,14 @@ function(pathwayid, cell_line = NA,

     }

     if (is.na(cell_line)){

-        edge_map <- edge_mapping_info(expanded_edges)

+        edge_map <- edge_mapping_info(expanded_edges, tidy_edge = tidy_edge)

     if (graph_title == "default"){

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

                             KGML@pathwayInfo@title)

         }

     }

     if (!is.na(cell_line) & !add_L1000_edge_data){

-        edge_map <- edge_mapping_info(expanded_edges)

+        edge_map <- edge_mapping_info(expanded_edges, tidy_edge = tidy_edge)

         if (graph_title == "default"){

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

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

@@ -101,7 +103,7 @@ function(pathwayid, cell_line = NA,

     }

     if (nrow(expanded_edges[expanded_edges$type == "maplink",]) == 

         nrow(expanded_edges) & only_mapped) {

-            edge_map <- edge_mapping_info(expanded_edges)

+            edge_map <- edge_mapping_info(expanded_edges, tidy_edge = tidy_edge)

             if (graph_title == "default"){

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

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

@@ -118,7 +120,8 @@ function(pathwayid, cell_line = NA,

                                             user_data, c(10,12), 

                                             only_mapped = only_mapped)

             edge_map <- edge_mapping_info(edges_plus_data, data_added = TRUE, 

-                                    significance_markup = significance_markup)

+                                    significance_markup = significance_markup,

+                                    tidy_edge = tidy_edge)

             if (graph_title == "default"){

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

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

@@ -126,7 +129,7 @@ function(pathwayid, cell_line = NA,

             }

         }

         else {

-            edge_map <- edge_mapping_info(expanded_edges)

+            edge_map <- edge_mapping_info(expanded_edges, tidy_edge = tidy_edge)

             if (graph_title == "default"){

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

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

@@ -8,6 +8,7 @@

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

 #' @return A data.frame object for edges that will be passed on to the function 

 #' get_graph_object

 #' @export

@@ -12,12 +12,14 @@

 get_drug_table <- function(pathwayid){

     url <- paste0("http://www.kegg.jp/kegg-bin/pathway_dd_list?map=",

-                  pathwayid)

+                    pathwayid)

     dd_table <- data.frame(

-                XML::readHTMLTable(url, header = T, which = 4, as.data.frame = FALSE), 

+                XML::readHTMLTable(url, header = TRUE, which = 4, 

+                                    as.data.frame = FALSE), 

                 stringsAsFactors = FALSE)

     if (nrow(dd_table) > 0){

-        d_table <- subset(dd_table, substring(dd_table$Disease.drug, 1, 1) == "D")

+        d_table <- subset(dd_table, 

+                            substring(dd_table$Disease.drug, 1, 1) == "D")

         if(nrow(d_table) == 0){

             warning("No associated drug targets in selected pathway")

             return()

@@ -34,10 +36,14 @@ get_drug_table <- function(pathwayid){

         long_drug <- data.frame("drug_KEGG_ID" = unlist(d_table$drug_KEGG_ID), 

                                 "drug_name" = unlist(d_table$drug_name), 

                                 "gene_target" = unlist(d_table$gene_target),

-                                 stringsAsFactors = FALSE)

+                                stringsAsFactors = FALSE)

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

-            long_drug$gene_id[i] <- strsplit(long_drug$gene_target[i], "\\(")[[1]][1]

-            long_drug$gene_symbol[i] <- regmatches(long_drug$gene_target[i], gregexpr("(?<=\\().*?(?=\\))", long_drug$gene_target[i], perl=T))[[1]]

+            long_drug$gene_id[i] <- strsplit(long_drug$gene_target[i], 

+                                            "\\(")[[1]][1]

+            long_drug$gene_symbol[i] <- regmatches(long_drug$gene_target[i], 

+                                                gregexpr("(?<=\\().*?(?=\\))", 

+                                                long_drug$gene_target[i], 

+                                                perl=TRUE))[[1]]

         }

         drops <- "gene_target"

         d_table <- long_drug[, names(long_drug) != drops]

@@ -55,10 +61,11 @@ get_disease_table <- function(pathwayid){

     url <- paste0("http://www.kegg.jp/kegg-bin/pathway_dd_list?map=",

                   pathwayid)

     dd_table <- data.frame(

-        XML::readHTMLTable(url, header = T, which = 4, as.data.frame = FALSE), 

+        XML::readHTMLTable(url, header = TRUE, which = 4, as.data.frame = FALSE), 

         stringsAsFactors = FALSE)

     if (nrow(dd_table) > 0){

-        d_table <- subset(dd_table, substring(dd_table$Disease.drug, 1, 1) == "H")

+        d_table <- subset(dd_table, 

+                          substring(dd_table$Disease.drug, 1, 1) == "H")

         if(nrow(d_table) == 0){

             warning("No diseases associated with selected pathway")

             return()

@@ -3,9 +3,11 @@

 #' @export

 #' @param edges The edge dataframe 

 #' @param edge_id The numeric value for the edge_id

+#' @param data_added A logical indicator; set to TRUE if data is added

 #' @param by_significance A logical indicator; option if data is added

 #' @param by_number A logical indicator; gives rough estimate of edge amount

 #' @return A data frame that has had the given edge condensed for viewing

+#' @importFrom grDevices col2rgb rgb

 #' @examples \dontrun{

 #' if (tidy_edge == TRUE) {

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

@@ -26,7 +28,7 @@

 #'}

 #'}

-tidy_edge <- function(edges, edge_id, data_added = TRUE, 

+tidy_edge <- function(edges, edge_id, data_added = FALSE, 

                       by_significance = FALSE, by_number = TRUE){

   edge <- edges[edges$edgeID == edge_id,]

   edges_1 <- edges[edges$edgeID != edge_id,]

@@ -8,7 +8,7 @@ KEGG_lincs(pathwayid, cell_line = NA, refine_by_cell_line = NA,

   add_L1000_edge_data = TRUE, significance_markup = TRUE,

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

   layered_nodes = FALSE, graph_title = "default", get_data = FALSE,

-  convert_KEGG_IDs = TRUE)

+  convert_KEGG_IDs = TRUE, tidy_edge = FALSE)

 }

 \arguments{

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

@@ -46,6 +46,8 @@ mapped to one location}

 \item{convert_KEGG_IDs}{A logical indicator; if set to TRUE KEGG 

 compounds will remain labeled via KEGG codes (do not need KEGGREST)}

+

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

 }

 \value{

 A dynamic map in Cytoscape automatically formatted for convenient 

@@ -17,6 +17,8 @@ been added (i.e. edges modified by function add_edge_data())}

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

 }

 \value{

 A data.frame object for edges that will be passed on to the function 

@@ -4,7 +4,7 @@

 \alias{tidy_edge}

 \title{Tidy up pathway by combining edges inside of edge_mapping_info}

 \usage{

-tidy_edge(edges, edge_id, data_added = TRUE, by_significance = FALSE,

+tidy_edge(edges, edge_id, data_added = FALSE, by_significance = FALSE,

   by_number = TRUE)

 }

 \arguments{

@@ -12,6 +12,8 @@ tidy_edge(edges, edge_id, data_added = TRUE, by_significance = FALSE,

 \item{edge_id}{The numeric value for the edge_id}

+\item{data_added}{A logical indicator; set to TRUE if data is added}

+

 \item{by_significance}{A logical indicator; option if data is added}

 \item{by_number}{A logical indicator; gives rough estimate of edge amount}