names in labels/tooltips

hipathia/convert_to_hipathia.R

@@ -97,6 +97,7 @@ get_hipathia_files <- function(raw_sif, node_prefix, model_elements, target_dir)
   ##### ID / label / X / Y / color / shape / type / label.cex / label.color / width / height / genesLis
   
   att_nodes <- sort(unique(c(raw_sif[,1],raw_sif[,3])))
+  att_labels <- sapply(att_nodes, function(x) with(model_elements, name[elementId == x]))
   node_ID <- paste0("N-",node_prefix,"-", att_nodes)
   ### Retrieve Entrez and type for the entire list of unique nodes
   entrez <- sapply(att_nodes, group_elements, model_elements, all_entrez)
@@ -106,14 +107,14 @@ get_hipathia_files <- function(raw_sif, node_prefix, model_elements, target_dir)
   colnames(xy) <- c("X", "Y")
   
   ### Combine into a single data frame
-  att_nodes_table <- data.frame(ID = node_ID, label = att_nodes,
+  att_nodes_table <- data.frame(ID = node_ID, label = att_labels,
                                 xy,
                                 color = "white", shape = "rectangle",
                                 type = type,
                                 label.cex = 0.5, label.color = "black",
                                 width = 46, height = 17,
                                 genesList = entrez,
-                                tooltip = att_nodes)
+                                tooltip = att_labels)
   
   ### Postprocess the att file
   ### nodes that are "complex" have '/' as a connector