#' Prepare edges for mapping
#' @description Modify the mapping information for desired look when graphed in
#' Cytoscape
#' @param expanded_edges The data frame object generated via the function
#' expand_KEGG_edges() OR has been modified by the function add_edge_data()
#' @param data_added A logical indicator; must be set to TRUE if user data has
#' been added (i.e. edges modified by function add_edge_data())
#' @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
#' @examples
#' p53_KGML <- get_KGML("hsa04115")
#' p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML)
#'
#' #Default; no data added to edges:
#'
#' p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)
#' p53_edge_mapping_info <- edge_mapping_info(p53_edges)
#'
#' #If data is added to edges as additional attribute[s]:
#'
#' p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings,
#' "HA1E", data_type = "100_bing")
#'
#' p53_edges_HA1E_data_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings,
#' p53_HA1E_data,
#' data_column_no = c(3, 10,12),
#' only_mapped = TRUE)
#'
#' p53_edge_mapping_HA1E <- edge_mapping_info(p53_edges_HA1E_data_MAPPED,
#' data_added = TRUE)
#'
edge_mapping_info <-
function(expanded_edges, data_added = FALSE, significance_markup = FALSE,
tidy_edge = TRUE){
#expanded_edges <- expanded_edges[,-c(1)]
for(i in 1:nrow(expanded_edges)){
if (expanded_edges$subtype1[i] == "activation"){
expanded_edges$color[i] = "#b20000"
}
else if (expanded_edges$subtype1[i] =="expression"){
expanded_edges$color[i] = "#b20000"
}
else if (expanded_edges$subtype1[i] =="inhibition"){
expanded_edges$color[i] = "#0015b2"
}
else if (expanded_edges$subtype1[i] =="irreversible"){
expanded_edges$color[i] = "#b20000"
}
else if (expanded_edges$subtype1[i] =="repression"){
expanded_edges$color[i] = "#0015b2"
}
else if (expanded_edges$subtype1[i] == "compound" |
expanded_edges$subtype1[i] == "indirect_effect" |
expanded_edges$subtype1[i] == "binding_association"){
expanded_edges$color[i] = "#000000"
}
else if (expanded_edges$subtype1[i] == "de_novo") {
expanded_edges$color[i] = "#808080"
}
else if (expanded_edges$subtype1[i] == "Not defined in KEGG" |
expanded_edges$type[i] == "dummy") {
expanded_edges$color[i] = "#808080"
}
else {
expanded_edges$color[i] = "#1c9900"
}
if (expanded_edges$color[i] == "#1c9900"){
expanded_edges$edge_label[i] = expanded_edges$value[i]
}
else {
expanded_edges$edge_label[i] = NA
}
if (is.na(expanded_edges$subtype2[i]) == FALSE &
expanded_edges$subtype2[i] != "indirect"){
if (expanded_edges$subtype1[i] == "inhibition"){
expanded_edges$color[i] = "#690099"
}
else if (expanded_edges$subtype1[i] == "activation"){
expanded_edges$color[i] = "#FF6600"
}
expanded_edges$edge_label[i] = expanded_edges$value2[i]
}
if(data_added){
if (expanded_edges$premapped[i] == 1){
if (expanded_edges$value[i] == "--|"){
expanded_edges$tooltip[i] <-
paste0(expanded_edges$entry1symbol[i]," --| ",
expanded_edges$entry2symbol[i])
}
else {
expanded_edges$tooltip[i] <-
paste0(expanded_edges$entry1symbol[i], " --> ",
expanded_edges$entry2symbol[i])
}
}
else {
expanded_edges$tooltip[i] <- paste0(expanded_edges$entry1symbol[i],
" - ",
expanded_edges$entry2symbol[i])
}
}
else {
if (expanded_edges$value[i] == "--|"){
expanded_edges$tooltip[i] <-
paste0(expanded_edges$entry1symbol[i], " --| ",
expanded_edges$entry2symbol[i])
}
else {
expanded_edges$tooltip[i] <-
paste0(expanded_edges$entry1symbol[i], " --> ",
expanded_edges$entry2symbol[i])
}
}
}
expanded_edges$name <- paste0(expanded_edges$entry1,
" (", expanded_edges$type, ") ",
expanded_edges$entry2)
if (significance_markup){
for (i in 1:nrow(expanded_edges)){
if (expanded_edges$has_data[i] == 1){
if (expanded_edges$summary_score[i] > 0 &
expanded_edges$significant[i] == 1){
expanded_edges$color[i] <- "#b20000"
}
else if (expanded_edges$summary_score[i] > 0 &
expanded_edges$significant[i] == 0){
expanded_edges$color[i] <- "#FF6600"
}
else if (expanded_edges$summary_score[i] <= 0 &
expanded_edges$significant[i] == 1){
expanded_edges$color[i] <- "#0015b2"
}
else {
expanded_edges$color[i] <- "#690099"
}
}
else {
expanded_edges$color[i] = "#808080"
}
}
}
#edge_map <- edge_map[,c(2,5,3,1,4:ncol(edge_map))]
expanded_edges<- cbind(expanded_edges[,c("entry1", "entry2","edgeID",
"entry1accession", "entry2accession")],
expanded_edges[,c(6:ncol(expanded_edges))])
expanded_edges <- expanded_edges[order(expanded_edges$edgeID),]
if (tidy_edge == TRUE) {
edge_IDs <- seq(min(expanded_edges$edgeID), max(expanded_edges$edgeID))
for (i in edge_IDs){
if(data_added == TRUE){
expanded_edges <- tidy_edge(edges = expanded_edges,
edge_id = edge_IDs[i],
data_added = TRUE,
by_significance = TRUE)
}
if(data_added == FALSE){
expanded_edges <- tidy_edge(edges = expanded_edges,
edge_id = edge_IDs[i],
data_added = FALSE)
}
}
}
return(expanded_edges)
}
