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+#' Add in edges to map documented in other pathways |
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+#' @description For a specific pathway entity(gene), search KEGG databases |
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| 3 |
+#' to see if it has any other documented relationships in KEGG. |
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+#' expand_KEGG_edges |
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+#' @export |
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+#' @param entry_accession The Accession # of the pathway entity to 'keggerize' |
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+#' @param KGML The KGML file of the current pathway |
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+#' @param KEGG_mappings KEGG mappings for the current pathway |
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+#' @param edges The expanded edges for the current pathway |
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+#' @return A modified expanded edges data frame with additional rows for new |
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+#' entries |
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+#' @examples \dontrun{
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+#' KGML <- get_KGML("hsa04150")
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+#' KEGG_mappings <- expand_KEGG_mappings(KGML) |
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+#' edges <- expand_KEGG_edges(KGML, KEGG_mappings) |
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+#' entry_accession <- "2475" |
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+#' mtor_plus_mtor <- keggerize_edges(entry_accession = entry_accession, |
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+#' KGML = KGML,KEGG_mappings = KEGG_mappings, |
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+#' edges = edges) } |
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+#' |
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+ |
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+keggerize_edges <- function(entry_accession, KGML, KEGG_mappings, edges){
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| 23 |
+ if(!"primary_pathway" %in% names(edges)){
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+ edges$primary_pathwayID <- strsplit(KGML@pathwayInfo@name, ":")[[1]][2] |
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+ edges$primary_pathway <- KGML@pathwayInfo@title |
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+ } |
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+ entry_code <- paste0("hsa:",entry_accession)
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+ entry_info <- keggGet(entry_code) |
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+ entry_pathways <- entry_info[[1]]["PATHWAY"] |
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+ entry_pathways <- names(entry_pathways$PATHWAY[1:length(unlist(entry_pathways))]) |
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+ current_pathway <- strsplit(KGML@pathwayInfo@name, ":")[[1]][2] |
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+ entry_pathways <- entry_pathways[!entry_pathways %in% current_pathway] |
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+ |
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+ for(p in 1:length(entry_pathways)){
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+ pathway_KGML <- get_KGML(entry_pathways[p]) |
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+ pathway_KEGG_mappings <- expand_KEGG_mappings(pathway_KGML) |
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+ pathway_edges <- expand_KEGG_edges(pathway_KGML, pathway_KEGG_mappings) |
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+ entry_edges <- pathway_edges[pathway_edges$entry1accession == entry_accession | |
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+ pathway_edges$entry2accession == entry_accession, ] |
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+ entry_sources <- entry_edges[entry_edges$entry1accession != entry_accession & |
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+ entry_edges$entry1accession %in% KEGG_mappings$entryACCESSION,] |
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+ entry_sources <- entry_sources[!duplicated(entry_sources[,6:16]),] |
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+ if(nrow(entry_sources) > 0){
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| 44 |
+ for(i in 1:nrow(entry_sources)){
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+ entry1_locations <- KEGG_mappings$entryID[KEGG_mappings$entrySYMBOL == entry_sources$entry1symbol[i]] |
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| 46 |
+ entry2_locations <- KEGG_mappings$entryID[KEGG_mappings$entrySYMBOL == entry_sources$entry2symbol[i]] |
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| 47 |
+ if(length(entry1_locations) > 1 | length(entry2_locations > 1)){
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+ |
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+ distance_matrix <- matrix(nrow = length(entry2_locations), |
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+ ncol = length(entry1_locations)) |
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+ colnames(distance_matrix) <- entry1_locations |
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+ rownames(distance_matrix) <- entry2_locations |
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+ for(j in 1:nrow(distance_matrix)){
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+ for (k in 1:ncol(distance_matrix)){
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+ value <- |
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+ sqrt((KEGG_mappings$Xcoord[KEGG_mappings$entryID == |
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+ colnames(distance_matrix)[k]][1] |
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+ - KEGG_mappings$Xcoord[KEGG_mappings$entryID == |
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+ rownames(distance_matrix)[j]][1])^2 |
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+ + (KEGG_mappings$Ycoord[KEGG_mappings$entryID == |
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+ colnames(distance_matrix)[k]][1] |
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+ - KEGG_mappings$Ycoord[KEGG_mappings$entryID == |
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+ rownames(distance_matrix)[j]][1])^2) |
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+ # print(value) |
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+ distance_matrix[j,k] <- value |
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+ } |
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+ } |
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+ location <- which(distance_matrix == min(distance_matrix), arr.ind = TRUE) |
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+ entry_sources$entry1[i] <- colnames(distance_matrix)[location[1,2]] |
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+ entry_sources$entry2[i] <- rownames(distance_matrix)[location[1,1]] |
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+ } |
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+ if(length(entry1_locations) == 1 & length(entry2_locations) == 1){
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+ entry_sources$entry1[i] <- entry1_locations |
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+ entry_sources$entry2[i] <- entry2_locations |
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+ } |
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+ } |
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+ } |
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+ entry_targets <- entry_edges[entry_edges$entry1accession == entry_accession & |
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+ entry_edges$entry2accession %in% KEGG_mappings$entryACCESSION,] |
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+ entry_targets <- entry_targets[!duplicated(entry_targets[,6:16]),] |
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+ if(nrow(entry_targets) > 0){
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| 82 |
+ for(i in 1:nrow(entry_targets)){
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+ entry1_locations <- KEGG_mappings$entryID[KEGG_mappings$entrySYMBOL == entry_targets$entry1symbol[i]] |
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+ entry2_locations <- KEGG_mappings$entryID[KEGG_mappings$entrySYMBOL == entry_targets$entry2symbol[i]] |
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| 85 |
+ if(length(entry1_locations) > 1 | length(entry2_locations > 1)){
|
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+ |
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+ distance_matrix <- matrix(nrow = length(entry2_locations), |
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+ ncol = length(entry1_locations)) |
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+ colnames(distance_matrix) <- entry1_locations |
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+ rownames(distance_matrix) <- entry2_locations |
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| 91 |
+ for(j in 1:nrow(distance_matrix)){
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| 92 |
+ for (k in 1:ncol(distance_matrix)){
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+ value <- |
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+ sqrt((KEGG_mappings$Xcoord[KEGG_mappings$entryID == |
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| 95 |
+ colnames(distance_matrix)[k]][1] |
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| 96 |
+ - KEGG_mappings$Xcoord[KEGG_mappings$entryID == |
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+ rownames(distance_matrix)[j]][1])^2 |
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+ + (KEGG_mappings$Ycoord[KEGG_mappings$entryID == |
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+ colnames(distance_matrix)[k]][1] |
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+ - KEGG_mappings$Ycoord[KEGG_mappings$entryID == |
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+ rownames(distance_matrix)[j]][1])^2) |
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+ # print(value) |
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+ distance_matrix[j,k] <- value |
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| 104 |
+ } |
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| 105 |
+ } |
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| 106 |
+ location <- which(distance_matrix == min(distance_matrix), arr.ind = TRUE) |
|
| 107 |
+ entry_targets$entry1[i] <- colnames(distance_matrix)[location[1,2]] |
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| 108 |
+ entry_targets$entry2[i] <- rownames(distance_matrix)[location[1,1]] |
|
| 109 |
+ } |
|
| 110 |
+ if(length(entry1_locations) == 1 & length(entry2_locations) == 1){
|
|
| 111 |
+ entry_targets$entry1[i] <- entry1_locations |
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| 112 |
+ entry_targets$entry2[i] <- entry2_locations |
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| 113 |
+ } |
|
| 114 |
+ } |
|
| 115 |
+ } |
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| 116 |
+ new_edges <- rbind(entry_sources, entry_targets) |
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| 117 |
+ if(nrow(new_edges) > 0) {
|
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| 118 |
+ new_edges$primary_pathwayID <- strsplit(pathway_KGML@pathwayInfo@name, ":")[[1]][2] |
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| 119 |
+ new_edges$primary_pathway <- pathway_KGML@pathwayInfo@title |
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| 120 |
+ edges <- rbind(edges, new_edges) |
|
| 121 |
+ } |
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| 122 |
+ print(p) |
|
| 123 |
+ } |
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| 124 |
+ |
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| 125 |
+ edges$edge_entry_ID <- paste0(edges$entry1, ":", edges$entry2) |
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| 126 |
+ edge_ID_sets <- edges$edge_entry_ID[!duplicated(edges$edge_entry_ID)] |
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| 127 |
+ edge_ID_mapper <- data.frame("edges" = edge_ID_sets,
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| 128 |
+ edgeID = 1:length(edge_ID_sets), |
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| 129 |
+ stringsAsFactors = FALSE) |
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| 130 |
+ for(i in 1:nrow(edges)){
|
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| 131 |
+ edges$edgeID[i] <- edge_ID_mapper$edgeID[match(edges$edge_entry_ID[i], |
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| 132 |
+ edge_ID_mapper$edges)] |
|
| 133 |
+ } |
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| 134 |
+ edges <- edges[,names(edges) != "edge_entry_ID"] |
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| 135 |
+ return(edges) |
|
| 136 |
+} |
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| 137 |
+ |
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| 138 |
+ |
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| 139 |
+ |
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| 140 |
+# KGML <- get_KGML("hsa04150")
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| 141 |
+# KEGG_mappings <- expand_KEGG_mappings(KGML) |
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| 142 |
+# edges <- expand_KEGG_edges(KGML, KEGG_mappings) |
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| 143 |
+# |
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+ |
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| 145 |
+# |
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| 146 |
+# keggerize_edges <- function(entry_accession, KGML, KEGG_mappings, edges){
|
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| 147 |
+# if(!"primary_pathway" %in% names(edges)){
|
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| 148 |
+# edges$primary_pathwayID <- strsplit(KGML@pathwayInfo@name, ":")[[1]][2] |
|
| 149 |
+# edges$primary_pathway <- KGML@pathwayInfo@title |
|
| 150 |
+# } |
|
| 151 |
+# entry_code <- paste0("hsa:",entry_accession)
|
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| 152 |
+# entry_info <- keggGet(entry_code) |
|
| 153 |
+# entry_pathways <- entry_info[[1]]["PATHWAY"] |
|
| 154 |
+# entry_pathways <- names(entry_pathways$PATHWAY[1:length(unlist(entry_pathways))]) |
|
| 155 |
+# current_pathway <- strsplit(KGML@pathwayInfo@name, ":")[[1]][2] |
|
| 156 |
+# entry_pathways <- entry_pathways[!entry_pathways %in% current_pathway] |
|
| 157 |
+# for(i in 1:length(entry_pathways)){
|
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| 158 |
+# pathway_KGML <- get_KGML(entry_pathways[i]) |
|
| 159 |
+# pathway_KEGG_mappings <- expand_KEGG_mappings(pathway_KGML) |
|
| 160 |
+# pathway_edges <- expand_KEGG_edges(pathway_KGML, pathway_KEGG_mappings) |
|
| 161 |
+# entry_edges <- pathway_edges[pathway_edges$entry1accession == entry_accession | |
|
| 162 |
+# pathway_edges$entry2accession == entry_accession, ] |
|
| 163 |
+# entry_sources <- entry_edges[entry_edges$entry1accession != entry_accession & |
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| 164 |
+# entry_edges$entry1accession %in% KEGG_mappings$entryACCESSION,] |
|
| 165 |
+# # for(i in 1:nrow(entry_sources)){
|
|
| 166 |
+# # entry1_locations <- KEGG_mappings$entryID[KEGG_mappings$entrySYMBOL == entry_sources$entry1symbol[i]] |
|
| 167 |
+# # entry2_locations <- KEGG_mappings$entryID[KEGG_mappings$entrySYMBOL == entry_sources$entry2symbol[i]] |
|
| 168 |
+# # distance_matrix <- matrix(nrow = length(entry2_locations), |
|
| 169 |
+# # ncol = length(entry1_locations)) |
|
| 170 |
+# # colnames(distance_matrix) <- entry1_locations |
|
| 171 |
+# # rownames(distance_matrix) <- entry2_locations |
|
| 172 |
+# # for(j in 1:nrow(distance_matrix)){
|
|
| 173 |
+# # for (k in 1:ncol(distance_matrix)){
|
|
| 174 |
+# # value <- |
|
| 175 |
+# # sqrt((KEGG_mappings$Xcoord[KEGG_mappings$entryID == |
|
| 176 |
+# # colnames(distance_matrix)[k]][1] |
|
| 177 |
+# # - KEGG_mappings$Xcoord[KEGG_mappings$entryID == |
|
| 178 |
+# # rownames(distance_matrix)[j]][1])^2 |
|
| 179 |
+# # + (KEGG_mappings$Ycoord[KEGG_mappings$entryID == |
|
| 180 |
+# # colnames(distance_matrix)[k]][1] |
|
| 181 |
+# # - KEGG_mappings$Ycoord[KEGG_mappings$entryID == |
|
| 182 |
+# # rownames(distance_matrix)[j]][1])^2) |
|
| 183 |
+# # print(value) |
|
| 184 |
+# # distance_matrix[j,k] <- value |
|
| 185 |
+# # } |
|
| 186 |
+# # } |
|
| 187 |
+# # |
|
| 188 |
+# # |
|
| 189 |
+# # } |
|
| 190 |
+# # for(i in 1:nrow(entry_sources)){
|
|
| 191 |
+# # entry_sources$entry2[i] <- list(KEGG_mappings$entryID[KEGG_mappings$entrySYMBOL == entry_sources$entry2symbol[i]]) |
|
| 192 |
+# # } |
|
| 193 |
+# # } |
|
| 194 |
+# entry_targets <- entry_edges[entry_edges$entry1accession == entry_accession & |
|
| 195 |
+# entry_edges$entry2accession %in% KEGG_mappings$entryACCESSION,] |
|
| 196 |
+# new_edges <- rbind(entry_sources, entry_targets) |
|
| 197 |
+# if(nrow(new_edges) > 0) {
|
|
| 198 |
+# new_edges$primary_pathwayID <- strsplit(pathway_KGML@pathwayInfo@name, ":")[[1]][2] |
|
| 199 |
+# new_edges$primary_pathway <- pathway_KGML@pathwayInfo@title |
|
| 200 |
+# |
|
| 201 |
+# max_edge_ID <- max(edges$edgeID) |
|
| 202 |
+# for(j in 1:nrow(new_edges)){
|
|
| 203 |
+# new_edges$edgeID[j] <- max_edge_ID + j |
|
| 204 |
+# } |
|
| 205 |
+# edges <- rbind(edges, new_edges) |
|
| 206 |
+# } |
|
| 207 |
+# print(i) |
|
| 208 |
+# } |
|
| 209 |
+# edges$edge_entry_ID <- paste0(edges$entry1, ":", edges$entry2) |
|
| 210 |
+# edge_ID_sets <- edges$edge_entry_ID[!duplicated(edges$edge_entry_ID)] |
|
| 211 |
+# edge_ID_mapper <- data.frame("edges" = edge_ID_sets,
|
|
| 212 |
+# edgeID = 1:length(edge_ID_sets), |
|
| 213 |
+# stringsAsFactors = FALSE) |
|
| 214 |
+# for(i in 1:nrow(edges)){
|
|
| 215 |
+# edges$edgeID[i] <- edge_ID_mapper$edgeID[match(edges$edge_entry_ID[i], |
|
| 216 |
+# edge_ID_mapper$edges)] |
|
| 217 |
+# } |
|
| 218 |
+# edges <- edges[,names(edges) != "edge_entry_ID"] |
|
| 219 |
+# return(edges) |
|
| 220 |
+# } |
|
| 221 |
+# |
|
| 222 |
+# mtor_plus_mtor <- keggerize_edges(entry_accession = entry_accession, KGML = KGML, |
|
| 223 |
+# KEGG_mappings = KEGG_mappings, |
|
| 224 |
+# edges = edges) |
|
| 225 |
+# #dim(edges) |
|
| 226 |
+# #[1] 581 16 |
|
| 227 |
+# # dim(mtor_plus_mtor) |
|
| 228 |
+# # [1] 757 18 |
|
| 229 |
+# mtor_plus_mtor_plus_deptor <- keggerize_edges(entry_accession = "64798", KGML = KGML, |
|
| 230 |
+# KEGG_mappings = KEGG_mappings, |
|
| 231 |
+# edges = mtor_plus_mtor) |
|
| 232 |
+# |
|
| 233 |
+# |
|
| 234 |
+# |
|
| 235 |
+# |
|
| 236 |
+# |
|
| 237 |
+# na_sources <- KEGG_gene_edges[is.na(KEGG_gene_edges$source),] |
|
| 238 |
+# na_targets<- KEGG_gene_edges[is.na(KEGG_gene_edges$target),] |
|
| 239 |
+# na_sources_and_targets <- KEGG_gene_edges[is.na(KEGG_gene_edges$target)& is.na(KEGG_gene_edges$source),] |
|
| 240 |
+# |
|
| 241 |
+# edges_complete_targets <- KEGG_gene_edges[!is.na(KEGG_gene_edges$target),] |
|
| 242 |
+# complete_edges <- edges_complete_targets[!is.na(edges_complete_targets$source),] |
|
| 243 |
+# |
|
| 244 |
+# # > dim(na_sources) + dim(na_targets) - dim(na_sources_and_targets) |
|
| 245 |
+# # [1] 2176 10 |
|
| 246 |
+# # |
|
| 247 |
+# # > dim(KEGG_gene_edges) - dim(complete_edges) |
|
| 248 |
+# # [1] 2176 0 |
|
| 249 |
+# |
|
| 250 |
+# |
|
| 251 |
+# for(j in 1:nrow(distance_matrix)){
|
|
| 252 |
+# for (k in 1:ncol(distance_matrix)){
|
|
| 253 |
+# distance_matrix[j,k] < |
|
| 254 |
+# sqrt((KEGG_mappings$Xcoord[KEGG_mappings$entryID == |
|
| 255 |
+# colnames(distance_matrix)[1]][1] |
|
| 256 |
+# - KEGG_mappings$Xcoord[KEGG_mappings$entryID == |
|
| 257 |
+# rownames(distance_matrix)[1]][1])^2 |
|
| 258 |
+# + (KEGG_mappings$Ycoord[KEGG_mappings$entryID == |
|
| 259 |
+# colnames(distance_matrix)[1]][1] |
|
| 260 |
+# - KEGG_mappings$Ycoord[KEGG_mappings$entryID == |
|
| 261 |
+# rownames(distance_matrix)[1]][1])^2) |
|
| 262 |
+# } |
|
| 263 |
+# } |
|
| 264 |
+# |
|
| 265 |
+# KEGG_gene_edges <- complete_edges |
|
| 266 |
+# mtor_edges <- KEGG_gene_edges[KEGG_gene_edges$source == "MTOR" | KEGG_gene_edges$target == "MTOR",] |
|
| 267 |
+# |
|
| 268 |
+# unique_mtor_edges <- mtor_edges[!duplicated(mtor_edges),] |
|
| 269 |
+# mtor_edges_all_pathways <- unique_mtor_edges |
|
| 270 |
+# |
|
| 271 |
+# mtor_sources <- mtor_edges_all_pathways$source |
|
| 272 |
+# mtor_sources <- mtor_sources[!duplicated(mtor_sources)] |
|
| 273 |
+# # length(mtor_sources) |
|
| 274 |
+# # [1] 33 |
|
| 275 |
+# mtor_targets <- mtor_edges_all_pathways$target |
|
| 276 |
+# mtor_targets <- mtor_targets[!duplicated(mtor_targets)] |
|
| 277 |
+# # length(mtor_targets) |
|
| 278 |
+# # [1] 26 |
|
| 279 |
+# |
|
| 280 |
+# mtor_KGML <- get_KGML("hsa04150")
|
|
| 281 |
+# mtor_KEGG_mappings <- expand_KEGG_mappings(mtor_KGML) |
|
| 282 |
+# mtor_edges <- expand_KEGG_edges(mtor_KGML, mtor_KEGG_mappings) |
|
| 283 |
+# |
|
| 284 |
+# sources_in_mtor_pathway <- mtor_KEGG_mappings[mtor_KEGG_mappings$entrySYMBOL %in% mtor_sources,] |
|
| 285 |
+# # dim(sources_in_mtor_pathway) |
|
| 286 |
+# # [1] 28 16 |
|
| 287 |
+# targets_in_mtor_pathway <- mtor_KEGG_mappings[mtor_KEGG_mappings$entrySYMBOL %in% mtor_targets,] |
|
| 288 |
+# # dim(targets_in_mtor_pathway) |
|
| 289 |
+# # [1] 19 16 |
|
| 290 |
+# internal_mtor_edges <- mtor_edges_all_pathways[mtor_edges_all_pathways$pathway_code == "path:hsa04150",] |
| 0 | 291 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,37 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/keggerize_edges.R |
|
| 3 |
+\name{keggerize_edges}
|
|
| 4 |
+\alias{keggerize_edges}
|
|
| 5 |
+\title{Add in edges to map documented in other pathways}
|
|
| 6 |
+\usage{
|
|
| 7 |
+keggerize_edges(entry_accession, KGML, KEGG_mappings, edges) |
|
| 8 |
+} |
|
| 9 |
+\arguments{
|
|
| 10 |
+\item{entry_accession}{The Accession # of the pathway entity to 'keggerize'}
|
|
| 11 |
+ |
|
| 12 |
+\item{KGML}{The KGML file of the current pathway}
|
|
| 13 |
+ |
|
| 14 |
+\item{KEGG_mappings}{KEGG mappings for the current pathway}
|
|
| 15 |
+ |
|
| 16 |
+\item{edges}{The expanded edges for the current pathway}
|
|
| 17 |
+} |
|
| 18 |
+\value{
|
|
| 19 |
+A modified expanded edges data frame with additional rows for new |
|
| 20 |
+entries |
|
| 21 |
+} |
|
| 22 |
+\description{
|
|
| 23 |
+For a specific pathway entity(gene), search KEGG databases |
|
| 24 |
+to see if it has any other documented relationships in KEGG. |
|
| 25 |
+expand_KEGG_edges |
|
| 26 |
+} |
|
| 27 |
+\examples{
|
|
| 28 |
+\dontrun{
|
|
| 29 |
+KGML <- get_KGML("hsa04150")
|
|
| 30 |
+KEGG_mappings <- expand_KEGG_mappings(KGML) |
|
| 31 |
+edges <- expand_KEGG_edges(KGML, KEGG_mappings) |
|
| 32 |
+entry_accession <- "2475" |
|
| 33 |
+mtor_plus_mtor <- keggerize_edges(entry_accession = entry_accession, |
|
| 34 |
+ KGML = KGML,KEGG_mappings = KEGG_mappings, |
|
| 35 |
+ edges = edges) } |
|
| 36 |
+ |
|
| 37 |
+} |
