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R/prepare_kegg_hierachy.R

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+# Load the data
+  organism <- "ko"
+  pwMap <- readLines(paste0("https://www.kegg.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=", organism))
+
+# Get the positions of interest
+  lvl_one <- grep("<b>", pwMap)
+
+
+output <- matrix("NA", ncol=3, nrow=length(pwMap))
+current_row <- 1
+for(i in 1:(length(lvl_one)-1) ){
+  col_one <- pwMap[lvl_one[i]]
+  col_one <- gsub("<b>", "", col_one)
+  col_one <- gsub("</b>", "", col_one)
+  curLevel <- 1
+  for(j in (lvl_one[i]+1):(lvl_one[i+1]-1)){
+    if(length(grep("<ul>", pwMap[j])) == 1) {
+      curLevel <- curLevel + 1 
+    } else if(length(grep("</ul>", pwMap[j])) == 1){
+      curLevel <- curLevel - 1
+    } else {
+      if(curLevel==2){
+        col_two <- trimws(pwMap[j])
+      } else if(curLevel==3){
+        col_three <- gsub('&nbsp;&nbsp;<a href=\"/pathway/', '', pwMap[j])
+        col_three <- paste0(organism, strsplit(col_three, organism)[[1]][2])
+        col_three <- gsub('\">', '_', col_three)
+        col_three <- gsub('</a><br>', '', col_three)
+        output[current_row,] <- c(col_one, col_two, col_three)
+        current_row <- current_row + 1
+      }
+    }
+  }
+}
+
+output <- output[1:current_row,]
+output <-cbind(output, sapply(strsplit(output[,3], "_"),"[",1))
+output