support for high resolution image

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ggkegg
 Type: Package
 Title: KEGG pathway visualization by ggplot2
-Version: 1.1.10
+Version: 1.1.11
 Authors@R: person("Noriaki", "Sato", email = "nori@hgc.jp", role = c("cre", "aut"))
 Description: This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.
 License: MIT + file LICENSE

R/overlay_functions.R

@@ -16,6 +16,7 @@
 #' Override `adjust`
 #' @param use_cache whether to use BiocFileCache()
 #' @param interpolate parameter in annotation_raster()
+#' @param high_res Use high resolution (2x) image for the overlay
 #' @import magick
 #' @return ggplot2 object
 #' @export
@@ -34,7 +35,8 @@ overlay_raw_map <- function(pid=NULL, directory=NULL,
                             adjust_manual_y=NULL,
                             clip=FALSE,
                             use_cache=TRUE,
-                            interpolate=TRUE) {
+                            interpolate=TRUE,
+                            high_res=FALSE) {
     structure(list(pid=pid,
                     transparent_colors=transparent_colors,
                     adjust=adjust,
@@ -43,7 +45,8 @@ overlay_raw_map <- function(pid=NULL, directory=NULL,
                     adjust_manual_y=adjust_manual_y,
                     directory=directory,
                     use_cache=use_cache,
-                    interpolate=interpolate),
+                    interpolate=interpolate,
+                    high_res=high_res),
             class="overlay_raw_map")
 }
 
@@ -65,16 +68,26 @@ ggplot_add.overlay_raw_map <- function(object, plot, object_name) {
     if (is.null(object$pid)) {
         infer <- plot$data$pathway_id |> unique()
         object$pid <- infer[!is.na(infer)]
+        if (object$high_res) {
+        	## Convert to reference ID
+        	cur_id <- object$pid
+        	object$pid <- paste0("map",
+        		regmatches(cur_id, gregexpr("[[:digit:]]+", cur_id)) %>% unlist())
+        }
     }
     if (!grepl("[[:digit:]]", object$pid)) {
         warning("Looks like not KEGG ID for pathway")
         return(1)
     }
     ## Return the image URL, download and cache
-    url <- paste0(as.character(pathway(object$pid,
-                                    use_cache=object$use_cache,
-                                    directory=object$directory,
-                                    return_image=TRUE)))
+    ## From 1.1.10
+    url <- paste0("https://rest.kegg.jp/get/",object$pid,"/image")
+    if (object$high_res) {
+    	if (!startsWith(object$pid, "map")) {
+    		stop("High resolution image can be obtained for the reference pathway.")
+    	}
+    	url <- paste0(url, "2x")
+    }
     if (object$use_cache) {
         bfc <- BiocFileCache()
         path <- bfcrpath(bfc, url)