use_cache in highlight_entities

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ggkegg
 Type: Package
 Title: KEGG pathway visualization by ggplot2
-Version: 0.99.3
+Version: 0.99.4
 Authors@R: person("Noriaki", "Sato", email = "[email protected]", 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/highlight_functions.R

@@ -15,6 +15,7 @@
 #' @param show_type entitie type, default to 'gene'
 #' @param fill_color highlight color, default to 'tomato'
 #' @param legend_name legend name, NULL to suppress
+#' @param use_cache use cache or not
 #' @return overlaid map
 #' @examples
 #' highlight_entities("hsa04110", c("CDKN2A"), legend_name="interesting")
@@ -23,8 +24,8 @@
 highlight_entities <- function(pathway, set, how="any",
 	name="graphics_name", sep=",", no_sep=FALSE,
 	show_type="gene", fill_color="tomato",
-	legend_name=NULL) {
-	graph <- pathway(pathway, use_cache=TRUE)
+	legend_name=NULL, use_cache=FALSE) {
+	graph <- pathway(pathway, use_cache=use_cache)
 	x <- get.vertex.attribute(graph, name)
     vec <- vapply(seq_along(x), function(xn) {
         if (no_sep) {