Merge remote-tracking branch 'origin/main' into devel

DESCRIPTION

@@ -22,5 +22,5 @@ RoxygenNote: 7.2.3
 biocViews: Pathways, DataImport, KEGG
 VignetteBuilder: knitr
 URL: https://github.com/noriakis/ggkegg
-BugReport: https://github.com/noriakis/ggkegg/issues
+BugReports: https://github.com/noriakis/ggkegg/issues
 Config/testthat/edition: 3

NAMESPACE

@@ -6,6 +6,7 @@ S3method(ggplot_add,overlay_raw_map)
 export(append_cp)
 export(append_label_position)
 export(assign_deseq2)
+export(carrow)
 export(combine_with_bnlearn)
 export(convert_id)
 export(create_test_module)
@@ -36,7 +37,6 @@ export(node_matrix)
 export(node_numeric)
 export(obtain_sequential_module_definition)
 export(overlay_raw_map)
-export(parseMetaCycPathwayReactions)
 export(pathway)
 export(pathway_abundance)
 export(pathway_info)

R/network_functions.R

@@ -164,7 +164,7 @@ network_graph <- function (kne, type="definition") {
                 paste0(vs[,1],"_",nn,"_",kne@ID) ,vs[,1])
             vs <- do.call(rbind, lapply(vs[,1], function(j) {
                 c(j,bln,"in_block")
-            }))
+            })) |> data.frame() |> `colnames<-`(c("from","to","type"))
             list(rbind(es, vs), nn)
         }
     })

R/utils.R

@@ -635,7 +635,18 @@ obtain_map_and_cache <- function(org, pid=NULL, colon=TRUE) {
   convert_vec
 }
 
-
+#' carrow
+#' 
+#' make closed type arrow
+#' @param length arrow length in unit()
+#' @export
+#' @examples
+#' carrow()
+#' @return arrow()
+#' 
+carrow <- function(length=unit(2,"mm")) {
+	arrow(length=length, type="closed")
+}
 
 #' combine_with_bnlearn
 #' 

README.md

@@ -16,6 +16,13 @@ The detailed documentation is
 
 ## Installation
 
+Using `BiocManager`:
+
+``` r
+BiocManager::install("ggkegg")
+```
+Using `devtools`:
+
 ``` r
 devtools::install_github("noriakis/ggkegg")
 ```