getter functions documentation

R/module_functions.R

@@ -28,10 +28,25 @@ setMethod("show",
     }
 )
 
+
+#' get_module_attribute
+#' 
+#' get slot from `kegg_module` class
+#' 
+#' @param x kegg_module class object
+#' @param attribute pass to get_module_attribute
+#' @return attribute of kegg_module
 #' @export
 setGeneric("get_module_attribute",
-    function(x, ...) standardGeneric("get_module_attribute"))
+    function(x, attribute) standardGeneric("get_module_attribute"))
 
+#' get_module_attribute
+#' 
+#' get the kegg_module class attribute
+#' 
+#' @param x kegg_module class object
+#' @param attribute slot name
+#' @return attribute of kegg_module
 setMethod("get_module_attribute", "kegg_module",
     function(x, attribute) attr(x, attribute))
 

R/network_functions.R

@@ -22,10 +22,24 @@ setMethod("show",
     }
 )
 
+#' get_network_attribute
+#' 
+#' get slot from `kegg_network` class
+#' 
+#' @param x kegg_network class object
+#' @param attribute pass to get_network_attribute
+#' @return attribute of kegg_network
 #' @export
 setGeneric("get_network_attribute",
-    function(x, ...) standardGeneric("get_network_attribute"))
+    function(x, attribute) standardGeneric("get_network_attribute"))
 
+#' get_network_attribute
+#' 
+#' get the kegg_network class attribute
+#' 
+#' @param x kegg_network class object
+#' @param attribute slot name
+#' @return attribute of kegg_module
 setMethod("get_network_attribute", "kegg_network",
     function(x, attribute) attr(x, attribute))
 

R/pathway_functions.R

@@ -349,14 +349,15 @@ process_line <- function(g, invert_y=TRUE, verbose=FALSE) {
 #' 
 #' @param g graph
 #' @param single_edge discard one edge when edge type is `reversible`
+#' @param keep_no_reaction keep edges not related to reaction
 #' @importFrom tidygraph bind_nodes bind_edges
 #' @export
 #' @return tbl_graph
 #' @examples
 #' gm_test <- create_test_pathway(line=TRUE)
 #' test <- process_reaction(gm_test)
 #' 
-process_reaction <- function(g, single_edge=FALSE) {
+process_reaction <- function(g, single_edge=FALSE, keep_no_reaction=TRUE) {
     ## This is perhaps dirty ways to obtain edges. Perhaps directly
     ## parsing substrate -> product would be reasonable with
     ## assigning "reversible" and "irreversible"
@@ -366,6 +367,7 @@ process_reaction <- function(g, single_edge=FALSE) {
 
     ## Obtain raw edges
     eds <- g |> activate("edges") |> data.frame()
+    no_reacs <- eds[is.na(eds$reaction_id),]
     reacs <- eds$reaction_id |> unique()
     reacs <- reacs[!is.na(reacs)]
     ## Prepare new edges
@@ -427,6 +429,15 @@ process_reaction <- function(g, single_edge=FALSE) {
     new_eds <- new_eds[!duplicated(new_eds),]
     new_eds$from <- as.integer(new_eds$from)
     new_eds$to <- as.integer(new_eds$to)
+    if (keep_no_reaction) {
+        for (coln in colnames(no_reacs)) {
+            if (!coln %in% colnames(new_eds)) {
+                new_eds[[coln]] <- NA
+            }
+        }
+        new_eds <- new_eds[,colnames(no_reacs)]
+        new_eds <- rbind(no_reacs, new_eds)
+    }
     new_g <- tbl_graph(nodes=nds, edges=new_eds)
     new_g
 }