v1.3.4 various updates on finding names in node

Author: noriakis

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ggkegg
 Type: Package
 Title: Analyzing and visualizing KEGG information using the grammar of graphics
-Version: 1.3.3
+Version: 1.3.4
 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/ggkegg.R

@@ -217,6 +217,9 @@ ggkegg <- function(pid,
 #' @param white_background fill background color white
 #' @param how how to match the node IDs with the queries 'any' or 'all'
 #' @param infer if TRUE, append the prefix to queried IDs based on pathway ID
+#' @param name name of column to match for
+#' @param sep separater for name, default to " "
+#' @param remove_dot remove "..." in the name
 #' @export
 #' @examples
 #' if (require("clusterProfiler")) {
@@ -227,7 +230,8 @@ ggkegg <- function(pid,
 #' @return ggraph with overlaid KEGG map
 #' 
 rawMap <- function(enrich, pathway_number=1, pid=NULL,
-    fill_color="red", how="any", white_background=TRUE, infer=FALSE) {
+    fill_color="red", how="any", white_background=TRUE, infer=FALSE,
+    name="name", sep=" ", remove_dot=TRUE) {
 
     number <- length(enrich)
     if (length(fill_color) != number) {
@@ -257,17 +261,17 @@ rawMap <- function(enrich, pathway_number=1, pid=NULL,
         qqcat("Changing prefix of pathway ID from map to ko\n")
         pid <- gsub("map","ko",pid)
     }
-
     if (number == 1) {
-        g <- pathway(pid) |> mutate(cp=append_cp(enrich, how=how, pid=pid, infer=infer))
+        g <- pathway(pid) %>% mutate(cp=append_cp(!!enrich, how=!!how, pid=!!pid, infer=!!infer,
+            name=!!name, sep=!!sep, remove_dot=!!remove_dot))
         gg <- ggraph(g, layout="manual", x=.data$x, y=.data$y)+
             geom_node_rect(fill=fill_color, aes(filter=.data$cp))+
             overlay_raw_map()+theme_void()
     } else {
         g <- pathway(pid)
         for (i in seq_len(number)) {
             g <- g  |> mutate(!!paste0("cp",i) :=append_cp(enrich[[i]],
-                how=how, pid=pid, infer=infer))
+                how=!!how, pid=!!pid, infer=!!infer, name=!!name, sep=!!sep, remove_dot=!!remove_dot))
         }
         V(g)$space <- V(g)$width/number
         gg <- ggraph(g, layout="manual", x=.data$x, y=.data$y)
@@ -299,12 +303,14 @@ rawMap <- function(enrich, pathway_number=1, pid=NULL,
 #' 
 #' @param values named vector, or list of them
 #' @param pid pathway id
-#' @param column column name on node table of the graph
 #' @param white_background fill background color white
 #' @param how how to match the node IDs with the queries 'any' or 'all'
 #' @param auto_add automatically add prefix based on pathway prefix
 #' @param man_graph provide manual tbl_graph
 #' @param show_type type to be shown
+#' @param column name of column to match for
+#' @param sep separater for name, default to " "
+#' @param remove_dot remove "..." in the name
 #' typically, "gene", "ortholog", or "compound"
 #' @export
 #' @examples
@@ -314,7 +320,8 @@ rawMap <- function(enrich, pathway_number=1, pid=NULL,
 #' @return ggraph with overlaid KEGG map
 #' 
 rawValue <- function(values, pid=NULL, column="name", show_type="gene",
-    how="any", white_background=TRUE, auto_add=FALSE, man_graph=NULL) {
+    how="any", white_background=TRUE, auto_add=FALSE, man_graph=NULL,
+    sep=" ", remove_dot=TRUE) {
     if (is.list(values)) {
         number <- length(values)
         if (auto_add) {
@@ -337,7 +344,7 @@ rawValue <- function(values, pid=NULL, column="name", show_type="gene",
     }
     if (number == 1) {
         g <- pgraph |> mutate(value=node_numeric(values,
-            name=column, how=how))
+            name=column, how=how, sep=sep, remove_dot=remove_dot))
         gg <- ggraph(g, layout="manual", x=.data$x, y=.data$y)+
             geom_node_rect(aes(fill=.data$value,
                                 filter=.data$type %in% show_type))+