cleanup code

R/emapplot_utilities.R

@@ -217,36 +217,6 @@ node_add_alpha <- function(p, hilight_category, hilight_gene, alpha_nohilight, a
 
 
 
-# adj_layout <- function(g, layout, coords) {
-#     if (!is.null(layout)) {
-#         p <- ggraph(g, layout=layout)
-#     } else {
-#         p <- ggraph(g, layout="nicely")
-#         if (!is.null(coords)) {
-#             # ggData <- p$data
-#             # rownames(ggData) <- ggData$name
-#             # ids <- intersect(ggData$name, rownames(coords))
-#             # if (length(ids) > 0) {
-#             #     coords <- coords[ids, ]
-#             #     ggData[ids, "x"] <- coords$x
-#             #     ggData[ids, "y"] <- coords$y
-#             #     rownames(ggData) <- rownames(p$data)
-#             #     p$data <- ggData 
-#             ids <- match(p$data$name, rownames(coords))
-#             ids <- ids[!is.na(ids)]
-#             if (length(ids) > 0) {
-#                 p$data[ids, "x"] <- coords$x
-#                 p$data[ids, "y"] <- coords$y
-#             } else {
-#                 wm <-  paste("Invalid coords parameter, the rownames of the coords", 
-#                     "must be the term names found in the emapplot diagram")
-#                 warning(wm)
-#             }         
-#         }
-#     }
-#     return(p)
-# }
-