cleanup code

R/emapplot_utilities.R

@@ -216,71 +216,6 @@ node_add_alpha <- function(p, hilight_category, hilight_gene, alpha_nohilight, a
 
 
 
-# build_ggraph <- function(x, enrichDf, mergedEnrichDf, cex_category, pie, 
-#                          layout, coords, cex_line, min_edge, pair_sim,
-#                          method, with_edge, hilight_category, alpha_hilight,
-#                          alpha_nohilight){
-
-#     segment.size <- get_ggrepel_segsize()
-#     geneSets <- setNames(strsplit(as.character(mergedEnrichDf$geneID), "/",
-#                               fixed = TRUE), mergedEnrichDf$ID) 
-
-#     g <- build_emap_graph(enrichDf=mergedEnrichDf,geneSets=geneSets,color="p.adjust",
-#         cex_line=cex_line, min_edge=min_edge, pair_sim = x@termsim, 
-#         method = x@method)
-#     g <- edge_add_alpha(g, hilight_category, alpha_nohilight, alpha_hilight)
-#     # if (!is.null(hilight_category) && length(hilight_category) > 0) {     
-#     #     edges <- attr(E(g), "vnames")
-#     #     E(g)$alpha <- rep(alpha_nohilight, length(E(g)))
-#     #     hilight_edge <- grep(paste(hilight_category, collapse = "|"), edges)
-#     #     E(g)$alpha[hilight_edge] <- min(0.8, alpha_hilight)
-#     #     # E(g)$alpha[hilight_edge] <- alpha_hilight
-#     # } else {
-#     #     E(g)$alpha <- rep(min(0.8, alpha_hilight), length(E(g)))
-#     # }
-#     ## when enrichDf just have one line
-#     if(is.null(dim(enrichDf)) | nrow(enrichDf) == 1) {
-#         title <- enrichDf$Cluster
-#         p <- ggraph(g, "tree") + geom_node_point(color="red", size=5 * cex_category) +
-#             geom_node_text(aes_(label=~name)) + theme_void() +
-#             labs(title=title)
-#         return(p)
-#     }
-
-#     if(is.null(dim(mergedEnrichDf)) | nrow(mergedEnrichDf) == 1) {
-#         p <- ggraph(g, "tree")
-#         ID_Cluster_mat <- prepare_pie_category(enrichDf = enrichDf, pie=pie)
-
-#         ID_Cluster_mat <- cbind(ID_Cluster_mat,1,1,0.1*cex_category)
-#         colnames(ID_Cluster_mat) <- c(colnames(ID_Cluster_mat)[1:(ncol(ID_Cluster_mat)-3)],
-#             "x", "y", "radius")
-
-
-#         p <- p + geom_scatterpie(aes_(x=~x,y=~y,r=~radius), data=ID_Cluster_mat,
-#                 cols=names(ID_Cluster_mat)[1:(ncol(ID_Cluster_mat)-3)],
-#                 color=NA)+
-#             xlim(-3,3) + ylim(-3,3) + coord_equal()+
-#             geom_node_text(aes_(label=~name), repel=TRUE, segment.size = segment.size) +
-#             theme_void()+labs(fill = "Cluster")
-#         return(p)
-
-#     }
-
-#     p <- adj_layout(g = g, layout = layout, coords = coords)    
-#     p$data$alpha <- rep(1, nrow(p$data))
-#     if (!is.null(hilight_category) && length(hilight_category) > 0) {
-#         p$data$alpha <- rep(alpha_nohilight, nrow(p$data))
-#         ii <- match(hilight_category, p$data$name)
-#         p$data$alpha[ii] <- alpha_hilight      
-#     }
-#     ## add edges
-#     if (with_edge & length(E(g)$width) > 0) {
-#         p <- p + geom_edge_link(aes_(width=~I(width), alpha=~I(alpha)),
-#                                 colour='darkgrey', show.legend = FALSE)
-#     }
-#     return(p)
-# }
-
 
 # ' Adjust the layout
 # '