From aed3beeaa3d305eb694269545790b9bec5474083 Mon Sep 17 00:00:00 2001 From: Guangchuang Yu Date: Fri, 20 Dec 2024 12:16:30 +0800 Subject: [PATCH] cleanup code --- R/emapplot_utilities.R | 23 +---------------------- 1 file changed, 1 insertion(+), 22 deletions(-) diff --git a/R/emapplot_utilities.R b/R/emapplot_utilities.R index c29052a..ea88101 100644 --- a/R/emapplot_utilities.R +++ b/R/emapplot_utilities.R @@ -215,28 +215,7 @@ node_add_alpha <- function(p, hilight_category, hilight_gene, alpha_nohilight, a } -# ' Get the an ggraph object -# ' -# ' @importFrom ggplot2 ylim -# ' @param x enrichment result. -# ' @param enrichDf A data.frame of enrichment result. -# ' @param mergedEnrichDf A data.frame of merged enrichment result. -# ' @param cex_category Numeric, scale of pie plot. -# ' @param pie Proportion of clusters in the pie chart, one of 'equal' (default) or 'Count'. -# ' @param layout Layout of the map. -# ' @param color a string, the column name of y for nodes colours -# ' @param cex_line Numeric, scale of line width -# ' @param min_edge The minimum similarity threshold for whether -# ' two nodes are connected, should between 0 and 1, default value is 0.2. -# ' @param pair_sim Semantic similarity matrix. -# ' @param method Method of calculating the similarity between nodes, -# ' one of "Resnik", "Lin", "Rel", "Jiang" , "Wang" and -# ' "JC" (Jaccard similarity coefficient) methods. -# ' @param with_edge Logical, if TRUE (the default), draw the edges of the network diagram. -# ' @param hilight_category category nodes to be highlight. -# ' @param alpha_hilight alpha of highlighted nodes. -# ' @param alpha_nohilight alpha of unhighlighted nodes. -# ' @noRd + # build_ggraph <- function(x, enrichDf, mergedEnrichDf, cex_category, pie, # layout, coords, cex_line, min_edge, pair_sim, # method, with_edge, hilight_category, alpha_hilight,