From 48b95e2c573e2cb4398ae0d74a2d497d621be264 Mon Sep 17 00:00:00 2001
From: ThomasKAtkins <32600420+ThomasKAtkins@users.noreply.github.com>
Date: Wed, 26 Mar 2025 14:29:18 -0400
Subject: [PATCH] Added log transformation argument for color scale

---
 DESCRIPTION   | 2 +-
 R/utilities.R | 9 +++++++--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a271543..899abd4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -12,7 +12,7 @@ Imports:
     DOSE (>= 3.31.2),
     ggfun (>= 0.1.7),
     ggnewscale,
-    ggplot2,
+    ggplot2 (>= 3.5.0),
     ggrepel (>= 0.9.0),
     ggtangle (>= 0.0.5),
     graphics,
diff --git a/R/utilities.R b/R/utilities.R
index 241495b..8a040e6 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -19,7 +19,7 @@ get_enrichplot_color <- function(n = 2) {
 
     if (n != 2 && n != 3) stop("'n' should be 2 or 3")
 
-    colors = c("#e06663", "#327eba")
+    colors = c("#ec2b54", "#005087")
     if (n == 2) return(colors)
 
     if (n == 3) return(c(colors[1], "white", colors[2]))
@@ -34,6 +34,7 @@ get_enrichplot_color <- function(n = 2) {
 ##' @param name name of the color legend
 ##' @param .fun force to use user provided color scale function
 ##' @param reverse whether reverse the color scheme, default is TRUE as it is more significant for lower pvalue
+##' @param log_transform whether or not to log-transform the color scale, default is TRUE as p-values operate over a wide range of orders of magnitude
 ##' @param ... additional parameter that passed to the color scale function
 ##' @return a color scale
 ##' @importFrom ggplot2 scale_fill_continuous
@@ -42,7 +43,8 @@ get_enrichplot_color <- function(n = 2) {
 ##' @importFrom ggplot2 scale_color_gradientn
 ##' @export
 set_enrichplot_color <- function(colors = get_enrichplot_color(2), 
-                                type = "color", name = NULL, .fun = NULL, reverse=TRUE, ...) {
+                                type = "color", name = NULL, .fun = NULL, 
+                                reverse = TRUE, log_transform = TRUE, ...) {
 
     type <- match.arg(type, c("color", "colour", "fill"))
     if (!reverse) colors = rev(colors)
@@ -77,6 +79,9 @@ set_enrichplot_color <- function(colors = get_enrichplot_color(2),
 
     params$guide <- guide_colorbar(reverse=reverse, order=1)
     params$name <- name # no legend name setting by default as 'name = NULL'
+    if (log_transform) {
+        params$transform <- "log10"
+    }
 
     params <- modifyList(params, list(...))