From ae05dce69ad71dcf43aa9e5752c4336508ea483f Mon Sep 17 00:00:00 2001
From: Emma Lipinski <112364984+emmalipinski@users.noreply.github.com>
Date: Fri, 10 Apr 2026 10:19:07 -0400
Subject: [PATCH] Change color palette in genophenogram.R

Changed red to green and blue to purple to reflect MaveDB colors
---
 R/genophenogram.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/genophenogram.R b/R/genophenogram.R
index 511570a..a0d12e7 100644
--- a/R/genophenogram.R
+++ b/R/genophenogram.R
@@ -161,10 +161,10 @@ genophenogram <- function(wt.aa, pos, mut.aa, score, syn.med, stop.med,
 	syn.top <- syn.med+(syn.med-stop.med)
 	cm <- colmap(
 		valStops=c(stop.med, neutral.bottom, neutral.top, syn.top), 
-		colStops=c("royalblue3","white","white","firebrick3")
+		colStops=c("mediumorchid4","white","white","green4")
 	)
 	cols <- cm(score)
-	# colRamp <- colorRampPalette(c("royalblue3","white","firebrick3"))(11)
+	# colRamp <- colorRampPalette(c("mediumorchid4","white","green4"))(11)
 	# scoreToColIdx <- function(score) sapply(score,function(s) {
 	# 	if (is.na(s)) {
 	# 		NA
@@ -435,11 +435,11 @@ genophenogram.nc <- function(wt.nc, pos, mut.nc, score, syn.med, stop.med,
 	syn.top <- syn.med+(syn.med-stop.med)
 	cm <- colmap(
 		valStops=c(stop.med, neutral.bottom, neutral.top, syn.top), 
-		colStops=c("royalblue3","white","white","firebrick3")
+		colStops=c("mediumorchid4","white","white","green4")
 	)
 	cols <- cm(score)
 	
-	# colRamp <- colorRampPalette(c("royalblue3","white","firebrick3"))(11)
+	# colRamp <- colorRampPalette(c("mediumorchid4","white","green4"))(11)
 	# scoreToColIdx <- function(score) sapply(score,function(s) {
 	# 	if (is.na(s)) {
 	# 		NA