From 66de5bbdffeb8e04a9d948c3fb5014ffebca679b Mon Sep 17 00:00:00 2001
From: lkhilton <laura.k.hilton@gmail.com>
Date: Wed, 18 Dec 2024 15:24:42 -0800
Subject: [PATCH] Retain input factor levels for splitGeneGroups

---
 R/prettyOncoplot.R | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/R/prettyOncoplot.R b/R/prettyOncoplot.R
index be94626..879ef40 100644
--- a/R/prettyOncoplot.R
+++ b/R/prettyOncoplot.R
@@ -907,10 +907,14 @@ prettyOncoplot = function(
     }
 
 
-    if(missing(splitGeneGroups)){
-        row_split = rep("", length(genes))
-    }else{
-        row_split = factor(splitGeneGroups[genes], levels = unique(splitGeneGroups[genes]))
+    if (missing(splitGeneGroups)) {
+        row_split <- rep("", length(genes))
+    } else {
+        if(is.factor(splitGeneGroups)){
+            row_split <- splitGeneGroups[genes]
+        } else(
+            row_split <- factor(splitGeneGroups[genes], levels = unique(splitGeneGroups[genes]))
+        )
     }
 
     if(!missing(groupNames)){