From ad92d1602a5a5e103e971ac153daf5326d2d1015 Mon Sep 17 00:00:00 2001
From: Kdreval <k.dreval@gmail.com>
Date: Tue, 30 Jan 2024 11:31:04 -0800
Subject: [PATCH] bug fix: keep only relevant annotations in prettyOncoplot

---
 R/prettyOncoplot.R | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/R/prettyOncoplot.R b/R/prettyOncoplot.R
index d937539..e2d320e 100644
--- a/R/prettyOncoplot.R
+++ b/R/prettyOncoplot.R
@@ -691,6 +691,13 @@ prettyOncoplot = function(maf_df,
         drop = FALSE
     ]
   }
+  
+  # Only keep the annotation colors for the remaining patients
+  for(column in colnames(metadata_df)){
+    remaining <- unique(metadata_df[column] %>% mutate_if(is.factor, as.character)) %>% pull()
+    colours[[column]] <- (colours[column] %>% unname %>% unlist)[remaining]
+  }
+
   ch = ComplexHeatmap::oncoPrint(mat[intersect(genes, genes_kept),patients_kept],
                                  alter_fun = alter_fun,
                                  top_annotation = top_annotation,