From aa59828ce5dc723ab2cf94c997654e0c0f23f3ef Mon Sep 17 00:00:00 2001
From: TuomasBorman <tvborm@utu.fi>
Date: Wed, 9 Oct 2024 15:00:48 +0300
Subject: [PATCH] up

---
 R/plotAbundance.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/plotAbundance.R b/R/plotAbundance.R
index e3a6bed..63d2574 100644
--- a/R/plotAbundance.R
+++ b/R/plotAbundance.R
@@ -222,6 +222,9 @@ setMethod("plotAbundance", signature = c("SummarizedExperiment"), function(
             "the names.\nThe following names are not allowed: '",
             paste0(not_allowed, collapse = "', '"), "'", call. = FALSE)
     }
+    # Leave order.col.by out of the comparison, if it specifies a feature
+    order.col.by <- if(order.col.by %in% colnames(colData(x))) order.col.by else
+        NULL
     all_vars <- unique(c(order.col.by, col.var))
     if( sum(colnames(colData(x)) %in% all_vars) != length(all_vars) ){
         stop("colData(x) must have unique colnames.", call. = FALSE)