From 1dff633b1cce0693c1b52734c98659b5da70c42e Mon Sep 17 00:00:00 2001
From: TuomasBorman <tvborm@utu.fi>
Date: Mon, 21 Oct 2024 22:01:33 +0300
Subject: [PATCH] up

---
 vignettes/case_study.qmd | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/vignettes/case_study.qmd b/vignettes/case_study.qmd
index 604ed88..e1232f7 100644
--- a/vignettes/case_study.qmd
+++ b/vignettes/case_study.qmd
@@ -61,6 +61,7 @@ knitr::opts_chunk$set(
 
 ```{r}
 #| label: setup
+#| output: false
 
 # List of packages that we need
 packages <- c(
@@ -594,7 +595,7 @@ p <- plotExpression(
     altExp(mae[[1]], "relevant"),
     features = rownames(altExp(mae[[1]], "relevant")),
     x = "mass_scaled",
-    assay.type = "counts",
+    assay.type = "standardize",
     scales = "free"
     ) +
   geom_smooth(method = "lm")