From c152b3b0994f4a2fa2a929a71cd5eb9512e8cbca Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 18 Mar 2026 01:38:39 +0000
Subject: [PATCH 1/2] Initial plan


From 8c18f4697dc03e01ac0994531513e18b25d7c4bc Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 18 Mar 2026 01:39:38 +0000
Subject: [PATCH 2/2] Fix trailing comma in knitr chunk header in
 SCWorkflow-Visualizations.Rmd

Co-authored-by: phoman14 <21298645+phoman14@users.noreply.github.com>
---
 vignettes/SCWorkflow-Visualizations.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/SCWorkflow-Visualizations.Rmd b/vignettes/SCWorkflow-Visualizations.Rmd
index 14fcc6f..a0cea4c 100644
--- a/vignettes/SCWorkflow-Visualizations.Rmd
+++ b/vignettes/SCWorkflow-Visualizations.Rmd
@@ -331,7 +331,7 @@ The function supports both **Frequency** (percent) and **Counts** (absolute cell
 The method first aggregates metadata by annotation and group to compute percentages and counts. It then links these summaries to sample-level metadata and generates a composition-focused barplot for sample-level variability. Together, these plots help distinguish overall compositional shifts from replicate-level dispersion.
 
 
-```{r,eval=run_Chunks,}
+```{r,eval=run_Chunks}
 
 FigOut=compareCellPopulations(
             object=Anno_SO$object,