From e20a06e67ad6405d174a5652b2e32297eda93783 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 26 Mar 2026 02:20:34 +0000
Subject: [PATCH 1/2] Initial plan


From cdac902cfb1668f40f54199b57aa0fcbe3a36f95 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 26 Mar 2026 02:22:55 +0000
Subject: [PATCH 2/2] Fix patchwork::plot_layout unqualified usage in Harmony.R

Co-authored-by: phoman14 <21298645+phoman14@users.noreply.github.com>
Agent-Logs-Url: https://github.com/NIDAP-Community/SCWorkflow/sessions/9de58a68-7e10-4304-87be-6efae85ad882
---
 DESCRIPTION | 1 +
 NAMESPACE   | 1 +
 R/Harmony.R | 1 +
 3 files changed, 3 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index e74cdc5..38364a5 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -92,4 +92,5 @@ Imports:
     htmlwidgets,
     scDblFinder
     , BiocParallel
+    , patchwork
 Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
index 561bba6..49bc794 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -139,6 +139,7 @@ importFrom(gridExtra,arrangeGrob)
 importFrom(gridExtra,tableGrob)
 importFrom(htmlwidgets,saveWidget)
 importFrom(magrittr,"%>%")
+importFrom(patchwork,plot_layout)
 importFrom(plotly,as_widget)
 importFrom(plotly,ggplotly)
 importFrom(plotly,plot_ly)
diff --git a/R/Harmony.R b/R/Harmony.R
index 93824af..619eb1f 100644
--- a/R/Harmony.R
+++ b/R/Harmony.R
@@ -23,6 +23,7 @@
 #' @import gridExtra
 #' @import RColorBrewer
 #' @import ggplot2
+#' @importFrom patchwork plot_layout
 #'   
 #' @export
 #' @examples