From 071e843f8e8b30d6d2ebfb45d8a5bdae899cfce6 Mon Sep 17 00:00:00 2001
From: salzcamino <salamha@bu.edu>
Date: Tue, 16 Jan 2024 14:24:46 -0500
Subject: [PATCH 1/3] change seuratFindHVG to runSeuratFindHVG

---
 inst/rmarkdown/CeldaCG_Run.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/rmarkdown/CeldaCG_Run.Rmd b/inst/rmarkdown/CeldaCG_Run.Rmd
index 6c38912c..8f510de0 100644
--- a/inst/rmarkdown/CeldaCG_Run.Rmd
+++ b/inst/rmarkdown/CeldaCG_Run.Rmd
@@ -101,7 +101,7 @@ varFilter <-
 if (varFilter) {
   temp.sce <- sce
   temp.sce <-
-    seuratFindHVG(inSCE = temp.sce, useAssay = useAssay)
+    runSeuratFindHVG(inSCE = temp.sce, useAssay = useAssay)
   o <-
     head(
       order(

From 8359aa218fe5a176b892af16f556bc53c8bf2620 Mon Sep 17 00:00:00 2001
From: salzcamino <salamha@bu.edu>
Date: Thu, 4 Apr 2024 12:52:50 -0400
Subject: [PATCH 2/3] require multipanelfigure package in report plotting RMD

---
 inst/rmarkdown/CeldaCG_PlotResults.Rmd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/inst/rmarkdown/CeldaCG_PlotResults.Rmd b/inst/rmarkdown/CeldaCG_PlotResults.Rmd
index 200a79e5..23ee5435 100644
--- a/inst/rmarkdown/CeldaCG_PlotResults.Rmd
+++ b/inst/rmarkdown/CeldaCG_PlotResults.Rmd
@@ -38,6 +38,7 @@ require(knitr)
 require(ggplot2)
 require(gridExtra)
 require(SingleCellExperiment)
+require(multipanelfigure)
 
 sce <- params$sce
 features <- params$features

From ed0bf471c459495cf0f865ca30c2cdc736995f57 Mon Sep 17 00:00:00 2001
From: salzcamino <salamha@bu.edu>
Date: Mon, 8 Apr 2024 15:43:39 -0400
Subject: [PATCH 3/3] change multipanelfigure to gridExtra

---
 inst/rmarkdown/CeldaCG_PlotResults.Rmd | 47 ++++++--------------------
 1 file changed, 10 insertions(+), 37 deletions(-)

diff --git a/inst/rmarkdown/CeldaCG_PlotResults.Rmd b/inst/rmarkdown/CeldaCG_PlotResults.Rmd
index 23ee5435..10e2bc45 100644
--- a/inst/rmarkdown/CeldaCG_PlotResults.Rmd
+++ b/inst/rmarkdown/CeldaCG_PlotResults.Rmd
@@ -38,7 +38,6 @@ require(knitr)
 require(ggplot2)
 require(gridExtra)
 require(SingleCellExperiment)
-require(multipanelfigure)
 
 sce <- params$sce
 features <- params$features
@@ -200,42 +199,16 @@ for (i in seq_len(L)) {
     altExpName = altExpName,
     modules = i
   )
-  # p2 <- moduleHeatmap(
-  #   sce,
-  #   featureModule = i,
-  #   topCells = NULL,
-  #   displayName = displayName,
-  #   moduleLabel = "All cells",
-  #   useRaster = TRUE
-  # )
-  # p3 <- moduleHeatmap(
-  #   sce,
-  #   featureModule = i,
-  #   topCells = 100,
-  #   displayName = displayName,
-  #   moduleLabel = "Top 100 cells",
-  #   useRaster = TRUE
-  # )
-
-  fig <- multi_panel_figure(rows = 2,
-                            columns = 2,
-                            figure_name = paste0("fig", i))
-
-  fig <- fill_panel(fig,
-                    p1,
-                    row = 1,
-                    column = 1:2,
-                    label = "")
-  fig <- fill_panel(fig,
-                    p2[[i]],
-                    row = 2,
-                    column = 1,
-                    label = "")
-  fig <- fill_panel(fig,
-                    p3[[i]],
-                    row = 2,
-                    column = 2,
-                    label = "")
+  
+  plts <- list(p1,p2[[i]],p3[[i]])
+  fig <- gridExtra::marrangeGrob(plts,
+                                nrow = 2,
+                                ncol = 2,
+                                layout_matrix = matrix(c(1,1,2,3),
+                                                       nrow = 2,
+                                                       ncol = 2,
+                                                       byrow = TRUE),
+                                top = NA)
   fig.list[[i]] <- fig
 }
 for (i in seq_len(L)) {