From 45a8204a899e620918ee8766599e0f3673b6cf3c Mon Sep 17 00:00:00 2001
From: Ashastry2 <amulyashastry@gmail.com>
Date: Mon, 28 Oct 2024 10:14:25 -0400
Subject: [PATCH 1/2] Fixes notes about DataFrame

---
 DESCRIPTION        | 3 +--
 NAMESPACE          | 1 +
 R/plotSCEHeatmap.R | 5 +++++
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 50abc5683..dd88b77b6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -121,8 +121,7 @@ Imports:
     scuttle,
     utils,
     stats,
-    zellkonverter,
-    tidyr
+    zellkonverter
 RoxygenNote: 7.3.2
 Suggests:
     testthat,
diff --git a/NAMESPACE b/NAMESPACE
index c069ce18e..9862e0d55 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -273,6 +273,7 @@ import(eds)
 importFrom(BiocParallel,SerialParam)
 importFrom(ComplexHeatmap,anno_barplot)
 importFrom(S4Vectors,"metadata<-")
+importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,"counts<-")
 importFrom(SingleCellExperiment,"reducedDim<-")
diff --git a/R/plotSCEHeatmap.R b/R/plotSCEHeatmap.R
index ee78d12ff..4fc55bc91 100644
--- a/R/plotSCEHeatmap.R
+++ b/R/plotSCEHeatmap.R
@@ -113,6 +113,8 @@
 #' @importFrom grid gpar
 #' @importFrom ComplexHeatmap anno_barplot
 #' @importFrom rlang .data
+#' @importFrom S4Vectors DataFrame
+#' 
 #' 
 plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,
                            doLog = FALSE, featureIndex = NULL, cellIndex = NULL,
@@ -380,6 +382,9 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,
       stop('Breaks of `colorScheme` do not match with `trim`.')
   }
   
+  # Avoid documentation error by setting these values to NULL
+  # removed NOTE about namespaces.
+  n<-value<-NULL
   
   ### Generate HeatmapAnnotation object
   ca <- NULL

From 0d1d468f85ec33fdc78a8c46d65ad23de3dcf1f5 Mon Sep 17 00:00:00 2001
From: Ashastry2 <amulyashastry@gmail.com>
Date: Mon, 28 Oct 2024 10:44:55 -0400
Subject: [PATCH 2/2] Fixes NAMESPACE error

---
 R/plotSCEHeatmap.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/plotSCEHeatmap.R b/R/plotSCEHeatmap.R
index 4fc55bc91..f76c307bb 100644
--- a/R/plotSCEHeatmap.R
+++ b/R/plotSCEHeatmap.R
@@ -290,7 +290,7 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,
    #colData(SCE) <- colData(SCE)[,c(aggregateCol),drop=FALSE] ##change
     
     temp_df<-as.data.frame(colData(SCE)[,c(aggregateCol),drop=FALSE]) %>% 
-      unite("new_colnames",1:ncol(.),sep = "_",remove = FALSE) %>% 
+      unite("new_colnames",1:ncol(.data),sep = "_",remove = FALSE) %>% 
       remove_rownames() %>% 
     #  mutate(aggregated_column = new_colnames) %>%
     #  dplyr::select(new_colnames, aggregated_column) %>%