From efbfb3d4c8c0de3be56fd3ed21ab267f6e94b9a9 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Fri, 13 Sep 2024 11:21:14 -0400
Subject: [PATCH] chore: cleanup some remaining dep accessors

---
 R/auxiliary_giotto.R        |  5 +----
 R/differential_expression.R | 10 ++--------
 R/spatial_interaction.R     |  5 +----
 3 files changed, 4 insertions(+), 16 deletions(-)

diff --git a/R/auxiliary_giotto.R b/R/auxiliary_giotto.R
index 8fbb26857..cfee9403a 100644
--- a/R/auxiliary_giotto.R
+++ b/R/auxiliary_giotto.R
@@ -1763,10 +1763,7 @@ addCellStatistics <- function(
             )
             cell_metadata[][, c("nr_feats", "perc_feats", "total_expr") := NULL]
             ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-            gobject <- set_cell_metadata(gobject,
-                metadata = cell_metadata,
-                verbose = FALSE
-            )
+            gobject <- setGiotto(gobject, cell_metadata, verbose = FALSE)
             ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
         }
 
diff --git a/R/differential_expression.R b/R/differential_expression.R
index d84d06f53..68c557814 100644
--- a/R/differential_expression.R
+++ b/R/differential_expression.R
@@ -512,10 +512,7 @@ findGiniMarkers <- function(
         )
 
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-        gobject <- set_cell_metadata(gobject,
-            metadata = cell_metadata,
-            verbose = FALSE
-        )
+        gobject <- setGiotto(gobject, cell_metadata, verbose = FALSE)
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
     }
 
@@ -907,10 +904,7 @@ findMastMarkers <- function(
     )
 
     ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-    gobject <- set_cell_metadata(gobject,
-        metadata = cell_metadata,
-        verbose = FALSE
-    )
+    gobject <- setGiotto(gobject, cell_metadata, verbose = FALSE)
     ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
 
diff --git a/R/spatial_interaction.R b/R/spatial_interaction.R
index c009c84a2..1c69275fd 100644
--- a/R/spatial_interaction.R
+++ b/R/spatial_interaction.R
@@ -427,10 +427,7 @@ addCellIntMetadata <- function(gobject,
 
     if (return_gobject == TRUE) {
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-        gobject <- set_cell_metadata(gobject,
-            metadata = cell_metadata,
-            verbose = FALSE
-        )
+        gobject <- setGiotto(gobject, cell_metadata, verbose = FALSE)
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
         ## update parameters used ##