See if importing SummarizedExperiment fixes the issue

LieberInstitute · Oct 24, 2023 · 5618f5d · 5618f5d
1 parent a92e592
commit 5618f5d
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Showing 3 changed files with 13 additions and 11 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -24,4 +24,5 @@ Imports:
     viridisLite,
     spatialLIBD,
     ggplot2,
-    SpatialExperiment
+    SpatialExperiment,
+    SummarizedExperiment
diff --git a/NAMESPACE b/NAMESPACE
@@ -2,6 +2,7 @@
 
 export(spot_plot)
 import(SpatialExperiment)
+import(SummarizedExperiment)
 import(ggplot2)
 import(spatialLIBD)
 import(viridisLite)
diff --git a/R/spot_plot.R b/R/spot_plot.R
@@ -37,7 +37,7 @@
 #'
 #' @export
 #' @author Nicholas J. Eagles
-#' @import viridisLite spatialLIBD ggplot2 SpatialExperiment
+#' @import viridisLite spatialLIBD ggplot2 SpatialExperiment SummarizedExperiment
 #' 
 #' @examples 
 #' 
@@ -79,15 +79,15 @@ spot_plot <- function(
     }
 
     #   State assumptions about columns expected to be in the colData
-    # expected_cols <- c("array_row", "array_col", "sample_id", "exclude_overlapping")
-    # if (!all(expected_cols %in% colnames(colData(spe)))) {
-    #     stop(
-    #         sprintf(
-    #             'Missing at least one of the following colData columns: "%s"',
-    #             paste(expected_cols, collapse = '", "')
-    #         )
-    #     )
-    # }
+    expected_cols <- c("array_row", "array_col", "sample_id", "exclude_overlapping")
+    if (!all(expected_cols %in% colnames(colnames(colData(spe))))) {
+        stop(
+            sprintf(
+                'Missing at least one of the following colData columns: "%s"',
+                paste(expected_cols, collapse = '", "')
+            )
+        )
+    }
 
     #   Subset to specific sample ID, and ensure overlapping spots are dropped
     subset_cols <- (spe$sample_id == sample_id) &