update to use inherets() for SPE check across functions

MicTott · Dec 24, 2024 · f0df01e · f0df01e
1 parent 9f16259
commit f0df01e
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Showing 4 changed files with 12 additions and 12 deletions.
diff --git a/R/findArtifacts.R b/R/findArtifacts.R
@@ -60,8 +60,9 @@ findArtifacts <- function(
     shape = "hexagonal", log = TRUE, name = "artifact", var_output = TRUE) {
 
   # ===== Validity checks =====
-  if (!("SpatialExperiment" %in% class(spe))) {
-    stop("Input data must be a SpatialExperiment object.")
+  # Check if 'spe' is (or inherits from) SpatialExperiment
+  if (!inherits(spe, "SpatialExperiment")) {
+    stop("Input data must be a SpatialExperiment or inherit from SpatialExperiment.")
   }
 
   if (!all(mito_percent %in% colnames(colData(spe)))) {

diff --git a/R/flagVisiumOutliers.R b/R/flagVisiumOutliers.R
@@ -33,10 +33,9 @@
 #'
 flagVisiumOutliers <- function(spe) {
 
-  # Check if 'spe' is a SpatialExperiment object
-  # Check if 'spe' is a valid object with required components
-  if (!("SpatialExperiment" %in% class(spe))) {
-    stop("Input data must be either a SpatialExperiment")
+  # Check if 'spe' is (or inherits from) SpatialExperiment
+  if (!inherits(spe, "SpatialExperiment")) {
+    stop("Input data must be a SpatialExperiment or inherit from SpatialExperiment.")
   }
 
   # Load the biased_spots dataset

diff --git a/R/localOutliers.R b/R/localOutliers.R
@@ -59,9 +59,9 @@ localOutliers <- function(
     log = TRUE, cutoff = 3, workers=1) {
 
   # ===== Validity checks =====
-  # Check if 'spe' is a valid object with required components
-  if (!("SpatialExperiment" %in% class(spe) || "SingleCellExperiment" %in% class(spe))) {
-    stop("Input data must be either a SpatialExperiment or SingleCellExperiment object.")
+  # Check if 'spe' is (or inherits from) SpatialExperiment
+  if (!inherits(spe, "SpatialExperiment")) {
+    stop("Input data must be a SpatialExperiment or inherit from SpatialExperiment.")
   }
 
   # Validate 'direction'

diff --git a/R/localVariance.R b/R/localVariance.R
@@ -62,9 +62,9 @@ localVariance <- function(spe, n_neighbors = 36,
                           workers = 1) {
 
   # ===== Validity checks =====
-  # Check if 'spe' is a valid object with required components
-  if (!("SpatialExperiment" %in% class(spe))) {
-    stop("Input data must be a SpatialExperiment object.")
+  # Check if 'spe' is (or inherits from) SpatialExperiment
+  if (!inherits(spe, "SpatialExperiment")) {
+    stop("Input data must be a SpatialExperiment or inherit from SpatialExperiment.")
   }
 
   # Validate 'metric' is a character vector