Merge pull request #299 from stemangiola/fix-bug-reduce_dimension

Fix bug reduce dimension

R/functions.R

@@ -2259,7 +2259,7 @@ get_reduced_dimensions_UMAP_bulk <-
            of_samples = TRUE,
            transform = log1p,
            scale = TRUE,
-           calculate_for_pca_dimensions = 20,
+           calculate_for_pca_dimensions = min(20, top),
            ...) {
 
     if(!is.null(calculate_for_pca_dimensions) & (

R/functions_SE.R

@@ -419,7 +419,7 @@ get_reduced_dimensions_UMAP_bulk_SE <-
            of_samples = TRUE,
            transform = log1p,
            scale = NULL, # This is only a dummy argument for making it compatibble with PCA
-           calculate_for_pca_dimensions = 20,
+           calculate_for_pca_dimensions = min(20, top),
            ...) {
     # Comply with CRAN NOTES
     . = NULL

R/methods.R

@@ -1140,6 +1140,17 @@ setGeneric("reduce_dimensions", function(.data,
 	col_names = get_abundance_norm_if_exists(.data, .abundance)
 	.abundance = col_names$.abundance
 
+	# adjust top for the max number of features I have
+	if(top > .data |> distinct(!!.feature) |> nrow()){
+	  warning(sprintf(
+	    "tidybulk says: the \"top\" argument %s is higher than the number of features %s", 
+	    top, 
+	    .data |> distinct(!!.feature) |> nrow()
+	  ))
+
+	  top = min(top, .data |> distinct(!!.feature) |> nrow())
+	}
+
 	# Validate data frame
 	if(do_validate()) {
 	validation(.data, !!.element, !!.feature, !!.abundance)

R/methods_SE.R

@@ -467,6 +467,17 @@ setMethod("cluster_elements",
   if(.abundance |> quo_is_symbolic()) my_assay = quo_name(.abundance)
   else my_assay = get_assay_scaled_if_exists_SE(.data)
 
+  # adjust top for the max number of features I have
+  if(top > nrow(.data)){
+    warning(sprintf(
+      "tidybulk says: the \"top\" argument %s is higher than the number of features %s", 
+      top, 
+      nrow(.data)
+    ))
+
+    top = min(top, nrow(.data))
+  }
+
 	my_assay =
 		.data %>%