From 67b61d5f06b994c8de22d5b63194436e9b3c2d3f Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Sat, 28 Oct 2023 18:09:08 +1100
Subject: [PATCH] I cannot have calculate_for_pca_dimensions bigger than top

---
 R/functions.R    | 2 +-
 R/functions_SE.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/functions.R b/R/functions.R
index d55fde13..09937d08 100755
--- a/R/functions.R
+++ b/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) & (
diff --git a/R/functions_SE.R b/R/functions_SE.R
index 5f067aec..1e671c03 100755
--- a/R/functions_SE.R
+++ b/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