Refactor ggplot method registration to use S7::method directly for improved clarity and compatibility with ggplot2.

Author: stemangiola

R/ggplot2_methods.R

@@ -33,13 +33,13 @@ ggplot.SummarizedExperiment <- function(data=NULL, mapping=aes(),
 # S7 method for ggplot2 4.0.0+ compatibility
 register_s7_ggplot_method <- function() {
     if (requireNamespace("S7", quietly = TRUE)) {
-        S7 <- getNamespace("S7")
         # Check if ggplot and SummarizedExperiment are S7 classes
         is_s7_class <- function(x) inherits(x, "S7_class")
         ggplot_s7 <- tryCatch(get("ggplot", envir = asNamespace("ggplot2")), error = function(e) NULL)
         se_s7 <- tryCatch(get("SummarizedExperiment", envir = asNamespace("SummarizedExperiment")), error = function(e) NULL)
         if (!is.null(ggplot_s7) && !is.null(se_s7) && is_s7_class(ggplot_s7) && is_s7_class(se_s7)) {
-            S7$method(ggplot_s7, se_s7) <- function(data=NULL, mapping=aes(), ..., environment=parent.frame()) {
+            # Use S7::method directly for the assignment
+            S7::method(ggplot_s7, se_s7) <- function(data=NULL, mapping=aes(), ..., environment=parent.frame()) {
                 .cols <- enquos(..., .ignore_empty="all") %>% 
                     map(~ quo_name(.x)) %>% unlist()
                 if (is_sample_feature_deprecated_used(data, .cols)) {