Refactor ggplot2 method to simplify compatibility with ggplot2 4.0.0 by removing S7 method registration. Update DESCRIPTION to remove S7 as a suggested dependency and enhance NEWS documentation for clarity.

Author: stemangiola

DESCRIPTION

@@ -46,8 +46,7 @@ Suggests:
     markdown,
     rmarkdown,
     plotly,
-    rbibutils,
-    S7
+    rbibutils
 VignetteBuilder: 
     knitr
 RdMacros:

R/ggplot2_methods.R

@@ -29,30 +29,3 @@ ggplot.SummarizedExperiment <- function(data=NULL, mapping=aes(),
         as_tibble() %>%
         ggplot2::ggplot(mapping=mapping)
 }
-
-# S7 method for ggplot2 4.0.0+ compatibility
-register_s7_ggplot_method <- function() {
-    if (requireNamespace("S7", quietly = TRUE)) {
-        # 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)) {
-            # 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)) {
-                    data <- ping_old_special_column_into_metadata(data)
-                }
-                data %>%
-                    as_tibble() %>%
-                    ggplot2::ggplot(mapping=mapping)
-            }
-        }
-    }
-}
-
-.onLoad <- function(libname, pkgname) {
-    register_s7_ggplot_method()
-}

inst/NEWS.rd

@@ -3,9 +3,8 @@
 
 \section{Changes in version 1.16.0, Bioconductor 3.22 Release}{
 \itemize{
-    \item Prepared for ggplot2 4.0.0 compatibility with S7 methods.
-    \item Added conditional S7 method for ggplot while maintaining S3 method for current ggplot2 versions.
-    \item Added S7 as suggested dependency for future ggplot2 4.0.0 compatibility.
+    \item Updated documentation to properly reflect S3 method structure.
+    \item Simplified ggplot2 compatibility - S3 method continues to work with ggplot2 4.0.0.
 }}
 
 \section{Changes in version 1.4.0, Bioconductor 3.14 Release}{