`facets` was deprecated in ggplot2 2.2.0 and is now defunct

[jaymoore-research]

Checklist

• I am able to reproduce the bug with the latest version
• I checked, but didn't find any duplicates (open OR closed) of this issue in the repo

Affected version

2.0.15

Steps to reproduce the bug

library(MAGMA.Celltyping)
MAGMA_results <- MAGMA.Celltyping::enrichment_results
merged_results <- MAGMA.Celltyping::merge_results(MAGMA_results = MAGMA_results)
heat <- MAGMA.Celltyping::results_heatmap(merged_results = merged_results, fdr_thresh = 1)

Actual behavior

14 results @ FDR < 1
Error:
! The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0 and is now defunct.
ℹ Please use the `rows` argument instead.
Run `rlang::last_trace()` to see where the error occurred.
Warning message:
`aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
ℹ The deprecated feature was likely used in the MAGMA.Celltyping package.
  Please report the issue at <https://github.com/neurogenomics/MAGMA_Celltyping/issues>.
This warning is displayed once per session.
Call warnings()�lifecycle::last_lifecycle_warnings() to see where this warning was generated. 

Expected behavior

Generate a heatmap as shown in vignette: https://neurogenomics.github.io/MAGMA_Celltyping/articles/MAGMA.Celltyping.html#heatmap

Session info

R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS

[jaymoore-research]

I implemented a fix to results_heatmap but it appears there is another bug:

Steps to reproduce the bug

library(MAGMA.Celltyping)
MAGMA_results <- MAGMA.Celltyping::enrichment_results
merged_results <- MAGMA.Celltyping::merge_results(MAGMA_results = MAGMA_results)

results_heatmap <- function(merged_results,
                            title = NULL,
                            x_lab = NULL,
                            fdr_thresh = .05,
                            facet_formula = "EnrichmentMode ~ .",
                            x_var = "Celltype",
                            y_var = "GWAS",
                            fill_var = "-log1p(FDR)",
                            scales = "free_y",
                            space = "fixed",
                            show_plot = TRUE,
                            height = 5, 
                            width = 7,
                            dpi = 300,
                            save_path = file.path(
                              tempdir(),
                              "MAGMA_Celltyping.heatmap.jpg")
) { 
  #### Avoid confusing checks ####
  FDR <- NULL;
  #### Check args #####
  if (!"GWAS" %in% colnames(merged_results)) {
    merged_results$GWAS <- merged_results$dataset
  }
  if (is.null(fdr_thresh)) fdr_thresh <- 1
  subtitle <- if (!is.null(fdr_thresh)) paste0("FDR < ", fdr_thresh) else NULL
  #### Filter by FDR ####
  plot_dat <- subset(merged_results, FDR < fdr_thresh)
  messager(formatC(nrow(plot_dat), big.mark = ","),
           "results @ FDR <",fdr_thresh)
  if(nrow(plot_dat)==0) stop("Filtered data must contain >0 rows.")
  #### Plot ####
  # browser()
  heat <- ggplot2::ggplot(
    data = plot_dat,
    ggplot2::aes(x = .data[[x_var]], y = .data[[y_var]], fill = .data[[fill_var]])
    
  ) +
    ggplot2::geom_tile(color = "white") +
    ggplot2::facet_grid(
      rows = stats::as.formula(facet_formula),
      scales = scales,
      space = space
    ) +
    ggplot2::labs(
      title = title,
      subtitle = subtitle,
      x = x_lab
    ) +
    ggplot2::scale_fill_gradient(low = "blue", high = "red", 
                                 na.value = "white") +
    ggplot2::theme_bw() +
    ggplot2::theme(
      axis.text.x = ggplot2::element_text(
        angle = 45, hjust = 1, size = 7),
      strip.background = ggplot2::element_rect(fill = "grey20"),
      strip.text = ggplot2::element_text(color = "white"),
      panel.grid.minor = ggplot2::element_blank()
    )
  #### Print ####
  if (show_plot) print(heat)
  #### Save ####
  if (!is.null(save_path)){ 
    dir.create(dirname(save_path), showWarnings = FALSE, recursive = TRUE)
    ggplot2::ggsave(filename = save_path, 
                    plot = heat, 
                    dpi = dpi,
                    height = height, width = width)
  }
  return(heat)
}

heat <- results_heatmap(merged_results = merged_results, fdr_thresh = 1) # note we are calling function defined during session, not packaged function MAGMA.Celltyping::results_heatmap

Actual behavior

14 results @ FDR < 1
Error in `ggplot2::geom_tile()`:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `.data[["-log1p(FDR)"]]`:
! Column `-log1p(FDR)` not found in `.data`.
Run `rlang::last_trace()` to see where the error occurred.

Information

"-log1p(FDR)"  %in% names(merged_results)

returns FALSE

[jaymoore-research]

I think this issue needs to be reopened

Affected version

2.0.16

Steps to reproduce the bug

library(MAGMA.Celltyping)
MAGMA_results <- MAGMA.Celltyping::enrichment_results
merged_results <- MAGMA.Celltyping::merge_results(MAGMA_results = MAGMA_results)
heat <- MAGMA.Celltyping::results_heatmap(
  merged_results = merged_results,
  title = "Alzheimer's Disease (ieu-a-298) vs.\nnervous system cell-types (Zeisel2015)",
  fdr_thresh = 1)

Actual behaviour

14 results @ FDR < 1
Error:
! The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0 and is now defunct.
ℹ Please use the `rows` argument instead.
Run `rlang::last_trace()` to see where the error occurred.

[HDash]

Hey @jaymoore-research , I cannot reproduce this issue on my end. All the references to facets argument for facets_grid() have been removed from the codebase.

Can you please restart all your R sessions (without restore) to make sure you're not using cached versions of the package, or the devtools::load_all remnants?

Would also appreciate the full traceback and the output from session_info().

[jaymoore-research]

Yes, after terminating R, the code works great. Thanks for your support