Updates to ggplot label access in testing ggplot labels (#24)

* Updates to ggplot label access Testing ggplot labels
Fixes #23

* Other updates to pass test with ggplot4.0.0

* Revert coord_trans --> coord_transform pending ggplot release

* Improve testing in changed code

Author: pbulsink

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("-",gg)
+S3method("-",ggplot)
 export(absorbance_to_transmittance)
 export(add_band)
 export(add_scalar_value)

NEWS.md

@@ -1,5 +1,7 @@
 # PlotFTIR (development version)
 
+* Updates (mostly to testing) to comply with pending ggplot2 4.0.0 release (#23)
+
 # PlotFTIR 1.2.0
 
 * Patch update to expose `check_ftir_data` for downstream packages. (related to #19)

R/io.R

@@ -219,11 +219,12 @@ read_ftir_directory <- function(path, files, sample_names = NA, ...) {
           }
         }
       },
-      error = function(e)
+      error = function(e) {
         cli::cli_warn(c(
           "{e}",
           i = "{.fn PlotFTIR::read_ftir_directory} will try to continue with the next file."
         ))
+      }
     )
   }
   if (nrow(ftir) > 0) {
@@ -504,7 +505,7 @@ save_plot <- function(ftir_spectra_plot, filename, ...) {
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::save_plt}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )

R/manipulations.R

@@ -46,7 +46,7 @@ zoom_in_on_range <- function(ftir_spectra_plot, zoom_range = c(1000, 1900)) {
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::zoom_in_on_range}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -150,22 +150,22 @@ compress_trans <- function(intercept = 2000, ratio = 5) {
 #'
 #' @keywords internal
 #'
-#' @references From https://stackoverflow.com/a/64011534
+#' @references modified from https://stackoverflow.com/a/64011534
 #'
 #' @md
-`-.gg` <- function(plot, layer) {
+`-.ggplot` <- function(plot, layer = NULL) {
   if (is.null(layer) || missing(layer)) {
     cli::cli_abort(c(
       "Cannot use {.code -.gg()} with a single argument, it must be followed by a {.arg layer}.",
       i = "Did you accidentally put {.code -} on a new line?"
     ))
   }
-  if (!ggplot2::is.ggplot(plot)) {
-    cli::cli_abort(
-      "You need to have a ggplot on the left side. You provided {.obj_type_friendly { plot }}."
-    )
-  }
-  plot$layers <- c(layer, plot$layers)
+
+  layers_count <- length(plot$layers)
+
+  plot <- plot + layer
+  # reorganize plot layers to put the recently added one 'first' in the list - underneath everything else
+  plot$layers <- c(plot$layers[[layers_count + 1]], plot$layers[1:layers_count])
   plot
 }
 
@@ -228,7 +228,7 @@ compress_low_energy <- function(
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::compress_low_energy}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -397,12 +397,32 @@ add_wavenumber_marker <- function(
     text <- as.character(as.integer(wavenumber))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::add_wavenumber_marker}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
   }
 
+  if (is.null(line_aesthetics)) {
+    line_aesthetics <- list()
+  }
+
+  if (is.null(label_aesthetics)) {
+    label_aesthetics <- list()
+  }
+
+  if (!is.list(line_aesthetics)) {
+    cli::cli_abort(
+      "Error in {.fn PlotFTIR::add_wavenumber_marker}. {.arg line_aesthetics} must be a named list. You provided {.obj_type_friendly {line_aesthetics}}."
+    )
+  }
+
+  if (!is.list(label_aesthetics)) {
+    cli::cli_abort(
+      "Error in {.fn PlotFTIR::add_wavenumber_marker}. {.arg label_aesthetics} must be a named list. You provided {.obj_type_friendly {label_aesthetics}}."
+    )
+  }
+
   data <- ftir_spectra_plot$data
   if (wavenumber < min(data$wavenumber) || wavenumber > max(data$wavenumber)) {
     cli::cli_abort(
@@ -484,7 +504,7 @@ rename_plot_sample_ids <- function(ftir_spectra_plot, sample_ids) {
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::rename_plot_sample_ids}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -608,7 +628,7 @@ move_plot_legend <- function(
       i = "Install {.pkg ggplot2} with {.run install.packages('ggplot2')}"
     ))
   }
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::move_plot_legend}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -708,7 +728,7 @@ highlight_sample <- function(ftir_spectra_plot, sample_ids, ...) {
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::highlight_sample}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -803,7 +823,7 @@ add_band <- function(
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::add_band}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )

R/plot_ftir.R

@@ -310,9 +310,9 @@ plot_ftir_stacked <- function(
   suppressMessages(p <- p + ggplot2::coord_cartesian(ylim = c(0, NA)))
 
   if (grepl("absorbance", mode)) {
-    p$labels$y <- "Absorbance (a.u.)"
+    p <- p + ggplot2::ylab("Absorbance (a.u.)")
   } else {
-    p$labels$y <- "Transmittance (a.u.)"
+    p <- p + ggplot2::ylab("Transmittance (a.u.)")
   }
 
   attr(p, "spectra_style") <- "stacked"

R/utils.R

@@ -33,7 +33,7 @@ get_plot_sample_ids <- function(ftir_spectra_plot) {
       i = "Install {.pkg ggplot2} with {.run install.packages('ggplot2')}"
     ))
   }
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::get_plot_sample_ids}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )

R/zzz.R

@@ -9,7 +9,7 @@
     options("PlotFTIR.lang" = "en")
     packageStartupMessage(
       'Plotting spectra with PlotFTIR. Please cite if plots are used in publishing (`citation("plotFTIR")`).\n',
-      'PlotFTIR is set to English as default. Changer au fran\u00e7ais par la fonction `options("PlotFTIR.lang" = "en")`'
+      'PlotFTIR is set to English as default. Changer au fran\u00e7ais par la fonction `options("PlotFTIR.lang" = "fr")`'
     )
   } else {
     if (

cran-comments.md

@@ -2,7 +2,4 @@
 
 0 errors | 0 warnings | 0 notes
 
-* This is a minor version release with improvements
-  * Exposes a function for downstream package(s) use.
-  * Adds import for .jdx filetype.
-
+* This is a patch release with updates to test code to resolve upstream changes in ggplot2 4.0.0. 

man/dot-gg.Rd man/dot-ggplot.Rdman/dot-gg.Rd renamed to man/dot-ggplot.Rd

@@ -307,10 +307,12 @@ test_that("reading .jdx works", {
   )
   # 2D NMR Data
   expect_error(
-    read_ftir(
-      path = system.file("extdata", "isasspc1.dx", package = "readJDX")
-    ),
-    "Could not confirm `infrared` data file."
+    suppressWarnings(
+      read_ftir(
+        path = system.file("extdata", "isasspc1.dx", package = "readJDX")
+      ),
+      "Could not confirm `infrared` data file."
+    )
   )
 })