Fixed warning from upstream ggplot2 chnages

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tRNA
 Title: Analyzing tRNA sequences and structures
-Version: 1.21.1
-Date: 2024-01-17
+Version: 1.21.2
+Date: 2024-03-24
 Authors@R: person("Felix GM", 
  "Ernst",
  email = "felix.gm.ernst@outlook.com",
@@ -53,5 +53,5 @@ Collate:
  'tRNA-utils.R'
  'utils.R'
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 BugReports: https://github.com/FelixErnst/tRNA/issues

R/tRNA-plot.R

@@ -261,10 +261,10 @@ setMethod(
  min <- min(df[[name]]$value)
  max <- max(df[[name]]$value)
  plot <- ggplot2::ggplot(df[[name]],
- ggplot2::aes_(x = ~score,
-  y = ~value,
-  group = ~id,
-  colour = ~id)) +
+ ggplot2::aes(x = !!ggplot2::sym('score'),
+ y = !!ggplot2::sym('value'),
+ group = !!ggplot2::sym('id'),
+ colour = !!ggplot2::sym('id'))) +
  ggplot2::scale_y_continuous(name = writtenNames[[name]]) +
  ggplot2::scale_colour_brewer(name = "Sample",
  palette = colour_palette) + 
@@ -282,10 +282,10 @@ setMethod(
  if(!is.na(dataType[[name]]) &&
  dataType[[name]] == "percent"){
  plot <- ggplot2::ggplot(df[[name]],
- ggplot2::aes_(x = ~score,
-  y = ~value,
-  group = ~id,
-  colour = ~id)) +
+ ggplot2::aes(x = !!ggplot2::sym('score'),
+ y = !!ggplot2::sym('value'),
+ group = !!ggplot2::sym('id'),
+ colour = !!ggplot2::sym('id'))) +
  ggplot2::geom_point() +
  ggplot2::scale_y_continuous(name = writtenNames[[name]],
  breaks = c(0,0.25,0.5,0.75,1),
@@ -302,10 +302,10 @@ setMethod(
  df[[name]][df[[name]]$value == 1,"value"] <- "Yes"
  df[[name]][df[[name]]$value == 0,"value"] <- "No"
  plot <- ggplot2::ggplot(df[[name]],
- ggplot2::aes_(x = ~score,
-  y = ~value,
-  group = ~id,
-  colour = ~id)) +
+ ggplot2::aes(x = !!ggplot2::sym('score'),
+ y = !!ggplot2::sym('value'),
+ group = !!ggplot2::sym('id'),
+ colour = !!ggplot2::sym('id'))) +
  ggplot2::geom_jitter(height = 0.2) +
  ggplot2::scale_y_discrete(name = writtenNames[[name]]) +
  ggplot2::scale_colour_brewer(name = "Sample",
@@ -329,9 +329,9 @@ setMethod(
  min <- min(df[[name]]$value)
  max <- max(df[[name]]$value)
  plot <- ggplot2::ggplot(df[[name]],
- ggplot2::aes_(x = ~id,
-  y = ~value,
-  colour = ~id)) +
+ ggplot2::aes(x = !!ggplot2::sym('id'),
+ y = !!ggplot2::sym('value'),
+ colour = !!ggplot2::sym('id'))) +
  ggplot2::geom_violin(scale = "width") +
  ggplot2::geom_jitter(width = 0.2,
  height = 0.2) +
@@ -369,9 +369,9 @@ setMethod(
  df[[name]][df[[name]]$value == 1,"value"] <- "Yes"
  df[[name]][df[[name]]$value == 0,"value"] <- "No"
  plot <- ggplot2::ggplot(df[[name]],
- ggplot2::aes_(x = ~id,
-  y = ~(ggplot2::after_stat(count)/sum(ggplot2::after_stat(count))),
-  fill = ~colour)) +
+ ggplot2::aes(x = !!ggplot2::sym('id'),
+ y = ggplot2::after_stat(count)/sum(ggplot2::after_stat(count)),
+ fill = !!ggplot2::sym('colour'))) +
  ggplot2::geom_bar(position = "fill") +
  ggplot2::scale_x_discrete(name = "Sample") +
  ggplot2::scale_y_continuous(name = writtenNames[[name]],