Fixes Open-Systems-Pharmacology#151 use coord_cartesian

- `coord_trans()` can't be used for the transformation because the method adding the watermark in background. Consequently, log and discrete transformations still use scale_x/y... 
- For the same reason, `coord_cartesian()` is used to set the axis limits
- suppressMessage is needed for the same reason as scale: multiple coord systems or scales lead to ggplot unwanted messages

R/plotconfiguration-axis.R

@@ -171,19 +171,23 @@ XAxisConfiguration <- R6::R6Class(
       validateIsOfType(plotObject, "ggplot")
       # Update font properties
       plotObject <- plotObject + ggplot2::theme(axis.text.x = private$.font$createPlotFont())
+      # Update limits using coor_cartesian to prevent ggplot to remove data and crash
+      suppressMessages(
+        plotObject <- plotObject + ggplot2::coord_cartesian(xlim = private$.limits)
+      )
       # Update scales and ticks
       if (isIncluded(private$.scale, Scaling$discrete)) {
         suppressMessages(
           plotObject <- plotObject +
-            ggplot2::scale_x_discrete(limits = private$.limits, breaks = private$.ticks, labels = private$.ticklabels)
+            ggplot2::scale_x_discrete(breaks = private$.ticks, labels = private$.ticklabels)
         )
         return(plotObject)
       }
       # Most of ggplot2 scales lead to unwanted warning messages
       # `try` should be added in cases of scale breaking because all the ggplot object elements are not yet in place
       suppressMessages(
         plotObject <- plotObject +
-          ggplot2::scale_x_continuous(trans = private$.scale, limits = private$.limits, breaks = private$.ticks, labels = private$.ticklabels)
+          ggplot2::scale_x_continuous(trans = private$.scale, breaks = private$.ticks, labels = private$.ticklabels)
       )
       return(plotObject)
     }
@@ -207,19 +211,22 @@ YAxisConfiguration <- R6::R6Class(
       validateIsOfType(plotObject, "ggplot")
       # Update font properties
       plotObject <- plotObject + ggplot2::theme(axis.text.y = private$.font$createPlotFont())
+      suppressMessages(
+        plotObject <- plotObject + ggplot2::coord_cartesian(ylim = private$.limits)
+      )
       # Update scales and ticks
       if (isIncluded(private$.scale, Scaling$discrete)) {
         suppressMessages(
           plotObject <- plotObject +
-            ggplot2::scale_y_discrete(limits = private$.limits, breaks = private$.ticks, labels = private$.ticklabels)
+            ggplot2::scale_y_discrete(breaks = private$.ticks, labels = private$.ticklabels)
         )
         return(plotObject)
       }
       # Most of ggplot2 scales lead to unwanted warning messages
       # `try` should be added in cases of scale breaking because all the ggplot object elements are not yet in place
       suppressMessages(
         plotObject <- plotObject +
-          ggplot2::scale_y_continuous(trans = private$.scale, limits = private$.limits, breaks = private$.ticks, labels = private$.ticklabels)
+          ggplot2::scale_y_continuous(trans = private$.scale, breaks = private$.ticks, labels = private$.ticklabels)
       )
       return(plotObject)
     }