Fixes Open-Systems-Pharmacology#249 allow data expansion to axes (Ope…

…n-Systems-Pharmacology#251)

* Fixes Open-Systems-Pharmacology#249 allow data expansion to axes

Default value for ddi ratio is TRUE

* Default axes scales and expand are managed using constants

* Remove usage of enum Scaling for constants to prevent build crash

R/boxwhisker-plotconfiguration.R

@@ -6,6 +6,9 @@ BoxWhiskerPlotConfiguration <- R6::R6Class(
   "BoxWhiskerPlotConfiguration",
   inherit = PlotConfiguration,
   public = list(
+    #' @field defaultXScale Default xAxis scale value when creating a `BoxWhiskerPlotConfiguration` object
+    defaultXScale = "discrete",
+
     #' @description Create a new `BoxWhiskerPlotConfiguration` object
     #' @param outliers logical defining if outliers should be included in boxplot
     #' @param ... parameters inherited from `PlotConfiguration`

R/plotconfiguration-axis.R

@@ -38,7 +38,6 @@ createPlotTicks <- function(ticks) {
   return(ticks)
 }
 
-
 #' @title AxisConfiguration
 #' @description  R6 class defining the configuration of axis
 #' @export
@@ -52,20 +51,26 @@ AxisConfiguration <- R6::R6Class(
     #' @param ticks numeric vector or function defining where to position axis ticks
     #' @param ticklabels character vector or function defining what to print on axis ticks
     #' @param font `Font` object defining the font of ticklabels
+    #' @param expand logical defining if data is expanded until axis.
+    #' If `TRUE`, data is expanded until axis
+    #' If `FALSE`, some space between data and axis is kept
     #' @return A new `AxisConfiguration` object
     initialize = function(limits = NULL,
                               scale = Scaling$lin,
                               ticks = NULL,
                               ticklabels = NULL,
-                              font = NULL) {
+                              font = NULL,
+                              expand = FALSE) {
       validateIsNumeric(limits, nullAllowed = TRUE)
       validateIsOfType(font, "Font", nullAllowed = TRUE)
+      validateIsLogical(expand)
       private$.limits <- limits
 
       scale <- scale %||% Scaling$lin
       private$.scale <- createPlotScale(scale)
       private$.ticks <- createPlotTicks(ticks)
       private$.ticklabels <- createPlotTicks(ticklabels)
+      private$.expand <- expand
 
       # Default axis font will use theme
       defaultFont <- Font$new()
@@ -90,6 +95,15 @@ AxisConfiguration <- R6::R6Class(
       )
     },
 
+    #' @description Get the `ggplot2` actual function for expansion
+    #' @return A `ggplot2` function
+    ggplotExpansion = function() {
+      if (private$.expand) {
+        return(ggplot2::expansion())
+      }
+      return(ggplot2::waiver())
+    },
+
     #' @description Get tick values for pretty default log plots
     #' @return User defined tick values or tlf default ticks
     prettyTicks = function() {
@@ -185,14 +199,26 @@ AxisConfiguration <- R6::R6Class(
       }
       private$.font <- value %||% defaultFont
       return(invisible())
+    },
+    #' @field expand logical defining if data is expanded until axis.
+    #' If `TRUE`, data is expanded until axis
+    #' If `FALSE`, some space between data and axis is kept
+    expand = function(value) {
+      if (missing(value)) {
+        return(private$.expand)
+      }
+      validateIsLogical(value)
+      private$.expand <- value
+      return(invisible())
     }
   ),
   private = list(
     .limits = NULL,
     .scale = NULL,
     .ticks = NULL,
     .ticklabels = NULL,
-    .font = NULL
+    .font = NULL,
+    .expand = NULL
   )
 )
 
@@ -219,15 +245,24 @@ XAxisConfiguration <- R6::R6Class(
       if (isIncluded(private$.scale, Scaling$discrete)) {
         suppressMessages(
           plotObject <- plotObject +
-            ggplot2::scale_x_discrete(breaks = private$.ticks, labels = private$.ticklabels)
+            ggplot2::scale_x_discrete(
+              breaks = private$.ticks,
+              labels = private$.ticklabels,
+              expand = self$ggplotExpansion()
+            )
         )
         return(plotObject)
       }
       # Most of ggplot2 scales lead to unwanted warning messages
       # `try` should be added in cases of scale breaking because all the ggplot object elements are not yet in place
       suppressMessages(
         plotObject <- plotObject +
-          ggplot2::scale_x_continuous(trans = self$ggplotScale(), breaks = self$prettyTicks(), labels = self$prettyTickLabels())
+          ggplot2::scale_x_continuous(
+            trans = self$ggplotScale(),
+            breaks = self$prettyTicks(),
+            labels = self$prettyTickLabels(),
+            expand = self$ggplotExpansion()
+          )
       )
       # Add special tick lines for pretty log plots
       suppressMessages(
@@ -268,15 +303,24 @@ YAxisConfiguration <- R6::R6Class(
       if (isIncluded(private$.scale, Scaling$discrete)) {
         suppressMessages(
           plotObject <- plotObject +
-            ggplot2::scale_y_discrete(breaks = private$.ticks, labels = private$.ticklabels)
+            ggplot2::scale_y_discrete(
+              breaks = private$.ticks,
+              labels = private$.ticklabels,
+              expand = self$ggplotExpansion()
+            )
         )
         return(plotObject)
       }
       # Most of ggplot2 scales lead to unwanted warning messages
       # `try` should be added in cases of scale breaking because all the ggplot object elements are not yet in place
       suppressMessages(
         plotObject <- plotObject +
-          ggplot2::scale_y_continuous(trans = self$ggplotScale(), breaks = self$prettyTicks(), labels = self$prettyTickLabels())
+          ggplot2::scale_y_continuous(
+            trans = self$ggplotScale(),
+            breaks = self$prettyTicks(),
+            labels = self$prettyTickLabels(),
+            expand = self$ggplotExpansion()
+          )
       )
       # Add special tick lines for pretty log plots
       suppressMessages(

R/plotconfiguration.R

@@ -1,6 +1,9 @@
 #' @title PlotConfiguration
 #' @description R6 class defining the configuration of a `ggplot` object
 #' @field export R6 class `ExportConfiguration` defining properties for saving/exporting plota
+#' @field defaultXScale Default xAxis scale value when creating a `PlotConfiguration` object
+#' @field defaultYScale Default yAxis scale value when creating a `PlotConfiguration` object
+#' @field defaultExpand Default expand value when creating a `PlotConfiguration` object
 #' @family PlotConfiguration classes
 #' @references For examples, see:
 #' <https://www.open-systems-pharmacology.org/TLF-Library/articles/plot-configuration.html>
@@ -9,6 +12,11 @@ PlotConfiguration <- R6::R6Class(
   "PlotConfiguration",
   public = list(
     export = NULL,
+    # Caution, helper enum Scaling doesn't work here 
+    # (even using @include to collate and define the variable beforehand)
+    defaultXScale = "lin",
+    defaultYScale = "lin",
+    defaultExpand = FALSE,
 
     #' @description Create a new `PlotConfiguration` object
     #' @param title character or `Label` object defining plot title
@@ -122,13 +130,19 @@ PlotConfiguration <- R6::R6Class(
 
       # X-Axis Configuration, overwrite some properties only if they are defined
       validateIsOfType(xAxis, "XAxisConfiguration", nullAllowed = TRUE)
-      private$.xAxis <- xAxis %||% XAxisConfiguration$new(scale = xAxisDefaultScale(self))
+      private$.xAxis <- xAxis %||% XAxisConfiguration$new(
+        scale = self$defaultXScale,
+        expand = self$defaultExpand
+      )
       private$.xAxis$limits <- xLimits %||% private$.xAxis$limits
       private$.xAxis$scale <- xScale %||% private$.xAxis$scale
 
       # Y-Axis configuration, overwrite some properties only if they are defined
       validateIsOfType(yAxis, "YAxisConfiguration", nullAllowed = TRUE)
-      private$.yAxis <- yAxis %||% YAxisConfiguration$new(scale = yAxisDefaultScale(self))
+      private$.yAxis <- yAxis %||% YAxisConfiguration$new(
+        scale = self$defaultYScale,
+        expand = self$defaultExpand
+      )
       private$.yAxis$limits <- yLimits %||% private$.yAxis$limits
       private$.yAxis$scale <- yScale %||% private$.yAxis$scale
 
@@ -272,20 +286,32 @@ TimeProfilePlotConfiguration <- R6::R6Class(
 
 #' @title PKRatioPlotConfiguration
 #' @description R6 class defining the configuration of a `ggplot` object for PK ratio plots
+#' @field defaultYScale Default yAxis scale value when creating a `PKRatioPlotConfiguration` object
 #' @export
 #' @family PlotConfiguration classes
 PKRatioPlotConfiguration <- R6::R6Class(
   "PKRatioPlotConfiguration",
-  inherit = PlotConfiguration
+  inherit = PlotConfiguration,
+  public = list(
+    defaultYScale = "log"
+  )
 )
 
 #' @title DDIRatioPlotConfiguration
 #' @description R6 class defining the configuration of a `ggplot` object for DDI ratio plots
+#' @field defaultXScale Default xAxis scale value when creating a `DDIRatioPlotConfiguration` object
+#' @field defaultYScale Default yAxis scale value when creating a `DDIRatioPlotConfiguration` object
+#' @field defaultExpand Default expand value when creating a `DDIRatioPlotConfiguration` object
 #' @export
 #' @family PlotConfiguration classes
 DDIRatioPlotConfiguration <- R6::R6Class(
   "DDIRatioPlotConfiguration",
-  inherit = PlotConfiguration
+  inherit = PlotConfiguration,
+  public = list(
+    defaultXScale = "log",
+    defaultYScale = "log",
+    defaultExpand = TRUE
+  )
 )
 
 #' @title ObsVsPredPlotConfiguration

R/tornado-plotconfiguration.R

@@ -12,6 +12,8 @@ TornadoPlotConfiguration <- R6::R6Class(
     colorPalette = NULL,
     #' @field dodge space between the bars/points
     dodge = NULL,
+    #' @field defaultYScale Default yAxis scale value when creating a `TornadoPlotConfiguration` object
+    defaultYScale = "discrete",
 
     #' @description Create a new `TornadoPlotConfiguration` object
     #' @param bar logical setting if tornado is uses a bar plot instead of regular points

R/utilities-axis.R

@@ -43,6 +43,7 @@ Scaling <- enum(c(
 #' @param ticks Optional values or function for axis ticks
 #' @param ticklabels Optional values or function for axis ticklabels
 #' @param font A `Font` object  defining font of ticklabels
+#' @param expand Logical defining if data is expanded until axis
 #' @return A `ggplot` object
 #' @export
 #' @examples
@@ -64,11 +65,13 @@ setXAxis <- function(plotObject,
                      limits = NULL,
                      ticks = NULL,
                      ticklabels = NULL,
-                     font = NULL) {
+                     font = NULL,
+                     expand = NULL) {
   validateIsOfType(plotObject, "ggplot")
   validateIsIncluded(scale, Scaling, nullAllowed = TRUE)
   validateIsNumeric(limits, nullAllowed = TRUE)
   validateIsOfType(font, "Font", nullAllowed = TRUE)
+  validateIsLogical(expand, nullAllowed = TRUE)
 
   # Clone plotConfiguration into a new plot object
   # Prevents update of R6 class being spread to plotObject
@@ -77,7 +80,7 @@ setXAxis <- function(plotObject,
 
   # R6 class not cloned will spread modifications into newPlotObject$plotConfiguration$xAxis
   xAxis <- newPlotObject$plotConfiguration$xAxis
-  eval(parseVariableToObject("xAxis", c("limits", "scale", "ticks", "ticklabels", "font"), keepIfNull = TRUE))
+  eval(parseVariableToObject("xAxis", c("limits", "scale", "ticks", "ticklabels", "font", "expand"), keepIfNull = TRUE))
   newPlotObject <- xAxis$updatePlot(newPlotObject, ylim = newPlotObject$plotConfiguration$yAxis$limits)
   return(newPlotObject)
 }
@@ -106,11 +109,13 @@ setYAxis <- function(plotObject,
                      limits = NULL,
                      ticks = NULL,
                      ticklabels = NULL,
-                     font = NULL) {
+                     font = NULL,
+                     expand = NULL) {
   validateIsOfType(plotObject, "ggplot")
   validateIsIncluded(scale, Scaling, nullAllowed = TRUE)
   validateIsNumeric(limits, nullAllowed = TRUE)
   validateIsOfType(font, "Font", nullAllowed = TRUE)
+  validateIsLogical(expand, nullAllowed = TRUE)
 
   # Clone plotConfiguration into a new plot object
   # Prevents update of R6 class being spread to plotObject
@@ -119,70 +124,11 @@ setYAxis <- function(plotObject,
 
   # R6 class not cloned will spread modifications into newPlotObject$plotConfiguration$yAxis
   yAxis <- newPlotObject$plotConfiguration$yAxis
-  eval(parseVariableToObject("yAxis", c("limits", "scale", "ticks", "ticklabels", "font"), keepIfNull = TRUE))
+  eval(parseVariableToObject("yAxis", c("limits", "scale", "ticks", "ticklabels", "font", "expand"), keepIfNull = TRUE))
   newPlotObject <- yAxis$updatePlot(newPlotObject, xlim = newPlotObject$plotConfiguration$xAxis$limits)
   return(newPlotObject)
 }
 
-#' @title xAxisDefaultScale
-#' @description Return x-axis default scale from a plot configuration
-#' @param plotConfiguration A `PlotConfiguration` object
-#' @return The default scale.
-#' The enum `Scaling` provides a list of available scales.
-#' @examples
-#' \dontrun{
-#' # Regular plots use continuous linear scale for x-axis
-#' plotConfiguration <- PlotConfiguration$new()
-#' xAxisDefaultScale(plotConfiguration)
-#'
-#' # DDI plots use log scale for x-axis
-#' ddiPlotConfiguration <- DDIRatioPlotConfiguration$new()
-#' xAxisDefaultScale(ddiPlotConfiguration)
-#'
-#' # Boxplots use discrete scale for x-axis
-#' boxPlotConfiguration <- BoxWhiskerPlotConfiguration$new()
-#' xAxisDefaultScale(boxPlotConfiguration)
-#' }
-#' @keywords internal
-xAxisDefaultScale <- function(plotConfiguration) {
-  if (isOfType(plotConfiguration, c("DDIRatioPlotConfiguration"))) {
-    return(Scaling$log)
-  }
-  if (isOfType(plotConfiguration, c("BoxWhiskerPlotConfiguration"))) {
-    return(Scaling$discrete)
-  }
-  return(Scaling$lin)
-}
-
-#' @title yAxisDefaultScale
-#' @description Return y-axis default scale from a plot configuration
-#' @param plotConfiguration A `PlotConfiguration` object
-#' @return The default scale.
-#' The enum `Scaling` provides a list of available scales.
-#' @examples
-#' \dontrun{
-#' # Regular plots use continuous linear scale for x-axis
-#' plotConfiguration <- PlotConfiguration$new()
-#' yAxisDefaultScale(plotConfiguration)
-#'
-#' # DDI plots use log scale for y-axis
-#' ddiPlotConfiguration <- DDIRatioPlotConfiguration$new()
-#' yAxisDefaultScale(ddiPlotConfiguration)
-#'
-#' # Tornado plots use discrete scale for y-axis
-#' tornadoPlotConfiguration <- TornadoPlotConfiguration$new()
-#' yAxisDefaultScale(tornadoPlotConfiguration)
-#' }
-#' @keywords internal
-yAxisDefaultScale <- function(plotConfiguration) {
-  if (isOfType(plotConfiguration, c("PKRatioPlotConfiguration", "DDIRatioPlotConfiguration"))) {
-    return(Scaling$log)
-  }
-  if (isOfType(plotConfiguration, c("TornadoPlotConfiguration"))) {
-    return(Scaling$discrete)
-  }
-  return(Scaling$lin)
-}
 
 #' @title getLogTickLabels
 #' @description Get ticklabels expressions for log scale plots