format with {styler} (#366)

Open-Systems-Pharmacology · Aug 11, 2022 · e30924b · e30924b
1 parent 7bdcb83
commit e30924b
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Showing 8 changed files with 43 additions and 46 deletions.
diff --git a/R/aaa-utilities.R b/R/aaa-utilities.R
@@ -110,11 +110,11 @@
 #' @return A `ggplot` object
 #' @keywords internal
 .updateSameAxes <- function(plotObject, data, dataMapping) {
-  if(!all(
+  if (!all(
     plotObject$plotConfiguration$defaultSymmetricAxes,
     isEmpty(plotObject$plotConfiguration$xAxis$limits),
     isEmpty(plotObject$plotConfiguration$yAxis$limits)
-  )){
+  )) {
     return(plotObject)
   }
   limits <- .getSameLimitsFromMapping(data, dataMapping)
@@ -131,14 +131,13 @@
 #' @return A `ggplot` object
 #' @keywords internal
 .updateSymmetricAxes <- function(plotObject, data, dataMapping) {
-  if(!all(
+  if (!all(
     plotObject$plotConfiguration$defaultSymmetricAxes,
     isEmpty(plotObject$plotConfiguration$yAxis$limits)
-  )){
+  )) {
     return(plotObject)
   }
   limits <- getSymmetricLimits(data[, dataMapping$y])
   plotObject$plotConfiguration$yAxis$limits <- limits
   return(plotObject)
 }
-
diff --git a/R/helpers.R b/R/helpers.R
@@ -3,15 +3,15 @@
 #' @param values numeric values
 #' @return An array of 2 symmetric values equally distant from 0
 #' @export
-#' @examples 
+#' @examples
 #' getSymmetricLimits(seq(-3, 8))
-#' 
-getSymmetricLimits <- function(values){
+#'
+getSymmetricLimits <- function(values) {
   validateIsNumeric(values, nullAllowed = TRUE)
   # Remove Inf and NA values
   values <- values[!is.infinite(values)]
   values <- values[!is.na(values)]
-  if(isEmpty(values)){
+  if (isEmpty(values)) {
     return(NULL)
   }
   return(c(-max(abs(values)), max(abs(values))))
@@ -23,17 +23,17 @@ getSymmetricLimits <- function(values){
 #' @param ... numeric values
 #' @return An array of 2 values
 #' @export
-#' @examples 
+#' @examples
 #' getSameLimits(seq(-3, 8), seq(-12, 4))
-#' 
-getSameLimits <- function(...){
+#'
+getSameLimits <- function(...) {
   values <- c(...)
   validateIsNumeric(values, nullAllowed = TRUE)
   # Remove Inf and NA values
   values <- values[!is.infinite(values)]
   values <- values[!is.na(values)]
-  if(isEmpty(values)){
+  if (isEmpty(values)) {
     return(NULL)
   }
   return(c(min(values), max(values)))
-}
+}
diff --git a/R/plot-timeprofile.R b/R/plot-timeprofile.R
@@ -389,46 +389,46 @@ updateTimeProfileLegend <- function(plotObject, caption) {
     linetype = ggplot2::scale_linetype_manual,
     fill = ggplot2::scale_fill_manual
   )
-  
+
   unDefinedNames <- list()
-  for(property in c("shape", "linetype", "fill")){
-    # Use suppressMessages to prevent ggplot2 to 
+  for (property in c("shape", "linetype", "fill")) {
+    # Use suppressMessages to prevent ggplot2 to
     # throw message that scale was updated
-      suppressMessages(
-        plotObject <- plotObject +
-          scaleFunction[[property]](
-            breaks = caption[[property]]$names,
-            labels = caption[[property]]$labels,
-            values = caption[[property]]$values
-          )
-      )
+    suppressMessages(
+      plotObject <- plotObject +
+        scaleFunction[[property]](
+          breaks = caption[[property]]$names,
+          labels = caption[[property]]$labels,
+          values = caption[[property]]$values
+        )
+    )
     # Get legend names that are not scaled but in final legend
     unDefinedNames[[property]] <- setdiff(
-      caption$color$names, 
+      caption$color$names,
       caption[[property]]$colorNames
     )
     # Fill in the caption guide for shape, linetype and fill
     caption[[property]] <- rbind.data.frame(
       caption[[property]],
       data.frame(
-        names = unDefinedNames[[property]], 
+        names = unDefinedNames[[property]],
         labels = unDefinedNames[[property]],
-        colorNames = unDefinedNames[[property]], 
+        colorNames = unDefinedNames[[property]],
         values = rep(blankValues[[property]], length(unDefinedNames[[property]]))
       ),
       stringsAsFactors = FALSE
     )
     # Keep only names and order provided by color legend
     captionOrder <- sapply(
       caption$color$names,
-      function(colorName){
+      function(colorName) {
         head(which(caption[[property]]$colorNames == colorName), 1)
-        }
-      )
+      }
+    )
     caption[[property]] <- caption[[property]][captionOrder, ]
   }
-  
-  # Update color scale and use color caption 
+
+  # Update color scale and use color caption
   # as reference for displaying final legend
   suppressMessages(
     plotObject <- plotObject +
@@ -446,11 +446,10 @@ updateTimeProfileLegend <- function(plotObject, caption) {
             shape = caption$shape$values,
             fill = caption$fill$values,
             linetype = caption$linetype$values
-            )
+          )
         )
       )
   )
   plotObject$plotConfiguration$legend$caption <- caption
   return(plotObject)
 }
-
diff --git a/R/plotconfiguration-axis.R b/R/plotconfiguration-axis.R
@@ -150,7 +150,7 @@ AxisConfiguration <- R6::R6Class(
         private$.ticks
       )
     },
-    
+
     #' @description Get tick values for pretty default log plots
     #' @return User defined tick values or tlf default ticks
     prettyMinorTicks = function() {
@@ -160,7 +160,7 @@ AxisConfiguration <- R6::R6Class(
         return(private$.minorTicks)
       }
       # Default tick values as a function of scale
-      if(isIncluded(private$.scale, Scaling$log)){
+      if (isIncluded(private$.scale, Scaling$log)) {
         return(tlfEnv$logMinorTicks)
       }
       return(private$.minorTicks)

diff --git a/R/plotconfiguration-background.R b/R/plotconfiguration-background.R
@@ -55,8 +55,8 @@ BackgroundConfiguration <- R6::R6Class(
         panel.grid.major.x = private$.xGrid$createPlotElement(),
         panel.grid.major.y = private$.yGrid$createPlotElement(),
         # Minor grid is same as Major grid but less thick
-        panel.grid.minor.x = private$.xGrid$createPlotElement(size = as.numeric(private$.xGrid$size)/2),
-        panel.grid.minor.y = private$.yGrid$createPlotElement(size = as.numeric(private$.yGrid$size)/2)
+        panel.grid.minor.x = private$.xGrid$createPlotElement(size = as.numeric(private$.xGrid$size) / 2),
+        panel.grid.minor.y = private$.yGrid$createPlotElement(size = as.numeric(private$.yGrid$size) / 2)
       )
       return(plotObject)
     }

diff --git a/R/tlf-env.R b/R/tlf-env.R
@@ -168,7 +168,7 @@ setDefaultWatermark <- function(watermark = NULL) {
 tlfEnv$logTicks <- 10^seq(-10, 10)
 tlfEnv$lnTicks <- exp(seq(-10, 10))
 # Log minor ticks for every integer
-tlfEnv$logMinorTicks <- rep(seq(1,9), 21)*rep(10^seq(-10, 10), each = 9)
+tlfEnv$logMinorTicks <- rep(seq(1, 9), 21) * rep(10^seq(-10, 10), each = 9)
 
 #' @title setDefaultLogTicks
 #' @description Set default values for log ticks

diff --git a/R/utilities-aesthetics.R b/R/utilities-aesthetics.R
@@ -159,14 +159,14 @@
 #' @param propertyName Name of aesthetic property (e.g. `"shape"`...)
 #' @return Selected levels of `data[,columnNames$color]`
 #' @keywords internal
-.getColorNamesForFirstAesValues <- function(data, columnNames, propertyName){
+.getColorNamesForFirstAesValues <- function(data, columnNames, propertyName) {
   colorNames <- sapply(
     levels(data[, columnNames[[propertyName]]]),
-    function(propertyLevel){
+    function(propertyLevel) {
       head(data[which(data[, columnNames[[propertyName]]] %in% propertyLevel), columnNames$color], 1)
     }
   )
-  return(colorNames) 
+  return(colorNames)
 }
 
 

diff --git a/R/utilities-mapping.R b/R/utilities-mapping.R
@@ -382,7 +382,6 @@ getLinesFromFoldDistance <- function(foldDistance) {
 #' @param data A data.frame with labels mapped to properties and obtained from a `DataMapping` object
 #' @param dataMapping A `ObsVsPredDataMapping` object
 #' @keywords internal
-.getSameLimitsFromMapping <- function(data, dataMapping){
-  getSameLimits(data[,dataMapping$x], data[,dataMapping$y], data[,dataMapping$xmin], data[,dataMapping$xmax])
+.getSameLimitsFromMapping <- function(data, dataMapping) {
+  getSameLimits(data[, dataMapping$x], data[, dataMapping$y], data[, dataMapping$xmin], data[, dataMapping$xmax])
 }
-