Fixes #1213 provide default axes settings in qualification workflows (#…

…1216)

R/qualification-time-profile.R

@@ -586,25 +586,6 @@ getTimeProfileObservedDataFromResults <- function(observedResults, molWeight, ax
   ))
 }
 
-#' @title getDefaultTimeProfileAxesSettings
-#' @description Get the default axes settings for mean and population time profiles
-#' for keeping compatibility with configuration plan from Matlab version
-#' @return List of `x` and `y` axes settings
-#' @keywords internal
-getDefaultTimeProfileAxesSettings <- function() {
-  xAxis <- list(
-    dimension = ospsuite::ospDimensions$Time, unit = ospsuite::ospUnits$Time$h,
-    min = NULL, max = NULL, scale = tlf::Scaling$lin,
-    grid = list(color = reEnv$theme$background$xGrid$color, linetype = reEnv$theme$background$xGrid$linetype)
-  )
-  yAxis <- list(
-    dimension = ospsuite::ospDimensions$`Concentration (mass)`, unit = ospsuite::ospUnits$`Concentration [mass]`$`µg/l`,
-    min = NULL, max = NULL, scale = tlf::Scaling$log,
-    grid = list(color = reEnv$theme$background$yGrid$color, linetype = reEnv$theme$background$yGrid$linetype)
-  )
-  return(list(x = xAxis, y = yAxis))
-}
-
 #' @title getObservedErrorValues
 #' @description
 #' Get the observed data error range to display on time profile plots

R/utilities-configuration-plan.R

@@ -122,6 +122,12 @@ getAxesProperties <- function(axesSettings) {
   return(list(x = xAxis, y = yAxis, y2 = y2Axis, y3 = y3Axis))
 }
 
+#' @title formatAxisProperties
+#' @description
+#' Format configuration plan field values to a list compatible with `tlf` package nomenclature
+#' @param axisField List of configuration plan field properties
+#' @return A list of properties compatible with `tlf` package nomenclature
+#' @keywords internal
 formatAxisProperties <- function(axisField) {
   list(
     dimension = axisField$Dimension,
@@ -137,6 +143,29 @@ formatAxisProperties <- function(axisField) {
   )
 }
 
+#' @title getAxesPropertiesFromName
+#' @description
+#' Get axes properties from global field `AxesSettings` of configuration plan if defined,
+#' otherwise use default values.
+#' @param configurationPlan A `ConfigurationPlan` object
+#' @param plotName Field name of the plot in the configuration plan `AxesSettings`
+#' @return A list of properties for axes identified for `x`, `y` and `y2` axes.
+#' The identified properties are directly compatible with `tlf` package nomenclature
+#' @keywords internal
+#' @import jsonlite
+getAxesPropertiesFromName <- function(configurationPlan, plotName) {
+  axesProperties <- getAxesProperties(configurationPlan$plots$AxesSettings[[plotName]])
+  if (!isEmpty(axesProperties)) {
+    return(axesProperties)
+  }
+  # If no axes settings are defined, use default values stored in the package json file
+  defaultAxisSettings <- jsonlite::fromJSON(
+    txt = system.file("extdata", "qualification-axis-settings.json", package = "ospsuite.reportingengine"),
+    simplifyVector = FALSE
+  )
+  return(getAxesProperties(defaultAxisSettings[[plotName]]))
+}
+
 #' @title updatePlotAxes
 #' @description Update the axes, grid and legend properties of a plot object based on the identified axes properties
 #' @param plotObject A ggplot object
@@ -191,7 +220,7 @@ updatePlotAxes <- function(plotObject, axesProperties) {
 tlfLinetype <- function(configurationLinetype) {
   # Unknown or NULL value will translate as NULL
   # which will lead to use default behaviour
-  if (isOfLength(configurationLinetype, 0)) {
+  if (isEmpty(configurationLinetype)) {
     return()
   }
   # tolower is used to ensure that there is no issue with caps from field values

R/utilities-task.R

@@ -919,7 +919,10 @@ loadQualificationTimeProfilesTask <- function(workflow, configurationPlan) {
     workflowFolder = workflow$workflowFolder,
     active = active,
     message = defaultWorkflowMessages$plotTimeProfiles,
-    settings = list(axes = getAxesProperties(configurationPlan$plots$AxesSettings$TimeProfile) %||% getDefaultTimeProfileAxesSettings())
+    settings = list(axes = getAxesPropertiesFromName(
+      configurationPlan = configurationPlan,
+      plotName = "TimeProfile"
+    ))
   ))
 }
 
@@ -960,8 +963,14 @@ loadGOFMergedTask <- function(workflow, configurationPlan) {
     active = active,
     message = defaultWorkflowMessages$plotGOFMerged,
     settings = list(
-      predictedVsObserved = list(axes = getAxesProperties(configurationPlan$plots$AxesSettings$GOFMergedPlotsPredictedVsObserved)),
-      residualsOverTime = list(axes = getAxesProperties(configurationPlan$plots$AxesSettings$GOFMergedPlotsResidualsOverTime)),
+      predictedVsObserved = list(axes = getAxesPropertiesFromName(
+        configurationPlan = configurationPlan,
+        plotName = "GOFMergedPlotsPredictedVsObserved"
+      )),
+      residualsOverTime = list(axes = getAxesPropertiesFromName(
+        configurationPlan = configurationPlan,
+        plotName = "GOFMergedPlotsResidualsOverTime"
+      )),
       digits = reEnv$formatNumericsDigits,
       nsmall = reEnv$formatNumericsSmall,
       scientific = reEnv$formatNumericsScientific
@@ -1007,7 +1016,12 @@ loadQualificationComparisonTimeProfileTask <- function(workflow, configurationPl
     workflowFolder = workflow$workflowFolder,
     active = active,
     message = defaultWorkflowMessages$plotComparisonTimeProfiles,
-    settings = list(axes = getAxesProperties(configurationPlan$plots$AxesSettings$ComparisonTimeProfile))
+    settings = list(
+      axes = getAxesPropertiesFromName(
+        configurationPlan = configurationPlan,
+        plotName = "ComparisonTimeProfile"
+      )
+    )
   ))
 }
 
@@ -1049,7 +1063,10 @@ loadPlotPKRatioTask <- function(workflow, configurationPlan) {
     active = active,
     message = defaultWorkflowMessages$plotPKRatio,
     settings = list(
-      axes = getAxesProperties(configurationPlan$plots$AxesSettings$PKRatioPlots),
+      axes = getAxesPropertiesFromName(
+        configurationPlan = configurationPlan,
+        plotName = "PKRatioPlots"
+      ),
       digits = reEnv$formatNumericsDigits,
       nsmall = reEnv$formatNumericsSmall,
       scientific = reEnv$formatNumericsScientific,
@@ -1115,8 +1132,14 @@ loadPlotDDIRatioTask <- function(workflow, configurationPlan) {
     active = active,
     message = defaultWorkflowMessages$plotDDIRatio,
     settings = list(
-      predictedVsObserved = list(axes = getAxesProperties(configurationPlan$plots$AxesSettings$DDIRatioPlotsPredictedVsObserved)),
-      residualsOverTime = list(axes = getAxesProperties(configurationPlan$plots$AxesSettings$DDIRatioPlotsResidualsVsObserved)),
+      predictedVsObserved = list(axes = getAxesPropertiesFromName(
+        configurationPlan = configurationPlan,
+        plotName = "DDIRatioPlotsPredictedVsObserved"
+      )),
+      residualsOverTime = list(axes = getAxesPropertiesFromName(
+        configurationPlan = configurationPlan,
+        plotName = "DDIRatioPlotsResidualsVsObserved"
+      )),
       digits = reEnv$formatNumericsDigits,
       nsmall = reEnv$formatNumericsSmall,
       scientific = reEnv$formatNumericsScientific

inst/extdata/qualification-axis-settings.json

@@ -0,0 +1,114 @@
+{
+  "GOFMergedPlotsPredictedVsObserved": [
+    {
+      "Type": "X",
+      "Dimension": "Concentration (mass)",
+      "Unit": "µg/l",
+      "GridLines": false,
+      "Scaling": "Log"
+    },
+    {
+      "Type": "Y",
+      "Dimension": "Concentration (mass)",
+      "Unit": "µg/l",
+      "GridLines": false,
+      "Scaling": "Log"
+    }
+  ],
+  "GOFMergedPlotsResidualsOverTime": [
+    {
+      "Type": "X",
+      "Dimension": "Time",
+      "Unit": "h",
+      "GridLines": false,
+      "Scaling": "Linear"
+    },
+    {
+      "Type": "Y",
+      "Dimension": "Dimensionless",
+      "Unit": "",
+      "GridLines": false,
+      "Scaling": "Linear"
+    }
+  ],
+  "ComparisonTimeProfile": [
+    {
+      "Type": "X",
+      "Dimension": "Time",
+      "Unit": "h",
+      "GridLines": false,
+      "Scaling": "Linear"
+    },
+    {
+      "Type": "Y",
+      "Dimension": "Concentration (mass)",
+      "Unit": "µg/l",
+      "GridLines": false,
+      "Scaling": "Log"
+    }
+  ],
+  "DDIRatioPlotsPredictedVsObserved": [
+    {
+      "Type": "X",
+      "Dimension": "Dimensionless",
+      "Unit": "",
+      "GridLines": false,
+      "Scaling": "Log"
+    },
+    {
+      "Type": "Y",
+      "Dimension": "Dimensionless",
+      "Unit": "",
+      "GridLines": false,
+      "Scaling": "Log"
+    }
+  ],
+  "DDIRatioPlotsResidualsVsObserved": [
+    {
+      "Type": "X",
+      "Dimension": "Dimensionless",
+      "Unit": "",
+      "GridLines": false,
+      "Scaling": "Log"
+    },
+    {
+      "Type": "Y",
+      "Dimension": "Dimensionless",
+      "Unit": "",
+      "GridLines": false,
+      "Scaling": "Log"
+    }
+  ],
+  "PKRatioPlots": [
+    {
+      "Type": "X",
+      "Dimension": "Age",
+      "Unit": "year(s)",
+      "GridLines": false,
+      "Scaling": "Linear"
+    },
+    {
+      "Type": "Y",
+      "Dimension": "Dimensionless",
+      "Unit": "",
+      "GridLines": false,
+      "Scaling": "Log"
+    }
+  ],
+  "TimeProfile": [
+    {
+      "Type": "X",
+      "Dimension": "Time",
+      "Unit": "h",
+      "GridLines": false,
+      "Scaling": "Linear"
+    },
+    {
+      "Type": "Y",
+      "Dimension": "Concentration (mass)",
+      "Unit": "µg/l",
+      "GridLines": false,
+      "Scaling": "Log"
+    }
+  ]
+}