add option for generating guest function outputs for residualVsObserv…

R/aaa-utilities.R

@@ -125,7 +125,7 @@ parseAddLineLayer <- function(type, value, position) {
   parse(text = paste0(
     "plotObject <- plotObject + ",
     switch(type,
-      "horizontal" = paste0("ggplot2::geom_hline(yintercept = ", value, ","),
+      "horizontal" = paste0("ggplot2::geom_abline(slope=0, intercept = ", value, ","),
       "vertical" = paste0("ggplot2::geom_vline(xintercept = ", value, ","),
       "diagonal" = paste0("ggplot2::geom_abline(slope=1, intercept = ", value, ",")
     ),

R/ddiratio-datamapping.R

@@ -9,17 +9,21 @@ DDIRatioDataMapping <- R6::R6Class(
     minRange = NULL,
     #' @field deltaGuest Value of `delta` in Guest et al. equation
     deltaGuest = NULL,
+    #' @field residualsVsObserved if true, returns a mapping for generating a residuals (predicted/observed) vs observed DDI ratio plot.  If false (default) returns a mapping for predicted vs observed DDI ratio plot.
+    residualsVsObserved = NULL,
 
     #' @description Create a new `DDIRatioDataMapping` object
     #' @param deltaGuest Value of parameter `delta` in Guest et al. equation.
     #' Default value is 1.
     #' @param minRange Mininmum range for guest lines
     #' @param lines list of ratio limits to plot as diagonal lines
-    #' @param ... parameters inherited from `PKRatioDataMapping`
-    #' @return A new `DDIRatioDataMapping` object
+    #' @param residualsVsObserved if true, returns a mapping for generating a residuals (predicted/observed) vs observed DDI ratio plot.  If false (default) returns a mapping for predicted vs observed DDI ratio plot.
+    #' @param ... parameters inherited from \code{PKRatioDataMapping}
+    #' @return A new \code{DDIRatioDataMapping} object
     initialize = function(deltaGuest = 1,
                           minRange = c(1e-2, 1e2),
                           lines = DefaultDataMappingValues$ddiRatio,
+                          residualsVsObserved = FALSE,
                           ...) {
       super$initialize(...)
       # Apply log10 transformation to lines because
@@ -28,6 +32,7 @@ DDIRatioDataMapping <- R6::R6Class(
       self$lines <- lapply(lines, log10)
       self$minRange <- minRange
       self$deltaGuest <- deltaGuest
+      self$residualsVsObserved <- residualsVsObserved
     }
   )
 )

R/obs-vs-pred-datamapping.R

@@ -20,7 +20,11 @@ ObsVsPredDataMapping <- R6::R6Class(
       validateIsIncluded(smoother, c("lm", "loess"), nullAllowed = TRUE)
 
       super$initialize(...)
-      self$lines <- lines
+
+      # Apply log10 transformation to lines because
+      # plot is log scaled in by default and geom_abline
+      # requires the log transformed values in input of intercept
+      self$lines <- lapply(lines, log10)
       self$smoother <- smoother
     }
   )

R/pkratio-datamapping.R

@@ -20,7 +20,11 @@ PKRatioDataMapping <- R6::R6Class(
                           ...) {
       validateIsString(uncertainty, nullAllowed = TRUE)
       super$initialize(...)
-      self$lines <- lines
+
+      # Apply log10 transformation to lines because
+      # plot is log scaled in by default and geom_abline
+      # requires the log transformed values in input of intercept
+      self$lines <- lapply(lines, log10)
       self$uncertainty <- uncertainty
     },
 

R/plot-ddiratio.R

@@ -24,10 +24,15 @@ plotDDIRatio <- function(data,
 
   plotObject <- plotObject %||% initializePlot(plotConfiguration)
 
+  lineOrientation <- "diagonal"
+  if(dataMapping$residualsVsObserved){
+    lineOrientation <- "horizontal"
+  }
+
   # Include horizontal lines
   for (lineIndex in seq_along(dataMapping$lines)) {
     # position correspond to the number of layer lines already added
-    eval(parseAddLineLayer("diagonal", dataMapping$lines[[lineIndex]], lineIndex - 1))
+    eval(parseAddLineLayer(lineOrientation, dataMapping$lines[[lineIndex]], lineIndex - 1))
   }
   if (isOfLength(lineIndex, 0)) {
     lineIndex <- 0
@@ -81,22 +86,27 @@ getGuestValuesFromDataMapping <- function(data,
   xmax <- max(dataMapping$minRange, xData[xData > 0])
   # By default, use 500 points to get enough discretization for the plot
   x <- 10^(seq(log10(xmin), log10(xmax), length.out = 5e2))
-  return(getGuestValues(x, delta = dataMapping$deltaGuest))
+  return(getGuestValues(x, delta = dataMapping$deltaGuest, residualsVsObserved = dataMapping$residualsVsObserved))
 }
 
 #' @title getGuestValues
 #' @description Get a data.frame with Guest et al. ratio limits
 #' @param x input values of Guest function
 #' @param delta parameter of Guest function
+#' @param residualsVsObserved if true, returns a dataframe for a residuals (predicted/observed) vs observed DDI ratio plot
 #' @return A data.frame with x, ymin and ymax defining Guest et al. limits
 #' @export
-getGuestValues <- function(x, delta = 1) {
+getGuestValues <- function(x, delta = 1, residualsVsObserved = FALSE) {
   xSym <- x
   xSym[x < 1] <- 1 / x[x < 1]
   limit <- (delta + 2 * (xSym - 1)) / xSym
   ymin <- x / limit
   ymax <- x * limit
 
-  guestLines <- data.frame(x, ymin, ymax)
+  if(residualsVsObserved){
+    guestLines <- data.frame(x = x, ymin =1/limit, ymax = limit)
+    return(guestLines)
+  }
+  guestLines <- data.frame(x = x, ymin = ymin, ymax = ymax)
   return(guestLines)
 }

tests/testthat/test-pkratio.R

@@ -33,9 +33,9 @@ test_that("PK Ratio default settings work", {
   expect_null(pkRatioMapping$x)
   expect_null(pkRatioMapping$y)
   expect_equal(pkRatioMapping$lines, list(
-    pkRatio1 = 1,
-    pkRatio2 = c(1.5, 1 / 1.5),
-    pkRatio3 = c(2, 1 / 2)
+    pkRatio1 = log10(1),
+    pkRatio2 = log10(c(1.5, 1 / 1.5)),
+    pkRatio3 = log10(c(2, 1 / 2))
   ))
 
   expect_is(pkRatioConfig$labels$title, "Label")