Fixes Open-Systems-Pharmacology#390 Fixes Open-Systems-Pharmacology#391…

… observed and simulated time profiles (Open-Systems-Pharmacology#393)

DESCRIPTION

@@ -81,9 +81,11 @@ Collate:
     'plot-grid.R'
     'plot-histogram.R'
     'plot-obs-vs-pred.R'
+    'plot-observed-time-profile.R'
     'plot-pkratio.R'
     'plot-qq.R'
     'plot-res-vs-pred.R'
+    'plot-simulated-time-profile.R'
     'plot-timeprofile.R'
     'plot-tornado.R'
     'plotconfiguration-axis.R'

NAMESPACE

@@ -134,10 +134,12 @@ export(plotDDIRatio)
 export(plotGrid)
 export(plotHistogram)
 export(plotObsVsPred)
+export(plotObservedTimeProfile)
 export(plotPKRatio)
 export(plotQQ)
 export(plotResVsPred)
 export(plotResVsTime)
+export(plotSimulatedTimeProfile)
 export(plotTimeProfile)
 export(plotTornado)
 export(runPlotMaker)

R/plot-observed-time-profile.R

@@ -0,0 +1,65 @@
+#' @title plotObservedTimeProfile
+#' @description
+#' Producing Time Profile plots for observed data
+#'
+#' @inheritParams addScatter
+#' @param dataMapping
+#' An `ObservedDataMapping` object mapping `x`, `y`, `ymin`, `ymax` and aesthetic groups to their variable names of `observedData`.
+#' @param plotConfiguration
+#' An optional `TimeProfilePlotConfiguration` object defining labels, grid, background and watermark.
+#' @return A `ggplot` object
+#'
+#' @export
+#' @family molecule plots
+#' @examples
+#' # Produce a Time profile plot with observed data
+#' obsData <- data.frame(x = c(1, 2, 1, 2, 3), y = c(5, 0.2, 2, 3, 4))
+#' plotObservedTimeProfile(
+#'   data = obsData,
+#'   dataMapping = ObservedDataMapping$new(x = "x", y = "y")
+#' )
+plotObservedTimeProfile <- function(data = NULL,
+                                    metaData = NULL,
+                                    dataMapping = NULL,
+                                    plotConfiguration = NULL,
+                                    plotObject = NULL) {
+  #----- Validation and formatting of input arguments -----
+  validateIsNotEmpty(data)
+  validateIsOfType(data, "data.frame")
+  dataMapping <- .setDataMapping(dataMapping, ObservedDataMapping, data)
+  plotConfiguration <- .setPlotConfiguration(
+    plotConfiguration, TimeProfilePlotConfiguration,
+    data, metaData, dataMapping
+  )
+  plotObject <- .setPlotObject(plotObject, plotConfiguration)
+
+  mapData <- dataMapping$checkMapData(data)
+  mapLabels <- .getAesStringMapping(dataMapping)
+
+  #----- Build layers of molecule plot -----
+  # 1- Error bars if available
+  if (!any(isEmpty(dataMapping$ymin), isEmpty(dataMapping$ymax))) {
+    plotObject <- .addErrorbarLayer(
+      plotObject,
+      data = mapData,
+      mapLabels = mapLabels
+    )
+  }
+  # 2- Scatter points
+  plotObject <- .addScatterLayer(
+    plotObject,
+    data = mapData,
+    mapLabels = mapLabels
+  )
+
+  #----- Update properties using ggplot2::scale functions -----
+  plotObject <- .updateAesProperties(
+    plotObject,
+    plotConfigurationProperty = "points",
+    propertyNames = c("color", "shape"),
+    data = mapData,
+    mapLabels = mapLabels
+  )
+  plotObject <- .updateAxes(plotObject)
+  return(plotObject)
+}

R/plot-simulated-time-profile.R

@@ -0,0 +1,112 @@
+#' @title plotSimulatedTimeProfile
+#' @description
+#' Producing Time Profile plots
+#'
+#' @inheritParams addScatter
+#' @param dataMapping
+#' A `TimeProfileDataMapping` object mapping `x`, `y`, `ymin`, `ymax` and aesthetic groups to their variable names of `data`.
+#' @param plotConfiguration
+#' An optional `TimeProfilePlotConfiguration` object defining labels, grid, background and watermark.
+#' @return A `ggplot` object
+#'
+#' @export
+#' @family molecule plots
+#' @examples
+#' # Produce a Time profile plot with simulated data
+#' simTime <- seq(1, 10, 0.1)
+#' simData <- data.frame(
+#'   x = simTime,
+#'   y = 10 * exp(-simTime),
+#'   ymin = 8 * exp(-simTime),
+#'   ymax = 12 * exp(-simTime)
+#' )
+#'
+#' plotSimulatedTimeProfile(
+#'   data = simData,
+#'   dataMapping = TimeProfileDataMapping$new(x = "x", y = "y", ymin = "ymin", ymax = "ymax")
+#' )
+plotSimulatedTimeProfile <- function(data = NULL,
+                                     metaData = NULL,
+                                     dataMapping = NULL,
+                                     plotConfiguration = NULL,
+                                     plotObject = NULL) {
+  #----- Validation and formatting of input arguments -----
+  validateIsNotEmpty(data)
+  validateIsOfType(data, "data.frame")
+  dataMapping <- .setDataMapping(dataMapping, TimeProfileDataMapping, data)
+  plotConfiguration <- .setPlotConfiguration(
+    plotConfiguration, TimeProfilePlotConfiguration,
+    data, metaData, dataMapping
+  )
+  plotObject <- .setPlotObject(plotObject, plotConfiguration)
+
+  mapData <- dataMapping$checkMapData(data)
+  mapLabels <- .getAesStringMapping(dataMapping)
+
+  #----- Build layers of molecule plot -----
+  # 1- Ribbons if available
+  if (!any(isEmpty(dataMapping$ymin), isEmpty(dataMapping$ymax))) {
+    aestheticValues <- .getAestheticValuesFromConfiguration(
+      n = 1,
+      position = 0,
+      plotConfigurationProperty = plotObject$plotConfiguration$ribbons,
+      propertyNames = c("alpha")
+    )
+    plotObject <- plotObject +
+      ggplot2::geom_ribbon(
+        data = mapData,
+        mapping = ggplot2::aes_string(
+          x = mapLabels$x,
+          ymin = mapLabels$ymin,
+          ymax = mapLabels$ymax,
+          fill = mapLabels$fill,
+          group = mapLabels$linetype
+        ),
+        alpha = aestheticValues$alpha,
+        na.rm = TRUE,
+        show.legend = TRUE
+      )
+  }
+
+  # 2- Lines
+  if (!isEmpty(dataMapping$y)) {
+    aestheticValues <- .getAestheticValuesFromConfiguration(
+      n = 1,
+      position = 0,
+      plotConfigurationProperty = plotObject$plotConfiguration$lines,
+      propertyNames = c("alpha", "size")
+    )
+    plotObject <- plotObject +
+      ggplot2::geom_path(
+        data = mapData,
+        mapping = ggplot2::aes_string(
+          x = mapLabels$x,
+          y = mapLabels$y,
+          color = mapLabels$color,
+          linetype = mapLabels$linetype
+        ),
+        size = aestheticValues$size,
+        alpha = aestheticValues$alpha,
+        na.rm = TRUE,
+        show.legend = TRUE,
+      )
+  }
+
+  #----- Update properties using ggplot2::scale functions -----
+  plotObject <- .updateAesProperties(
+    plotObject,
+    plotConfigurationProperty = "ribbons",
+    propertyNames = "fill",
+    data = mapData,
+    mapLabels = mapLabels
+  )
+  plotObject <- .updateAesProperties(
+    plotObject,
+    plotConfigurationProperty = "lines",
+    propertyNames = c("color", "linetype"),
+    data = mapData,
+    mapLabels = mapLabels
+  )
+  plotObject <- .updateAxes(plotObject)
+  return(plotObject)
+}