tests/testthat/test-plot-observed-vs-simulated.R

In Open-Systems-Pharmacology/OSPSuite-R: R package to manipulate OSPSuite Models

# data to be used ---------------------------------------

# plotObservedVsSimulated


# load the simulation
sim <- loadTestSimulation("MinimalModel")
simResults <- importResultsFromCSV(
  simulation = sim,
  filePaths = getTestDataFilePath("Stevens_2012_placebo_indiv_results.csv")
)

# import observed data (will return a list of `DataSet` objects)
dataSet <- loadDataSetsFromExcel(
  xlsFilePath = getTestDataFilePath("CompiledDataSetStevens2012.xlsx"),
  importerConfiguration = loadDataImporterConfiguration(getTestDataFilePath("ImporterConfiguration.xml"))
)

# create a new instance and add datasets
myCombDat <- DataCombined$new()
myCombDat$addDataSets(dataSet)
myCombDat$addSimulationResults(
  simResults,
  quantitiesOrPaths = c(
    "Organism|Lumen|Stomach|Metformin|Gastric retention",
    "Organism|Lumen|Stomach|Metformin|Gastric retention distal",
    "Organism|Lumen|Stomach|Metformin|Gastric retention proximal"
  )
)

myCombDat$setGroups(
  names = c(
    "Organism|Lumen|Stomach|Metformin|Gastric retention",
    "Organism|Lumen|Stomach|Metformin|Gastric retention distal",
    "Organism|Lumen|Stomach|Metformin|Gastric retention proximal",
    "Stevens_2012_placebo.Placebo_total",
    "Stevens_2012_placebo.Placebo_distal",
    "Stevens_2012_placebo.Placebo_proximal"
  ),
  groups = c("Solid total", "Solid distal", "Solid proximal", "Solid total", "Solid distal", "Solid proximal")
)

test_that("It throws an error when foldDistance is lower that 1", {
  expect_error(plotObservedVsSimulated(myCombDat, foldDistance = 0.5),
    regexp = messages$plotObservedVsSimulatedWrongFoldDistance("foldDistance", 0.5)
  )

  expect_error(plotObservedVsSimulated(myCombDat, foldDistance = c(1, 0.5)),
    regexp = messages$plotObservedVsSimulatedWrongFoldDistance("foldDistance", c(1, 0.5))
  )
})

test_that("It creates default plots as expected", {
  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "defaults",
    fig = plotObservedVsSimulated(myCombDat)
  )
})

test_that("It creates default plots as expected without any identity or foldDistance line", {
  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "defaults without lines",
    fig = plotObservedVsSimulated(myCombDat, foldDistance = FALSE)
  )
})

test_that("It creates default plots as expected with 1 fold distance", {
  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "defaults 1 fold dist",
    fig = plotObservedVsSimulated(myCombDat, foldDistance = 2)
  )
})

test_that("It creates default plots as expected with several fold distances", {
  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "defaults 3 fold dist",
    fig = plotObservedVsSimulated(myCombDat, foldDistance = c(2, 4, 6))
  )
})

test_that("It issues warning when scale is linear", {
  myPlotConfiguration <- DefaultPlotConfiguration$new()
  myPlotConfiguration$xAxisScale <- tlf::Scaling$lin
  myPlotConfiguration$yAxisScale <- tlf::Scaling$lin

  set.seed(123)

  testthat::expect_warning({
    plot <- plotObservedVsSimulated(myCombDat, myPlotConfiguration, foldDistance = c(2, 4, 6))
  })

  vdiffr::expect_doppelganger(
    title = "linear scale",
    fig = plot
  )
})

test_that("It does not issue warning when no foldDistance are defined with linear scale", {
  myPlotConfiguration <- DefaultPlotConfiguration$new()
  myPlotConfiguration$xAxisScale <- tlf::Scaling$lin
  myPlotConfiguration$yAxisScale <- tlf::Scaling$lin

  set.seed(123)

  plot <- plotObservedVsSimulated(myCombDat, myPlotConfiguration)

  vdiffr::expect_doppelganger(
    title = "linear scale without foldDistance",
    fig = plot
  )
})


test_that("It respects custom plot configuration", {
  myPlotConfiguration <- DefaultPlotConfiguration$new()
  myPlotConfiguration$yUnit <- ospUnits$Fraction$`%`
  myPlotConfiguration$title <- "My Plot Title"
  myPlotConfiguration$subtitle <- "My Plot Subtitle"
  myPlotConfiguration$caption <- "My Sources"
  myPlotConfiguration$legendTitle <- "My legendary title"
  myPlotConfiguration$legendTitleColor <- "red"
  myPlotConfiguration$legendTitleSize <- 16
  myPlotConfiguration$legendKeysColor <- "brown"
  myPlotConfiguration$pointsSize <- 2.5
  myPlotConfiguration$legendPosition <- tlf::LegendPositions$outsideRight
  myPlotConfiguration$pointsColor <- tlf::ColorMaps$default
  myPlotConfiguration$linesLinetype <- names(tlf::Linetypes)
  myPlotConfiguration$foldLinesLegend <- TRUE
  myPlotConfiguration$foldLinesLegendDiagonal <- TRUE

  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "custom",
    fig = plotObservedVsSimulated(
      myCombDat,
      myPlotConfiguration,
      foldDistance = c(1.5, 2)
    )
  )

  # Since these were not specified by the user, they should not be updated
  # after plotting function is done with it.
  expect_null(myPlotConfiguration$xLabel)
  expect_null(myPlotConfiguration$yLabel)
})

test_that("It produces expected plot for Aciclovir data", {
  simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
  sim <- loadSimulation(simFilePath)

  simResults <- runSimulations(sim)[[1]]

  obsData <- lapply(
    c("ObsDataAciclovir_1.pkml", "ObsDataAciclovir_2.pkml", "ObsDataAciclovir_3.pkml"),
    function(x) loadDataSetFromPKML(system.file("extdata", x, package = "ospsuite"))
  )

  names(obsData) <- lapply(obsData, function(x) x$name)

  outputPaths <- "Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)"
  myDataCombined <- DataCombined$new()

  # Add simulated results
  myDataCombined$addSimulationResults(
    simulationResults = simResults,
    quantitiesOrPaths = outputPaths,
    groups = "Aciclovir PVB"
  )

  # Add observed data set
  myDataCombined$addDataSets(obsData$`Vergin 1995.Iv`, groups = "Aciclovir PVB")

  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "Aciclovir",
    fig = plotObservedVsSimulated(myDataCombined, foldDistance = 2)
  )
})

# edge cases ------------------------

test_that("It returns `NULL` when `DataCombined` is empty", {
  myCombDat <- DataCombined$new()

  expect_null(suppressWarnings(plotObservedVsSimulated(myCombDat)))
  expect_warning(
    plotObservedVsSimulated(myCombDat),
    messages$plottingWithEmptyDataCombined()
  )
})

test_that("It doesn't extrapolate past maximum simulated time point", {
  simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
  sim <- loadSimulation(simFilePath)

  simData <- withr::with_tempdir({
    df <- dplyr::tibble(
      IndividualId = c(0, 0, 0),
      `Time [min]` = c(0, 2, 4),
      `Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood) [µmol/l]` = c(0, 4, 8)
    )
    readr::write_csv(df, "SimResults.csv")
    importResultsFromCSV(sim, "SimResults.csv")
  })

  obsData <- DataSet$new(name = "Observed")
  obsData$setValues(xValues = c(1, 3, 3.5, 4, 5), yValues = c(1.9, 6.1, 7, 8.2, 1))
  obsData$xUnit <- "min"

  myDC <- DataCombined$new()
  myDC$addSimulationResults(simData, groups = "myGroup")
  myDC$addDataSets(obsData, groups = "myGroup")

  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "NA past max sim time",
    fig = plotObservedVsSimulated(myDC, foldDistance = 2)
  )
})

test_that("It returns `NULL` when `DataCombined` doesn't have any pairable datasets", {
  dataSet1 <- DataSet$new(name = "Dataset1")
  dataSet1$setValues(1, 1)
  dataSet1$yDimension <- ospDimensions$`Concentration (molar)`
  dataSet1$molWeight <- 1

  myCombDat <- DataCombined$new()
  myCombDat$addDataSets(dataSet1)

  expect_null(suppressWarnings(plotObservedVsSimulated(myCombDat)))
  expect_warning(
    plotObservedVsSimulated(myCombDat),
    messages$residualsCanNotBeComputed()
  )
})

test_that("Different symbols for data sets within one group", {
  simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
  sim <- loadSimulation(simFilePath)

  simData <- withr::with_tempdir({
    df <- dplyr::tibble(
      IndividualId = c(0, 0, 0),
      `Time [min]` = c(0, 2, 4),
      `Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood) [µmol/l]` = c(0, 4, 8)
    )
    readr::write_csv(df, "SimResults.csv")
    importResultsFromCSV(sim, "SimResults.csv")
  })

  obsData <- DataSet$new(name = "Observed")
  obsData$setValues(xValues = c(1, 3, 3.5, 4, 5), yValues = c(1.9, 6.1, 7, 8.2, 1))
  obsData$xUnit <- "min"
  obsData$yDimension <- ospDimensions$`Concentration (molar)`

  myDC <- DataCombined$new()
  myDC$addSimulationResults(simData, groups = "myGroup")
  myDC$addDataSets(obsData, groups = "myGroup")

  # Add second obs data
  obsData2 <- DataSet$new(name = "Observed 2")
  obsData2$setValues(xValues = c(0, 3, 4, 4.5, 5.5), yValues = c(2.9, 5.1, 3, 8.2, 1))
  obsData2$xUnit <- "min"
  obsData2$yDimension <- ospDimensions$`Concentration (molar)`
  myDC$addDataSets(obsData2, groups = "myGroup")

  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "multiple data sets one group",
    fig = plotObservedVsSimulated(myDC, foldDistance = 2)
  )
})

test_that("LLOQ is plotted", {
  simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
  sim <- loadSimulation(simFilePath)

  simData <- withr::with_tempdir({
    df <- dplyr::tibble(
      IndividualId = c(0, 0, 0),
      `Time [min]` = c(0, 2, 4),
      `Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood) [µmol/l]` = c(0, 4, 8)
    )
    readr::write_csv(df, "SimResults.csv")
    importResultsFromCSV(sim, "SimResults.csv")
  })

  obsData <- DataSet$new(name = "Observed")
  obsData$setValues(xValues = c(1, 3, 3.5, 4, 5), yValues = c(1.9, 6.1, 7, 8.2, 1))
  obsData$xUnit <- "min"
  obsData$yDimension <- ospDimensions$`Concentration (molar)`
  obsData$LLOQ <- 3

  myDC <- DataCombined$new()
  myDC$addSimulationResults(simData, groups = "myGroup")
  myDC$addDataSets(obsData, groups = "myGroup")

  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "lloq vertical",
    fig = plotObservedVsSimulated(myDC, foldDistance = 2)
  )

  DPC <- DefaultPlotConfiguration$new()
  DPC$lloqDirection <- "both"
  vdiffr::expect_doppelganger(
    title = "lloq both direction",
    fig = plotObservedVsSimulated(myDC,
      foldDistance = 2,
      defaultPlotConfiguration = DPC
    )
  )
})