sensitivitySpiderPlot: Sensitivity Spider Plot for Pharmacokinetic Parameters

In esqLABS/esqlabsR: esqLABS utilities package

Sensitivity Spider Plot for Pharmacokinetic Parameters

Description

Creates spider plots for sensitivity calculation. A spider plot is a visualization technique that displays the sensitivity of a model output to changes in model parameters. Each plot displays the sensitivity of a set of PK parameters for a single output path to changes in model parameters. The x-axis represents the value of model parameters (absolute or percent from default value), and the y-axis represents the sensitivity of the output to changes in the model parameter.

Usage

sensitivitySpiderPlot(
  sensitivityCalculation,
  outputPaths = NULL,
  parameterPaths = NULL,
  pkParameters = NULL,
  xAxisScale = NULL,
  yAxisScale = NULL,
  xAxisType = "percent",
  yAxisType = "percent",
  yAxisFacetScales = "fixed",
  defaultPlotConfiguration = NULL
)

Arguments

sensitivityCalculation	The SensitivityCalculation object returned by sensitivityCalculation().
outputPaths, parameterPaths, pkParameters	A single or a vector of the output path(s), parameter path(s), and PK parameters to be displayed, respectively. If NULL, all included paths and parameters present in the supplied SensitivityCalculation object will be displayed in the visualization. A separate plot will be generated for each output path. Each plot will contain a spider plot panel for each PK parameter, and the sensitivities for each parameter will be displayed as lines.
xAxisScale	Character string, either "log" (logarithmic scale) or "lin" (linear scale), to set the x-axis scale. Default is "log".
yAxisScale	Character string, either "log" or "lin", sets the y-axis scale similarly to xAxisScale. Default is "lin".
xAxisType	Character string, either "percent" (percentage change) or "absolute" (absolute values) for PK parameter values, for x-axis data normalization. Default is "percent".
yAxisType	Character string, either "percent" (percentage change) or "absolute" (absolute values) for PK parameter values, for y-axis data normalization. Default is "percent".
yAxisFacetScales	Character string, either "fixed" or "free", determines the scaling across y-axes of different facets. Default is "fixed". If "fixed", all facetes within one plot will have the same range, which allows for easier comparison between different PK parameters. If "free", each facet will have its own range, which allows for better visualization of the single PK parameters sensitivity.
defaultPlotConfiguration	An object of class DefaultPlotConfiguration used to customize plot aesthetics. Plot-specific settings provided directly to the function, such as xAxisScale, will take precedence over any modifications in defaultPlotConfiguration. Supported parameters include: legendPosition: Position of the legend on the plot. legendTitle: Title displayed for the legend. linesAlpha: Alpha transparency for line elements. linesColor: Color of the line elements. linesSize: Thickness of the line elements. pointsShape: Shape of the point elements. pointsSize: Size of the point elements. subtitle: Subtitle text for the plot. title: Main title text for the plot. titleSize: Font size of the plot title. xAxisScale: Scale type for the x-axis ("log" or "lin"). xLabel: Label text for the x-axis. xValuesLimits: Numeric vector specifying the limits for x-values. yAxisLimits: Numeric vector specifying the limits for y-values. yAxisScale: Scale type for the y-axis ("log" or "lin"). yAxisTicks: Number of ticks on the y-axis. yLabel: Label text for the y-axis. yValuesLimits: Numeric vector specifying the limits for y-values. Default values are set to provide a standardized look, but each parameter can be tailored to fit specific visual needs. Modifying these parameters will directly affect the aesthetics of the output plots.

Value

A patchwork object containing the combined ggplot objects if a single output path is specified, or a list of patchwork objects for multiple output paths.

See Also

Other sensitivity-calculation: sensitivityCalculation(), sensitivityTimeProfiles(), sensitivityTornadoPlot()

Examples

## Not run: 
simPath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
simulation <- loadSimulation(simPath)
outputPaths <- "Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)"
parameterPaths <- c(
  "Aciclovir|Lipophilicity",
  "Applications|IV 250mg 10min|Application_1|ProtocolSchemaItem|Dose",
  "Neighborhoods|Kidney_pls_Kidney_ur|Aciclovir|Glomerular Filtration-GFR|GFR fraction"
)

results <- sensitivityCalculation(
  simulation = simulation,
  outputPaths = outputPaths,
  parameterPaths = parameterPaths
)

# Print plots with default settings
sensitivitySpiderPlot(results)

# Print plots with absolute y-axis values
sensitivitySpiderPlot(results, yAxisType = "absolute", yAxisFacetScales = "free")

# Print plots with custom configuration settings
myPlotConfiguration <- createEsqlabsPlotConfiguration()
myPlotConfiguration$pointsShape <- 22
myPlotConfiguration$subtitle <- "Custom settings"
sensitivitySpiderPlot(results, defaultPlotConfiguration = myPlotConfiguration)

# Use named parameter paths to customize legend labels
namedParameterPaths <- c(
  "Lipophilicity" = "Aciclovir|Lipophilicity",
  "Dose" = "Applications|IV 250mg 10min|Application_1|ProtocolSchemaItem|Dose",
  "GFR fraction" = "Neighborhoods|Kidney_pls_Kidney_ur|Aciclovir|Glomerular Filtration-GFR|GFR fraction"
)

resultsNamed <- sensitivityCalculation(
  simulation = simulation,
  outputPaths = outputPaths,
  parameterPaths = namedParameterPaths
)

sensitivitySpiderPlot(resultsNamed)

## End(Not run)

esqLABS/esqlabsR documentation built on April 17, 2025, 10:51 a.m.