Plot configuration for OSP plots

R6 configuration class defining aesthetic properties of plots that can be created with plotIndividualTimeProfile(), plotPopulationTimeProfile(), plotObservedVsSimulated(), and plotResidualsVsTime().

To interactively explore various aesthetic properties and appearance of plots with these properties, you can use the Shiny app from {tlf} package.

The following sections provide more details on how to customize it further.

Specifying aesthetic properties

Aesthetic mappings describe how groups are mapped to visual properties (color, shape, size, etc.) of the geometries included in the plot (e.g. point, line, ribbon, etc.).

The supported values for each property can be seen using {tlf} lists:

color, fill: tlf::ColorMaps
shape: tlf::Shapes
legend position: tlf::LegendPositions
alignments: tlf::Alignments
linetype: tlf::Linetypes

For example, all parameters related to color (titleColor, yAxisLabelTicksColor, etc.) accept any of the palettes available in tlf::ColorMaps (e.g. tlf::ColorMaps$ospDefault).

Note that these are named lists, and, therefore, if you want to assign a specific element from a list to an object's public field, you will have to extract that element first.

For example, if you want to specify that the legend position should be outside the plot to the left and at bottom, you will have to do the following:

myPlotConfiguration <- DefaultPlotConfiguration$new()
myPlotConfiguration$legendPosition <- tlf::LegendPositions$outsideBottomLeft

Of course, the extracted element doesn't have to be a single value, and can also be an atomic vector. For example, if you want to assign a different line type to each group in a profile plot, you will have to assign a vector of line types.

myPlotConfiguration <- DefaultPlotConfiguration$new()
myPlotConfiguration$linesLinetype <- names(tlf::Linetypes)

If there are more number of elements in the vector than the number of groups, the additional elements will be ignored.

Specifying units

The available units for x-and y-axes depend on the dimensions of these quantities (ospsuite::ospDimensions). Supported units can be seen with ospsuite::ospUnits.

Specifying fonts

A font is a particular set of glyphs (character shapes), differentiated from other fonts in the same family by additional properties such as stroke weight, slant, relative width, etc.

A font face (aka typeface) is the design of lettering, characterized by variations in size, weight (e.g. bold), slope (e.g. italic), width (e.g. condensed), and so on. The available font faces can seen using tlf::FontFaces list.

A font family is a grouping of fonts defined by shared design styles.

The available font families will depend on which fonts have been installed on your computer. This information can be extracted by running the following code:

# install.packages("systemfonts")
library(systemfonts)
system_fonts()

Specifying scaling

Transformations for both x- and y-axes can be (independently) specified. The default is linear for both axes.

The available transformations can be seen in the tlf::Scaling list.

Specifying tick labels

tlf::TickLabelTransforms lists of all available tick label transformations. For example, selecting tlf::TickLabelTransforms$identity will display tick labels as they are, while selecting tlf::TickLabelTransforms$log will display tick labels in logarithmic scale format.

Saving plot

By default, the plots will be shown in plot pane of your IDE, but the plots can also be saved to a file using the ggplot2::ggsave() function.

myPlot <- plotIndividualTimeProfile(myDataComb, myPC)
ggplot2::ggsave(filename = "plot_1.png", plot = myPlot)

Public fields

xUnit, yUnit: Units for quantities plotted on x- and y-axes, respectively.
title, subtitle, caption, xLabel, yLabel, legendTitle, watermark: A character string providing plot annotations for plot title, subtitle, caption, x-axis label, y-axis label, plot legend, watermark, respectively.
titleColor, titleSize, titleFontFace, titleFontFamily, titleAngle, titleAlign, titleMargin: Aesthetic properties for the plot title.
subtitleColor, subtitleSize, subtitleFontFace, subtitleFontFamily, subtitleAngle, subtitleAlign, subtitleMargin: Aesthetic properties for the plot subtitle.
captionColor, captionSize, captionFontFace, captionFontFamily, captionAngle, captionAlign, captionMargin: Aesthetic properties for the plot caption.
xLabelColor, xLabelSize, xLabelFontFace, xLabelFontFamily, xLabelAngle, xLabelAlign, xLabelMargin: Aesthetic properties for the plot xLabel.
yLabelColor, yLabelSize, yLabelFontFace, yLabelFontFamily, yLabelAngle, yLabelAlign, yLabelMargin: Aesthetic properties for the plot yLabel.
legendPosition: A character string defining the legend position. Available options can be seen using tlf::LegendPositions list.
legendTitleSize, legendTitleColor, legendTitleFontFamily, legendTitleFontFace, legendTitleAngle, legendTitleAlign, legendTitleMargin: Aesthetic properties for the legend title.
legendKeysSize, legendKeysColor, legendKeysFontFamily, legendKeysFontFace, legendKeysAngle, legendKeysAlign, legendKeysMargin: Aesthetic properties for the legend caption.
legendBackgroundColor, legendBackgroundAlpha, legendBorderColor, legendBorderType, legendBorderSize: Aesthetic properties for the legend box
xAxisTicksLabels, xAxisLabelTicksSize, xAxisLabelTicksColor, xAxisLabelTicksFontFamily, xAxisLabelTicksFontFace, xAxisLabelTicksAngle, xAxisLabelTicksAlign, xAxisLabelTicksMargin, xAxisExpand: Aesthetic properties for the x-axis label.
yAxisTicksLabels, yAxisLabelTicksSize, yAxisLabelTicksColor, yAxisLabelTicksFontFamily, yAxisLabelTicksFontFace, yAxisLabelTicksAngle, yAxisLabelTicksAlign, yAxisLabelTicksMargin, yAxisExpand: Aesthetic properties for the y-axis label.
xAxisLimits, yAxisLimits: A numeric vector of axis limits for the x-and y-axis, respectively. This will preserve all data points but zoom in the plot.
xValuesLimits, yValuesLimits: A numeric vector of values limits for the x-and y-axis, respectively. This will filter out the data points outside the specified ranges before plotting.
xAxisTicks, yAxisTicks: A numeric vector or a function defining where to position x-and y-axis ticks, respectively.
xAxisScale, yAxisScale: A character string defining axis scale. Available options can be seen using tlf::Scaling list.
watermarkSize, watermarkColor, watermarkFontFamily, watermarkFontFace, watermarkAngle, watermarkAlign, watermarkMargin: A character string specifying the aesthetic properties for the watermark.
plotBackgroundFill, plotBackgroundColor, plotBackgroundSize, plotBackgroundLinetype: A character string specifying the aesthetic properties for the plot background.
plotPanelBackgroundFill, plotPanelBackgroundColor, plotPanelBackgroundSize, plotPanelBackgroundLinetype: A character string specifying the aesthetic properties for the plot panel (inside of plot) background.
xAxisColor, xAxisSize, xAxisLinetype: A character string specifying the aesthetic properties for the x-axis.
yAxisColor, yAxisSize, yAxisLinetype: A character string specifying the aesthetic properties for the y-axis.
xGridColor, xGridSize, xGridLinetype: A character string specifying the aesthetic properties for the x-axis grid.
yGridColor, yGridSize, yGridLinetype: A character string specifying the aesthetic properties for the y-axis grid.
linesColor, linesSize, linesLinetype, linesAlpha: A selection key or values for choice of color, fill, shape, size, linetype, alpha, respectively, for lines.
pointsColor, pointsShape, pointsSize, pointsAlpha: A selection key or values for choice of color, fill, shape, size, linetype, alpha, respectively, for points.
ribbonsFill, ribbonsSize, ribbonsLinetype, ribbonsAlpha: A selection key or values for choice of color, fill, shape, size, linetype, alpha, respectively, for ribbons.
errorbarsSize, errorbarsLinetype, errorbarsAlpha, errorbarsCapSize: A selection key or values for choice of color, fill, shape, size, linetype, alpha, cap width/height, respectively, for error bars.
displayLLOQ: A Boolean controlling display Lower Limit of Quantification lines. Default to True.
lloqDirection: A string controlling how the LLOQ lines are plotted. Can be "vertical", "horizontal" or "both". Default to NULL to respect specific plot configurations.
foldLinesLegend: A Boolean controlling the drawing of the fold lines in the legend. Default to False.
foldLinesLegendDiagonal: A Boolean controlling whether the fold lines legend should be horizontal or diagonal lines.

Active bindings

xUnit, yUnit: Units for quantities plotted on x- and y-axes, respectively.
title, subtitle, caption, xLabel, yLabel, legendTitle, watermark: A character string providing plot annotations for plot title, subtitle, caption, x-axis label, y-axis label, plot legend, watermark, respectively.
titleColor, titleSize, titleFontFace, titleFontFamily, titleAngle, titleAlign, titleMargin: Aesthetic properties for the plot title.
subtitleColor, subtitleSize, subtitleFontFace, subtitleFontFamily, subtitleAngle, subtitleAlign, subtitleMargin: Aesthetic properties for the plot subtitle.
captionColor, captionSize, captionFontFace, captionFontFamily, captionAngle, captionAlign, captionMargin: Aesthetic properties for the plot caption.
xLabelColor, xLabelSize, xLabelFontFace, xLabelFontFamily, xLabelAngle, xLabelAlign, xLabelMargin: Aesthetic properties for the plot xLabel.
yLabelColor, yLabelSize, yLabelFontFace, yLabelFontFamily, yLabelAngle, yLabelAlign, yLabelMargin: Aesthetic properties for the plot yLabel.
legendTitleSize, legendTitleColor, legendTitleFontFamily, legendTitleFontFace, legendTitleAngle, legendTitleAlign, legendTitleMargin: Aesthetic properties for the legend title.
legendKeysSize, legendKeysColor, legendKeysFontFamily, legendKeysFontFace, legendKeysAngle, legendKeysAlign, legendKeysMargin: Aesthetic properties for the legend caption.
legendBackgroundColor, legendBackgroundAlpha, legendBorderColor, legendBorderType, legendBorderSize: Aesthetic properties for the legend box
xAxisTicksLabels, xAxisLabelTicksSize, xAxisLabelTicksColor, xAxisLabelTicksFontFamily, xAxisLabelTicksFontFace, xAxisLabelTicksAngle, xAxisLabelTicksAlign, xAxisLabelTicksMargin, xAxisExpand: Aesthetic properties for the x-axis label.
yAxisTicksLabels, yAxisLabelTicksSize, yAxisLabelTicksColor, yAxisLabelTicksFontFamily, yAxisLabelTicksFontFace, yAxisLabelTicksAngle, yAxisLabelTicksAlign, yAxisLabelTicksMargin, yAxisExpand: Aesthetic properties for the y-axis label.
xAxisLimits, yAxisLimits: A numeric vector of axis limits for the x-and y-axis, respectively. This will preserve all data points but zoom in the plot.
xValuesLimits, yValuesLimits: A numeric vector of values limits for the x-and y-axis, respectively. This will filter out the data points outside the specified ranges before plotting.
xAxisTicks, yAxisTicks: A numeric vector or a function defining where to position x-and y-axis ticks, respectively.
xAxisScale, yAxisScale: A character string defining axis scale. Available options can be seen using tlf::Scaling list.
watermarkSize, watermarkColor, watermarkFontFamily, watermarkFontFace, watermarkAngle, watermarkAlign, watermarkMargin: A character string specifying the aesthetic properties for the watermark.
plotBackgroundFill, plotBackgroundColor, plotBackgroundSize, plotBackgroundLinetype: A character string specifying the aesthetic properties for the plot background.
plotPanelBackgroundFill, plotPanelBackgroundColor, plotPanelBackgroundSize, plotPanelBackgroundLinetype: A character string specifying the aesthetic properties for the plot panel (inside of plot) background.
xAxisColor, xAxisSize, xAxisLinetype: A character string specifying the aesthetic properties for the x-axis.
yAxisColor, yAxisSize, yAxisLinetype: A character string specifying the aesthetic properties for the y-axis.
xGridColor, xGridSize, xGridLinetype: A character string specifying the aesthetic properties for the x-axis grid.
yGridColor, yGridSize, yGridLinetype: A character string specifying the aesthetic properties for the y-axis grid.
linesColor, linesSize, linesLinetype, linesAlpha: A selection key or values for choice of color, fill, shape, size, linetype, alpha, respectively, for lines.
pointsColor, pointsShape, pointsSize, pointsAlpha: A selection key or values for choice of color, fill, shape, size, linetype, alpha, respectively, for points.
ribbonsFill, ribbonsSize, ribbonsLinetype, ribbonsAlpha: A selection key or values for choice of color, fill, shape, size, linetype, alpha, respectively, for ribbons.
errorbarsSize, errorbarsLinetype, errorbarsAlpha, errorbarsCapSize: A selection key or values for choice of color, fill, shape, size, linetype, alpha, cap width/height, respectively, for error bars.

Methods

Public methods

DefaultPlotConfiguration$clone()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

DefaultPlotConfiguration$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


# Create a new instance of this class
myPlotConfiguration <- DefaultPlotConfiguration$new()

# Change defaults
myPlotConfiguration$title <- "My Plot Title"
myPlotConfiguration$pointsSize <- 2.5
myPlotConfiguration$legendTitle <- "My Legend Title"

# Checking new values
myPlotConfiguration$pointsSize
#> [1] 2.5

# To check all default values, you can print the object
myPlotConfiguration
#> <DefaultPlotConfiguration>
#>   Public:
#>     caption: NULL
#>     captionAlign: right
#>     captionAngle: 0
#>     captionColor: black
#>     captionFontFace: plain
#>     captionFontFamily: 
#>     captionMargin: 2 2 5 2
#>     captionSize: 8
#>     clone: function (deep = FALSE) 
#>     displayLLOQ: TRUE
#>     errorbarsAlpha: 0.75
#>     errorbarsCapSize: 4
#>     errorbarsLinetype: solid
#>     errorbarsSize: 1
#>     foldLinesLegend: FALSE
#>     foldLinesLegendDiagonal: FALSE
#>     legendBackgroundAlpha: 0
#>     legendBackgroundColor: white
#>     legendBorderColor: NULL
#>     legendBorderSize: NULL
#>     legendBorderType: 1
#>     legendKeysAlign: left
#>     legendKeysAngle: 0
#>     legendKeysColor: black
#>     legendKeysFontFace: plain
#>     legendKeysFontFamily: 
#>     legendKeysMargin: 2 0 2 0
#>     legendKeysSize: 10
#>     legendPosition: NULL
#>     legendTitle: My Legend Title
#>     legendTitleAlign: left
#>     legendTitleAngle: 0
#>     legendTitleColor: black
#>     legendTitleFontFace: plain
#>     legendTitleFontFamily: 
#>     legendTitleMargin: 2 2 2 2
#>     legendTitleSize: 10
#>     linesAlpha: 0.75
#>     linesColor: NULL
#>     linesLinetype: NULL
#>     linesSize: 1
#>     lloqDirection: NULL
#>     plotBackgroundColor: black
#>     plotBackgroundFill: white
#>     plotBackgroundLinetype: blank
#>     plotBackgroundSize: 0.5
#>     plotPanelBackgroundColor: black
#>     plotPanelBackgroundFill: white
#>     plotPanelBackgroundLinetype: solid
#>     plotPanelBackgroundSize: 0.5
#>     pointsAlpha: 0.75
#>     pointsColor: #5050FFFF #CE3D32FF #749B58FF #F0E685FF #466983FF #BA633 ...
#>     pointsShape: circle diamond triangle square invertedTriangle cross th ...
#>     pointsSize: 2.5
#>     ribbonsAlpha: 0.5
#>     ribbonsFill: #5050FFFF #CE3D32FF #749B58FF #F0E685FF #466983FF #BA633 ...
#>     ribbonsLinetype: solid longdash dotted dashed twodash dotdash blank
#>     ribbonsSize: 1
#>     subtitle: NULL
#>     subtitleAlign: left
#>     subtitleAngle: 0
#>     subtitleColor: black
#>     subtitleFontFace: plain
#>     subtitleFontFamily: 
#>     subtitleMargin: 0 2 10 2
#>     subtitleSize: 10
#>     title: My Plot Title
#>     titleAlign: left
#>     titleAngle: 0
#>     titleColor: black
#>     titleFontFace: plain
#>     titleFontFamily: 
#>     titleMargin: 20 2 10 2
#>     titleSize: 12
#>     watermark: NULL
#>     watermarkAlign: center
#>     watermarkAngle: 30
#>     watermarkColor: grey40
#>     watermarkFontFace: plain
#>     watermarkFontFamily: 
#>     watermarkMargin: 1 1 1 1
#>     watermarkSize: 20
#>     xAxisColor: black
#>     xAxisExpand: FALSE
#>     xAxisLabelTicksAlign: center
#>     xAxisLabelTicksAngle: 0
#>     xAxisLabelTicksColor: black
#>     xAxisLabelTicksFontFace: plain
#>     xAxisLabelTicksFontFamily: 
#>     xAxisLabelTicksMargin: 2 2 2 2
#>     xAxisLabelTicksSize: 8
#>     xAxisLimits: NULL
#>     xAxisLinetype: solid
#>     xAxisScale: NULL
#>     xAxisSize: 0.5
#>     xAxisTicks: NULL
#>     xAxisTicksLabels: identity
#>     xGridColor: grey
#>     xGridLinetype: blank
#>     xGridSize: 0.25
#>     xLabel: NULL
#>     xLabelAlign: center
#>     xLabelAngle: 0
#>     xLabelColor: black
#>     xLabelFontFace: plain
#>     xLabelFontFamily: 
#>     xLabelMargin: 10 2 5 2
#>     xLabelSize: 10
#>     xUnit: NULL
#>     xValuesLimits: NULL
#>     yAxisColor: black
#>     yAxisExpand: FALSE
#>     yAxisLabelTicksAlign: center
#>     yAxisLabelTicksAngle: 90
#>     yAxisLabelTicksColor: black
#>     yAxisLabelTicksFontFace: plain
#>     yAxisLabelTicksFontFamily: 
#>     yAxisLabelTicksMargin: 2 2 2 2
#>     yAxisLabelTicksSize: 8
#>     yAxisLimits: NULL
#>     yAxisLinetype: solid
#>     yAxisScale: NULL
#>     yAxisSize: 0.5
#>     yAxisTicks: NULL
#>     yAxisTicksLabels: identity
#>     yGridColor: grey
#>     yGridLinetype: blank
#>     yGridSize: 0.25
#>     yLabel: NULL
#>     yLabelAlign: center
#>     yLabelAngle: 90
#>     yLabelColor: black
#>     yLabelFontFace: plain
#>     yLabelFontFamily: 
#>     yLabelMargin: 5 2 10 2
#>     yLabelSize: 10
#>     yUnit: NULL
#>     yValuesLimits: NULL