Package 'tlf'

Title: TLF Library
Description: An implementation of the Table, Listing and Figure concepts in R. This library provides a standardized approach to creating tables and graphs based on conventions over configurations.
Authors: Open-Systems-Pharmacology Community [cph], Michael Sevestre [aut, cre], Pierre Chelle [aut], Abdullah Hamadeh [aut], Indrajeet Patil [ctb] (ORCID: <https://orcid.org/0000-0003-1995-6531>, Twitter: @patilindrajeets)
Maintainer: Michael Sevestre <[email protected]>
License: GPL-2 | file LICENSE
Version: 1.6.2
Built: 2026-07-06 12:18:55 UTC
Source: https://github.com/Open-Systems-Pharmacology/TLF-Library

Help Index

Sanitize Label Text

Description

ggtext does not allow certain characters that can be converted to html tags but that are not supported. This function removes this forbidden characters.

Usage

.sanitizeLabel(text)

Arguments

text

a character string

Value

a sanitized character string

addErrorbar

Description

Add an errorbar layer to a ggplot object.

Usage

addErrorbar(
  data = NULL,
  metaData = NULL,
  x = NULL,
  ymin = NULL,
  ymax = NULL,
  caption = NULL,
  color = NULL,
  size = NULL,
  linetype = NULL,
  capSize = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
x

Numeric values to plot along the x axis. Only used instead of data if data is NULL.
ymin

Numeric values to plot along the y axis. Only used instead of data if data is NULL.
ymax

Numeric values to plot along the y axis. Only used instead of data if data is NULL.
caption

Optional character values defining the legend captions of the plot.
color

Optional character values defining the colors of the plot layer. See grDevices::colors() to get names of colors
size

Optional numeric values defining the size of the plot layer.
linetype

Optional character values defining the linetype of the plot layer. See enum Linetypes to get names of linetype.
capSize

Numeric extent of the error bars caps Caution the value corresponds to the ratio of the mean spacing between plotted error bars. For instance, an extent of 1 will fill the caps until the next error bar
dataMapping

A RangeDataMapping object mapping x, ymin, ymax and aesthetic groups to their variable names of data.
plotConfiguration

An optional PlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

References

For examples, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/atom-plots.html

See Also

Other atom plots: addLine(), addRibbon(), addScatter(), initializePlot()

Examples

# Add errorbar using x, ymin and ymax
addErrorbar(
  x = c(1, 2, 1, 2, 3),
  ymin = c(5, 0, 2, 3, 4),
  ymax = c(6, 2, 6, 2.5, 5)
)

# Add errorbar using a data.frame
time <- seq(0, 30, 0.5)
errorbarData <- data.frame(x = time, ymin = cos(time) - 1, ymax = cos(time) + 1)

addErrorbar(
  data = errorbarData,
  dataMapping = RangeDataMapping$new(x = "x", ymin = "ymin", ymax = "ymax")
)

# Or for simple cases a smart mapping will get directly x, ymin and ymax from data
addErrorbar(data = errorbarData)

# Add a errorbar with caption
addErrorbar(data = errorbarData, caption = "My errorbar plot")

# Add a errorbar with specific properties
addErrorbar(data = errorbarData, color = "blue", size = 0.5, caption = "My data")

# Add a errorbar with specific properties
p <- addErrorbar(
  data = errorbarData,
  color = "blue", size = 0.5, caption = "My data"
)
addScatter(
  x = time, y = cos(time),
  color = "red", size = 1, caption = "My data",
  plotObject = p
)

addLine

Description

Add a line layer to a ggplot object.

Usage

addLine(
  data = NULL,
  metaData = NULL,
  x = NULL,
  y = NULL,
  caption = NULL,
  color = NULL,
  shape = NULL,
  size = NULL,
  linetype = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
x

Numeric values to plot along the x axis. Only used instead of data if data is NULL.
y

Numeric values to plot along the y axis. Only used instead of data if data is NULL.
caption

Optional character values defining the legend captions of the plot.
color

Optional character values defining the colors of the plot layer. See grDevices::colors() to get names of colors
shape

Optional character values defining the shapes/symbols of the plot layer. See enum Shapes to get names of shapes.
size

Optional numeric values defining the size of the plot layer.
linetype

Optional character values defining the linetype of the plot layer. See enum Linetypes to get names of linetype.
dataMapping

A XYGDataMapping object mapping x, y and aesthetic groups to their variable names of data.
plotConfiguration

An optional PlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

References

For examples, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/atom-plots.html

See Also

Other atom plots: addErrorbar(), addRibbon(), addScatter(), initializePlot()

Examples

# Add line using x and y
addLine(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

# Add line using a data.frame
time <- seq(0, 30, 0.1)
lineData <- data.frame(x = time, y = cos(time))

addLine(
  data = lineData,
  dataMapping = XYGDataMapping$new(x = "x", y = "y")
)

# Or for simple cases a smart mapping will get directly x and y from data
addLine(data = lineData)

# Add a line with caption
addLine(data = lineData, caption = "My line plot")

# Add a line with specific properties
addLine(
  data = lineData,
  color = "blue", linetype = "longdash", size = 0.5, caption = "My data"
)

# Add a line with specific properties
p <- addLine(
  data = lineData,
  color = "blue", linetype = "longdash", size = 0.5, caption = "My data"
)
addLine(
  x = c(0, 1), y = c(1, 0),
  color = "red", linetype = "solid", size = 1,
  plotObject = p
)

addRibbon

Description

Add a ribbon layer to a ggplot object.

Usage

addRibbon(
  data = NULL,
  metaData = NULL,
  x = NULL,
  ymin = NULL,
  ymax = NULL,
  caption = NULL,
  fill = NULL,
  color = NULL,
  size = NULL,
  linetype = NULL,
  alpha = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
x

Numeric values to plot along the x axis. Only used instead of data if data is NULL.
ymin

Numeric values to plot along the y axis. Only used instead of data if data is NULL.
ymax

Numeric values to plot along the y axis. Only used instead of data if data is NULL.
caption

Optional character values defining the legend captions of the plot.
fill

Optional character values defining the colors of the plot layer. See grDevices::colors() to get names of colors
color

Optional character values defining the colors of the plot layer. See grDevices::colors() to get names of colors
size

Optional numeric values defining the size of the plot layer.
linetype

Optional character values defining the linetype of the plot layer. See enum Linetypes to get names of linetype.
alpha

Numeric value between 0 and 1 corresponding to transparency of the ribbon. The closer to 0, the more transparent the ribbon is. The closer to 1, the more opaque the ribbon is.
dataMapping

A RangeDataMapping object mapping x, ymin, ymax and aesthetic groups to their variable names of data.
plotConfiguration

An optional PlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

References

For examples, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/atom-plots.html

See Also

Other atom plots: addErrorbar(), addLine(), addScatter(), initializePlot()

Examples

# Add ribbon using x, ymin and ymax
addRibbon(
  x = c(1, 2, 1, 2, 3),
  ymin = c(5, 0, 2, 3, 4),
  ymax = c(6, 2, 6, 2.5, 5)
)

# Add ribbon using a data.frame
time <- seq(0, 30, 0.1)
ribbonData <- data.frame(x = time, ymin = cos(time) - 1, ymax = cos(time) + 1)

addRibbon(
  data = ribbonData,
  dataMapping = RangeDataMapping$new(x = "x", ymin = "ymin", ymax = "ymax")
)

# Or for simple cases a smart mapping will get directly x, ymin and ymax from data
addRibbon(data = ribbonData)

# Add a ribbon with caption
addRibbon(data = ribbonData, caption = "My ribbon plot")

# Add a ribbon with specific properties
addRibbon(data = ribbonData, fill = "blue", alpha = 0.5, caption = "My data")

# Add a ribbon with specific properties
p <- addRibbon(data = ribbonData, fill = "blue", alpha = 0.5, caption = "My data")
addRibbon(
  x = c(0, 1), ymin = c(-0.5, -0.5), ymax = c(0.5, 0.5),
  fill = "red", alpha = 1,
  plotObject = p
)

addScatter

Description

Add a scatter plot layer to a ggplot object

Usage

addScatter(
  data = NULL,
  metaData = NULL,
  x = NULL,
  y = NULL,
  caption = NULL,
  color = NULL,
  shape = NULL,
  size = NULL,
  linetype = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
x

Numeric values to plot along the x axis. Only used instead of data if data is NULL.
y

Numeric values to plot along the y axis. Only used instead of data if data is NULL.
caption

Optional character values defining the legend captions of the plot.
color

Optional character values defining the colors of the plot layer. See grDevices::colors() to get names of colors
shape

Optional character values defining the shapes/symbols of the plot layer. See enum Shapes to get names of shapes.
size

Optional numeric values defining the size of the plot layer.
linetype

Optional character values defining the linetype of the plot layer. See enum Linetypes to get names of linetype.
dataMapping

A XYGDataMapping object mapping x, y and aesthetic groups to their variable names of data.
plotConfiguration

An optional PlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

References

For examples, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/atom-plots.html

See Also

Other atom plots: addErrorbar(), addLine(), addRibbon(), initializePlot()

Examples

# Add scatter using x and y
addScatter(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

# Add scatter using a data.frame
time <- seq(0, 30, 0.1)
scatterData <- data.frame(x = time, y = cos(time))

addScatter(
  data = scatterData,
  dataMapping = XYGDataMapping$new(x = "x", y = "y")
)

# Or for simple cases a smart mapping will get directly x and y from data
addScatter(data = scatterData)

# Add a scatter with caption
addScatter(data = scatterData, caption = "My scatter plot")

# Add a scatter with specific properties
addScatter(
  data = scatterData,
  color = "blue", shape = "diamond", size = 2, caption = "My data"
)

# Add a scatter with specific properties
p <- addScatter(
  data = scatterData,
  color = "blue", shape = "diamond", size = 2, caption = "My data"
)
addScatter(
  x = c(0, 1), y = c(1, 0),
  color = "red", shape = "circle", size = 3,
  plotObject = p
)

addWatermark

Description

Creates a ggplot grob based on the label text and its font properties. Then, adds the grob to the ggplot object as a new layer using ggplot2::annotation_custom.

Usage

addWatermark(
  plotObject,
  watermark,
  color = NULL,
  size = NULL,
  angle = NULL,
  alpha = NULL
)

Arguments

plotObject

A ggplot object
watermark

A character value or a Label object
color

Color of the watermark.
size

Size of the watermark.
angle

Angle of the watermark (in degree).
alpha

Numeric value between 0 and 1 corresponding to transparency of the watermark The closer to 0, the more transparent the watermark is. The closer to 1, the more opaque the watermark is.

Value

A ggplot object

Examples

# Add a watermark to an empty plot
p <- ggplot2::ggplot()
addWatermark(p, "watermark")

# Watermark with font properties
watermarkLabel <- Label$new(text = "watermark", color = "blue")
addWatermark(p, watermarkLabel)

# Horizontal watermark
addWatermark(p, watermarkLabel, angle = 0)

# Watermark totally opaque
addWatermark(p, watermarkLabel, alpha = 1)

# As multiple layers of watermark:
p2 <- addWatermark(p, watermarkLabel, alpha = 1)
addWatermark(p2, "other watermark", color = "red", angle = 90)

AestheticFields

Description

List of all available aesthetic fields that manage aesthetic properties

Usage

AestheticFields

Format

An object of class list of length 4.

See Also

Other enum helpers: AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

AestheticProperties

Description

Enum of aesthetic property names of ggplot2

Usage

AestheticProperties

Format

An object of class list of length 6.

See Also

Other enum helpers: AestheticFields, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

AestheticSelectionKeys

Description

List of some ggplot2 shapes

Usage

AestheticSelectionKeys

Format

An object of class list of length 4.

See Also

Other enum helpers: AestheticFields, AestheticProperties, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

AggregationInput

Description

R6 class to be used to construct inputs to the AggregationSummary class

Public fields

aggregationFunction

list of functions to use for aggregation

aggregationFunctionName

vector of function names that will be used as variable name of the aggregation

aggregationUnit

unit of aggregation output

aggregationDimension

dimension of aggregation output

Methods

Public methods

Method new()

Create a new AggregationInput object

Usage
AggregationInput$new(
  aggregationFunction = NULL,
  aggregationFunctionName = NULL,
  aggregationUnit = NULL,
  aggregationDimension = NULL
)
Arguments
aggregationFunction

list of functions to use for aggregation

aggregationFunctionName

vector of function names that will be used as variable name of the aggregation

aggregationUnit

unit of aggregation output

aggregationDimension

dimension of aggregation output

Returns

A new AggregationInput object

Method clone()

The objects of this class are cloneable with this method.

Usage
AggregationInput$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

AggregationSummary

Description

R6 class to split a data.frame data into subsets defined by unique combinations of elements in the columns xColumnNames and groupingColumnNames. Applies functions defined in aggregationFunctionsVector to column yColumnNames. Returns a list of data.frame, one data.frame for each function listed in aggregationFunctionsVector. Each data.frame in list element is named after the function's corresponding string in aggregationFunctionNames. The summary statistic column name in each data.frame is the same as the name of the data.frame in the returned list.

Public fields

data

data.frame

metaData

list of information on data

xColumnNames

character names of grouping variables

groupingColumnNames

character names of grouping variables

yColumnNames

character names of dependent variables (that are grouped)

aggregationInputsVector

list of R6 class AggregationInput objects

aggregationFunctionsVector

list of functions to use for aggregation

aggregationFunctionNames

vector of function names that will be used as variable name of the aggregation

aggregationUnitsVector

character vector of units of aggregation output

aggregationDimensionsVector

character vector of dimensions of aggregation output

dfHelper

data.frame of aggregated values

metaDataHelper

list of information on dfHelper

Methods

Public methods

Method new()

Create a new AggregationSummary object

Usage
AggregationSummary$new(
  data,
  metaData = NULL,
  xColumnNames = NULL,
  groupingColumnNames = NULL,
  yColumnNames = NULL,
  aggregationInputsVector = NULL,
  aggregationFunctionsVector = NULL,
  aggregationFunctionNames = NULL,
  aggregationUnitsVector = NULL,
  aggregationDimensionsVector = NULL
)
Arguments
data

data.frame

metaData

list of information on data

xColumnNames

character names of grouping variables

groupingColumnNames

character names of grouping variables

yColumnNames

character names of dependent variables (that are grouped)

aggregationInputsVector

list of R6 class AggregationInput objects

aggregationFunctionsVector

list of functions to use for aggregation

aggregationFunctionNames

vector of function names that will be used as variable name of the aggregation

aggregationUnitsVector

character vector of units of aggregation output

aggregationDimensionsVector

character vector of dimensions of aggregation output

Returns

A new AggregationSummary object

Method applyAggregationFunctions()

Apply aggregation functions on x

Usage
AggregationSummary$applyAggregationFunctions(x)
Arguments
x

numeric vector

Returns

A list or vector of aggregated values

Method generateAggregatedValues()

Generate aggregated values

Usage
AggregationSummary$generateAggregatedValues()
Returns

A list or vector of aggregated values

Method clone()

The objects of this class are cloneable with this method.

Usage
AggregationSummary$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Alignments

Description

List of all available alignments/justifications for fonts

Usage

Alignments

Format

An object of class list of length 3.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

asLabel

Description

Set a character string into a Label object associating font properties to input If text is already a Label object, asLabel can be used to update its font properties

Usage

asLabel(text = "", font = NULL)

Arguments

text

A character value
font

A Font object defining the font properties of the Label

Value

A Label object

Examples

title <- "Title of Plot"
title <- asLabel(title)

AtomPlots

Description

List of all available atom plots

Usage

AtomPlots

Format

An object of class list of length 5.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

AxisConfiguration

Description

R6 class defining the configuration of axis

Active bindings

valuesLimits

numeric vector of length 2 defining limits of axis. A value of NULL is allowed and lead to default ggplot2 behaviour

axisLimits

numeric vector of length 2 defining limits of axis. A value of NULL is allowed and lead to default ggplot2 behaviour

scale

name of axis scale from Enum Scaling A value of NULL is allowed and will lead to a default linear scale

ticks

function or values defining where axis ticks are placed

minorTicks

function or values defining where axis minor ticks are placed

ticklabels

function or values defining the axis tick labels

font

Font object defining the font of the ticklabels

expand

logical defining if data is expanded until axis. If TRUE, data is expanded until axis If FALSE, some space between data and axis is kept

Methods

Public methods

Method new()

Create a new AxisConfiguration object

Usage
AxisConfiguration$new(
  valuesLimits = NULL,
  axisLimits = NULL,
  limits = lifecycle::deprecated(),
  scale = Scaling$lin,
  ticks = NULL,
  ticklabels = NULL,
  minorTicks = NULL,
  font = NULL,
  expand = FALSE
)
Arguments
valuesLimits

numeric vector of value limits (data outside these limits is removed)

axisLimits

numeric vector of axis limits (data outside these limits is kept but not plotted)

limits

[Deprecated]. Replaced by axisLimits argument.

scale

character defining axis scale Use enum Scaling to access predefined scales.

ticks

numeric vector or function defining where to position axis ticks

ticklabels

character vector or function defining what to print on axis ticks

minorTicks

numeric vector or function defining where to position minor axis ticks

font

Font object defining the font of ticklabels

expand

logical defining if data is expanded until axis. If TRUE, data is expanded until axis If FALSE, some space between data and axis is kept

Returns

A new AxisConfiguration object

Method ggplotScale()

Get the ggplot2 actual trans name of scale

Usage
AxisConfiguration$ggplotScale()
Returns

A character included in ggplot2 available trans names

Method ggplotExpansion()

Get the ggplot2 actual function for expansion

Usage
AxisConfiguration$ggplotExpansion()
Returns

A ggplot2 function

Method prettyTicks()

Get tick values for pretty default log plots

Usage
AxisConfiguration$prettyTicks()
Returns

User defined tick values or tlf default ticks

Method prettyMinorTicks()

Get tick values for pretty default log plots

Usage
AxisConfiguration$prettyMinorTicks()
Returns

User defined tick values or tlf default ticks

Method prettyTickLabels()

Get tick labels for pretty default log plots

Usage
AxisConfiguration$prettyTickLabels()
Returns

User defined tick labels or tlf default ticklabels

Method clone()

The objects of this class are cloneable with this method.

Usage
AxisConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

BackgroundConfiguration

Description

R6 class defining the configuration of background

Active bindings

watermark

Label object

plot

BackgroundElement object

panel

BackgroundElement object

xAxis

LineElement object

yAxis

LineElement object

y2Axis

LineElement object

xGrid

LineElement object

yGrid

LineElement object

y2Grid

LineElement object

Methods

Public methods

Method new()

Create a new BackgroundConfiguration object

Usage
BackgroundConfiguration$new(
  watermark = NULL,
  plot = NULL,
  panel = NULL,
  xAxis = NULL,
  yAxis = NULL,
  y2Axis = NULL,
  xGrid = NULL,
  yGrid = NULL,
  y2Grid = NULL
)
Arguments
watermark

Label object defining properties of watermark

plot

BackgroundElement object defining outside plot background properties

panel

BackgroundElement object defining panel (inside of plot) background properties

xAxis

LineElement object defining properties of x-axis

yAxis

LineElement object defining properties of y-axis

y2Axis

LineElement object defining properties of right y-axis

xGrid

LineElement object defining properties of x-grid

yGrid

LineElement object defining properties of y-grid

y2Grid

LineElement object defining properties of right y-grid

Returns

A new BackgroundConfiguration object

Method updatePlot()

Update background a ggplot object from BackgroundConfiguration properties

Usage
BackgroundConfiguration$updatePlot(plotObject)
Arguments
plotObject

a ggplot object

Returns

A ggplot object

Method clone()

The objects of this class are cloneable with this method.

Usage
BackgroundConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

BackgroundElement

Description

R6 class defining the properties of background elements

Public fields

fill

character defining the color filling of the background element

color

character defining the color of the background element frame/line

size

numeric defining the size of the background element frame/line

linetype

character defining the size of the background element frame/line

Methods

Public methods

Method new()

Create a new BackgroundElement object

Usage
BackgroundElement$new(fill = NULL, color = NULL, size = NULL, linetype = NULL)
Arguments
fill

character color filling of the background element

color

character color of the frame of the background element

size

character size of the frame of the background element

linetype

character linetype of the frame of the background element

Returns

A new BackgroundElement object

Method createPlotElement()

Create a ggplot2::element_rect directly usable by ggplot2::theme.

Usage
BackgroundElement$createPlotElement(
  fill = NULL,
  color = NULL,
  size = NULL,
  linetype = NULL
)
Arguments
fill

character color filling of the background element

color

character color of the frame of the background element

size

character size of the frame of the background element

linetype

character linetype of the frame of the background element

Returns

An element_rect object.

Method clone()

The objects of this class are cloneable with this method.

Usage
BackgroundElement$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

BoxWhiskerDataMapping

Description

R6 class for mapping y, GroupMapping, boxWhiskerLimits and outlierLimits to data

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> BoxWhiskerDataMapping

Public fields

outlierLimits

List of minOutlierLimit and maxOutlierLimit functions outside which data is flagged as outlier

boxWhiskerLimits

List of ymin, lower, middle, upper and ymax functions calculated on data to obtain box whiskers

Methods

Public methods

Inherited methods

Method new()

Create a new BoxWhiskerDataMapping object

Usage
BoxWhiskerDataMapping$new(
  x = NULL,
  y,
  ymin = tlfStatFunctions$`Percentile5%`,
  lower = tlfStatFunctions$`Percentile25%`,
  middle = tlfStatFunctions$`Percentile50%`,
  upper = tlfStatFunctions$`Percentile75%`,
  ymax = tlfStatFunctions$`Percentile95%`,
  minOutlierLimit = tlfStatFunctions$`Percentile25%-1.5IQR`,
  maxOutlierLimit = tlfStatFunctions$`Percentile75%+1.5IQR`,
  ...
)
Arguments
x

Name of x variable to map Default value is NULL in case of a unique box in the boxplot.

y

Name of y variable to map

ymin

Name of function used for calculating lower whisker. Default value is ⁠Percentile5%⁠.

lower

Name of function used for calculating lower line of box Default value is ⁠Percentile25%⁠.

middle

Name of function used for calculating middle line Default value is ⁠Percentile55%⁠.

upper

Name of function used for calculating upper line of box Default value is ⁠Percentile75%⁠.

ymax

Name of function used for calculating upper whisker Default value is ⁠Percentile95%⁠.

minOutlierLimit

Name of function used for calculating lower outlier limit Default value is ⁠Percentile25-1.5IQR%⁠.

maxOutlierLimit

Name of function used for calculating upper outlier limit Default value is ⁠Percentile75+1.5IQR%⁠.

...

parameters inherited from XYGDataMapping

Returns

A new BoxWhiskerDataMapping object

Method getBoxWhiskerLimits()

Get a data.frame with box-whisker limit by group

Usage
BoxWhiskerDataMapping$getBoxWhiskerLimits(data)
Arguments
data

data.frame to check

Returns

A data.frame with ymin, lower, middle, upper, ymax variables.

Method getOutliers()

Get a data.frame flagging outliers

Usage
BoxWhiskerDataMapping$getOutliers(data)
Arguments
data

data.frame to check

Returns

A data.frame with minOutliers and maxOutliers variables. Values not flagged are NA in the outliers variables

Method clone()

The objects of this class are cloneable with this method.

Usage
BoxWhiskerDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

BoxWhiskerPlotConfiguration

Description

R6 class defining the configuration of a ggplot object for boxplots

Super class

tlf::PlotConfiguration -> BoxWhiskerPlotConfiguration

Public fields

defaultXScale

Default xAxis scale value when creating a BoxWhiskerPlotConfiguration object

Active bindings

outliers

logical defining if outliers should be included in boxplot

Methods

Public methods

Method new()

Create a new BoxWhiskerPlotConfiguration object

Usage
BoxWhiskerPlotConfiguration$new(outliers = TRUE, ...)
Arguments
outliers

logical defining if outliers should be included in boxplot

...

parameters inherited from PlotConfiguration

Returns

A new BoxWhiskerPlotConfiguration object

Method clone()

The objects of this class are cloneable with this method.

Usage
BoxWhiskerPlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

ColorMaps

Description

List with some color maps for Theme object.

The ospDefault color map is based on colors in default_igv qualitative color palette from {ggsci} package.

Usage

ColorMaps

Format

An object of class list of length 6.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

ColorPalettes

Description

Enum of available color palettes First color palettes come from viridis Remaining color palettes are from RColorBrewer

Usage

ColorPalettes

Format

An object of class list of length 42.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

createWatermarkGrob

Description

Creates a ggplot grob based on the label text and its font properties.

Usage

createWatermarkGrob(label, alpha = NULL)

Arguments

label

A character value or Label object
alpha

Numeric value between 0 and 1 corresponding to transparency of the watermark The closer to 0, the more transparent the watermark is. The closer to 1, the more opaque the watermark is.

Value

A ggplot grob

CumulativeTimeProfileDataMapping

Description

R6 class for mapping x, y, GroupMapping variables to data

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> CumulativeTimeProfileDataMapping

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
CumulativeTimeProfileDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

CumulativeTimeProfilePlotConfiguration

Description

R6 class defining the configuration of a ggplot object for cumulative time profile plots

Super class

tlf::PlotConfiguration -> CumulativeTimeProfilePlotConfiguration

Public fields

defaultExpand

Default expand value when creating a CumulativeTimeProfilePlotConfiguration object

colorPalette

color palette property from ggplot2

Methods

Public methods

Method new()

Create a new CumulativeTimeProfilePlotConfiguration object

Usage
CumulativeTimeProfilePlotConfiguration$new(colorPalette = NULL, ...)
Arguments
colorPalette

color palette property from ggplot2

...

parameters inherited from PlotConfiguration

Returns

A new CumulativeTimeProfilePlotConfiguration object

Method clone()

The objects of this class are cloneable with this method.

Usage
CumulativeTimeProfilePlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

DataMappings

Description

List of all available molecule plots

Usage

DataMappings

Format

An object of class list of length 18.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

DDIRatioDataMapping

Description

R6 class for mapping x, y, GroupMapping and DDI ratio lines variables to data

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> tlf::PKRatioDataMapping -> DDIRatioDataMapping

Active bindings

deltaGuest

Value of delta in Guest et al. equation

minRange

Minimum range of x values for guest and ratio lines

residualsVsObserved

Logical defining if calculated DDI data are as residuals vs observed or predicted vs observed

Methods

Public methods

Inherited methods

Method new()

Create a new DDIRatioDataMapping object

Usage
DDIRatioDataMapping$new(
  deltaGuest = NULL,
  minRange = c(0.01, 100),
  lines = DefaultDataMappingValues$ddiRatio,
  residualsVsObserved = FALSE,
  ...
)
Arguments
deltaGuest

Value of delta in Guest et al. equation. Default value is 1.

minRange

Minimum range of x values for guest and ratio lines Default is [0.01 - 100]

lines

List of ratio limits to display as diagonal/horizontal lines

residualsVsObserved

Logical defining if calculated DDI data are as residuals vs observed or predicted vs observed

...

parameters inherited from PKRatioDataMapping

Returns

A new DDIRatioDataMapping object

Method clone()

The objects of this class are cloneable with this method.

Usage
DDIRatioDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

DDIRatioPlotConfiguration

Description

R6 class defining the configuration of a ggplot object for DDI ratio plots

Super class

tlf::PlotConfiguration -> DDIRatioPlotConfiguration

Public fields

defaultXScale

Default xAxis scale value when creating a DDIRatioPlotConfiguration object

defaultYScale

Default yAxis scale value when creating a DDIRatioPlotConfiguration object

defaultExpand

Default expand value when creating a DDIRatioPlotConfiguration object

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
DDIRatioPlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

DefaultDataMappingValues

Description

List of default values used in dataMapping

Usage

DefaultDataMappingValues

Format

An object of class list of length 7.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

Directions

Description

Enum of plotting directions for errorbars and lloq lines.

Usage

Directions

Format

An object of class list of length 3.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

ExportConfiguration

Description

R6 class defining properties for saving a ggplot object

Public fields

name

character defining the name of the file to be saved (without extension)

path

Path of the directory to save plot to: path and filename are combined to create the fully qualified file name. Defaults to the working directory.

format

character defining the format of the file to be saved

width

numeric values defining the width in units of the plot dimensions after saving

height

numeric values defining the height in units of the plot dimensions after saving

units

character defining the unit of the saving dimension

dpi

(dots per inch) numeric value defining plot resolution

Methods

Public methods

Method new()

Create a new ExportConfiguration object

Usage
ExportConfiguration$new(
  path = NULL,
  name = NULL,
  format = NULL,
  width = NULL,
  height = NULL,
  units = NULL,
  dpi = NULL
)
Arguments
path

Path of the directory to save plot to: path and filename are combined to create the fully qualified file name. Defaults to the working directory.

name

character defining the name of the file to be saved (without extension)

format

character defining the format of the file to be saved.

width

numeric values defining the width in units of the plot dimensions after saving

height

numeric values defining the height in units of the plot dimensions after saving

units

character defining the unit of the saving dimension

dpi

numeric value defining plot resolution (dots per inch)

Returns

A new ExportConfiguration object

Method print()

Print properties of export configuration

Usage
ExportConfiguration$print()
Returns

Export configuration properties

Method getFileName()

Print the default exported file name from the export configuration

Usage
ExportConfiguration$getFileName()
Returns

Default file name

Method savePlot()

Save/Export a plot

Usage
ExportConfiguration$savePlot(plotObject, fileName = NULL)
Arguments
plotObject

A ggplot object

fileName

character file name of the exported plot

Returns

The file name of the exported plot

Method convertPixels()

If unit is in pixels, convert all export dimensions to inches to keep compatibility with older versions of ggplot2

Usage
ExportConfiguration$convertPixels()

Method clone()

The objects of this class are cloneable with this method.

Usage
ExportConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

ExportFormats

Description

List of all available formats to export a ggplot object

Usage

ExportFormats

Format

An object of class list of length 10.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

exportPlot

Description

Save a ggplot object according to its export properties

Usage

exportPlot(
  plotObject,
  fileName = NULL,
  name = NULL,
  format = NULL,
  width = NULL,
  height = NULL,
  units = NULL,
  dpi = NULL
)

Arguments

plotObject

Graphical object created from ggplot
fileName

name of exported file (with extension)
name

character defining the name of the file to be saved (without extension)
format

character defining the format of the file to be saved.
width

numeric values defining the width in units of the plot dimensions after saving
height

numeric values defining the height in units of the plot dimensions after saving
units

character defining the unit of the saving dimension
dpi

numeric value defining plot resolution (dots per inch)

Value

The file name of the exported plot

exportPlotConfigurationCode

Description

Export a plot configuration as R code

Usage

exportPlotConfigurationCode(plotConfiguration, name = "plotConfiguration")

Arguments

plotConfiguration

A PlotConfiguration object
name

Name of PlotConfiguration object in the created code

Value

R code to recreate the plot configuration as character

ExportUnits

Description

List of all available units for width and height to export a ggplot object

Usage

ExportUnits

Format

An object of class list of length 4.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

Font

Description

R6 class defining font properties

Public fields

size

numeric defining the size of font

color

character defining the color of font

fontFamily

character defining the family of font

fontFace

character defining the font face as defined in helper enum FontFaces.

angle

numeric defining the angle of font

align

character defining the alignment of font as defined in helper enum Alignments.

maxWidth

numeric that will be converted to a ggplot2::unit object (in "pt" unit) defining the maximum width of text box.

margin

a numeric vector of length 4 defining the size of the area (in pt) around the text in the followin order: top, right, bottom, left.

Methods

Public methods

Method new()

Create a new Font object. Default font properties are defined directly in the object field, so NULL input is allowed will lead to default properties.

Usage
Font$new(
  color = NULL,
  size = NULL,
  fontFamily = NULL,
  fontFace = NULL,
  angle = NULL,
  align = NULL,
  maxWidth = NULL,
  margin = NULL
)
Arguments
color

character defining the color of font.

size

numeric defining the size of font.

fontFamily

character defining the family of font.

fontFace

character defining the font face as defined in helper enum FontFaces.

angle

numeric defining the angle of font.

align

character defining the alignment of font as defined in helper enum Alignments.

maxWidth

numeric that will be converted to a ggplot2::unit object (in "pt" unit) defining the maximum width of text box.

margin

a numeric vector of length 4 defining the size of the area (in pt) around the text in the followin order: top, right, bottom, left.

Returns

A new Font object

Method createPlotTextFont()

Create a ggplot2::element_text directly convertible by ggplot2::theme.

Usage
Font$createPlotTextFont(
  size = NULL,
  color = NULL,
  fontFamily = NULL,
  fontFace = NULL,
  angle = NULL,
  align = NULL,
  margin = NULL
)
Arguments
size

numeric defining the size of font

color

character defining the color of font

fontFamily

character defining the family of font

fontFace

character defining the font face as defined in helper enum FontFaces.

angle

numeric defining the angle of font.

align

character defining the alignment of font as defined in helper enum Alignments.

margin

a numeric vector of length 4 defining the size of the area (in pt) around the text in the followin order: top, right, bottom, left.

Returns

An element_text object.

Method createPlotTextBoxFont()

Create a ggplot2::element_text directly convertible by ggplot2::theme.

Usage
Font$createPlotTextBoxFont(
  size = NULL,
  color = NULL,
  fontFamily = NULL,
  fontFace = NULL,
  angle = NULL,
  align = NULL,
  maxWidth = NULL,
  margin = NULL
)
Arguments
size

numeric defining the size of font

color

character defining the color of font

fontFamily

character defining the family of font

fontFace

character defining the font face as defined in helper enum FontFaces.

angle

numeric defining the angle of font.

align

character defining the alignment of font as defined in helper enum Alignments.

maxWidth

numeric that will be converted to a ggplot2::unit object (in "pt" unit) defining the maximum width of text box.

margin

a numeric vector of length 4 defining the size of the area (in pt) around the text in the followin order: top, right, bottom, left.

Returns

An ggtext::element_textbox object.

Method clone()

The objects of this class are cloneable with this method.

Usage
Font$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

FontFaces

Description

List of all available font faces

Usage

FontFaces

Format

An object of class list of length 4.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

geomTLFPoint

Description

geom similar to geom_point() but that leverage fonts to draw its shapes

Usage

geomTLFPoint(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

Arguments

mapping

mapping from ggplot2 package as provided by aes()
data

data.frame
stat

stat name from ggplot2
position

position name from ggplot2
na.rm

a logical value indicating
show.legend

= NA,
inherit.aes

a logical value indicating if aesthetics are inherited
...

other arguments.

getBoxWhiskerMeasure

Description

Get a summary table of Box Whisker percentiles

Usage

getBoxWhiskerMeasure(
  data,
  dataMapping = NULL,
  y = NULL,
  group = NULL,
  quantiles = c(0.05, 0.25, 0.5, 0.75, 0.95)
)

Arguments

data

A data.frame to use for plot.
dataMapping

A BoxWhiskerDataMapping object mapping x, y and aesthetic groups to their variable names of data.
y

Name of y variable in data.
group

Name of grouping variable in data.
quantiles

Numeric values between 0 and 1 defining the quantiles to summarize

Value

A data.frame of summary statistics

Examples

# Get box-and-whisker plots of log-normal distributed data
boxData <- data.frame(x = c(rep("A", 500), rep("B", 500)), y = rlnorm(1000))

getBoxWhiskerMeasure(data = boxData, dataMapping = BoxWhiskerDataMapping$new(x = "x", y = "y"))

getDefaultCaptions

Description

Creates default legend captions by concatenating the values of the data and metaData of variableList variables from data.

Usage

getDefaultCaptions(
  data,
  metaData = NULL,
  variableList = colnames(data),
  sep = "-"
)

Arguments

data

data.frame used for legend caption
metaData

list of lists containing metaData on data
variableList

ordered vector of variables used for specifying the caption
sep

characters separating variables in caption

Value

Factor levels corresponding to the legend captions

Examples

data <- data.frame(
  Population = c("Caucasian", "Asian", "Caucasian", "Asian"),
  Gender = c("Male", "Male", "Female", "Female"),
  Dose = c(50, 100, 100, 50),
  Compound = c("Midazolam", "Midazolam", "Midazolam", "Midazolam")
)

metaData <- list(Dose = list(unit = "mg"))

# Get captions using every variable of data
getDefaultCaptions(data, metaData)

# Get captions using specific variables of data
getDefaultCaptions(data, metaData, variableList = c("Gender", "Population"))

# Get captions separating variables witha space (character " ")
getDefaultCaptions(data, metaData, sep = " ")

getDualAxisPlot

Description

Check if dual Y Axis is needed

Usage

getDualAxisPlot(leftPlotObject, rightPlotObject)

Arguments

leftPlotObject

A ggplot object with left y-axis
rightPlotObject

A ggplot object with right y-axis

Value

A ggplot object with dual y-axis

getGreekTickLabels

Description

Get ticklabels expressions for discrete scale plots with greek letters

Usage

getGreekTickLabels(ticks)

Arguments

ticks

numeric values of the ticks

Value

Expressions to use in ticklabels input parameter of setXAxis and setYAxis functions

Examples

ticks <- c(1, 5, 10, 50, 100, 500)
getGreekTickLabels(ticks)

getGuestValues

Description

Get a data.frame with Guest et al. ratio limits with:

  • ymax = x.limit

  • ymin = x/limit

  • limit = (delta+2(x-1))/x

Usage

getGuestValues(x, delta = 1, residualsVsObserved = FALSE)

Arguments

x

Numeric values input of Guest function
delta

Numeric value parameter of Guest function
residualsVsObserved

Logical value defining if limits are calculated as residuals vs observed, instead of predicted vs observed.

Value

A data.frame with x, ymin and ymax defining Guest et al. limits

References

https://dmd.aspetjournals.org/content/39/2/170

Examples

# Get predicted vs observed Guest et al. limits
getGuestValues(x = 10^seq(-2, 2, 0.2))

# Get residuals vs observed Guest et al. limits
getGuestValues(x = 10^seq(-2, 2, 0.2), residualsVsObserved = TRUE)

getGuestValuesFromDataMapping

Description

Get a data.frame with Guest et al. ratio limits from data and its DDIRatioDataMapping

Usage

getGuestValuesFromDataMapping(data, dataMapping)

Arguments

data

A data.frame to use for plot.
dataMapping

A DDIRatioDataMapping object mapping x, y and aesthetic groups to their variable names of data.

Value

A data.frame with x, ymin and ymax defining Guest et al. limits

Examples

# Get the data.frame of Guest et al. limits
ddiData <- data.frame(x = c(1, 2, 1, 2, 3), y = c(5, 0.2, 2, 3, 4))

getGuestValuesFromDataMapping(
  data = ddiData,
  dataMapping = DDIRatioDataMapping$new(x = "x", y = "y")
)

getLabelWithUnit

Description

Get label with its unit within square brackets when available

Usage

getLabelWithUnit(label, unit = NULL)

Arguments

label

text of axis label
unit

Character value corresponding to unit of label

Value

label [unit] or label depending if unit is NULL or ""

Examples

getLabelWithUnit("Time", "min")

getLabelWithUnit("Label without unit")

getLegendCaption

Description

Get the legend caption

Usage

getLegendCaption(plotObject)

Arguments

plotObject

ggplot graphical object

Value

A data.frame corresponding to legend caption

getLegendPosition

Description

Get the legend position

Usage

getLegendPosition(plotObject)

Arguments

plotObject

ggplot graphical object

Value

Position of legend as defined in enum LegendPositions

See Also

LegendPositions

getLinesFromFoldDistance

Description

Get list of values to provide to lines argument of dataMapping objects. The lines are internally used as argument of geom_hline and geom_abline from ggplot2

Usage

getLinesFromFoldDistance(foldDistance)

Arguments

foldDistance

Numeric values Caution: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive. In particular, line of identity corresponds to a foldDistance of 1.

Value

A list of numeric values

Examples

# Get lines for identity and 2-fold distance
getLinesFromFoldDistance(c(1, 2))

# Create dataMapping with lines identity and 2-fold distance
dataMapping <- ObsVsPredDataMapping$new(
  x = "predicted",
  y = "observed",
  lines = getLinesFromFoldDistance(c(1, 2))
)

getLnTickLabels

Description

Get ticklabels expressions for ln scale plots

Usage

getLnTickLabels(ticks)

Arguments

ticks

numeric values of the ticks

Value

Expressions to use in ticklabels input parameter of setXAxis and setYAxis functions

Examples

ticks <- exp(c(1, 5, 10, 50, 100, 500))
getLnTickLabels(ticks)

getLogTickLabels

Description

Get ticklabels expressions for log scale plots

Usage

getLogTickLabels(ticks)

Arguments

ticks

numeric values of the ticks

Value

Expressions to use in ticklabels input parameter of setXAxis and setYAxis functions

Examples

ticks <- c(1, 5, 10, 50, 100, 500)
getLogTickLabels(ticks)

getPercentileTickLabels

Description

Get ticklabels expressions for percentiles of normal distribution scale plots

Usage

getPercentileTickLabels(ticks)

Arguments

ticks

numeric values of the ticks

Value

Expressions to use in ticklabels input parameter of setXAxis and setYAxis functions

Examples

ticks <- rnorm(5)
getPercentileTickLabels(ticks)

# Get percentile of normal distribution
ticks <- qnorm(seq(1, 9) / 10)
getPercentileTickLabels(ticks)

getPiTickLabels

Description

Get ticklabels expressions for plots with values as ratios of Pi

Usage

getPiTickLabels(ticks)

Arguments

ticks

numeric values of the ticks

Value

Expressions to use in ticklabels input parameter of setXAxis and setYAxis functions

Examples

ticks <- seq(0, 2 * pi, pi / 2)
getPiTickLabels(ticks)

getPKRatioMeasure

Description

Get a summary table of PK Ratio within specific limits

Usage

getPKRatioMeasure(data, dataMapping = NULL, ratioLimits = c(1.5, 2))

Arguments

data

A data.frame to use for plot.
dataMapping

A PKRatioDataMapping object mapping x, y and aesthetic groups to their variable names of data.
ratioLimits

Numeric positive values limits

Value

A data.frame of summary of PK Ratio within specific limits

Examples

# Get summary of usual PK Ratio limits
pkData <- data.frame(x = c(1, 2, 1, 2, 3), y = c(5, 0.2, 2, 3, 4))

getPKRatioMeasure(data = pkData, dataMapping = PKRatioDataMapping$new(x = "x", y = "y"))

# Get summary of other PK Ratio limits
getPKRatioMeasure(
  data = pkData,
  dataMapping = PKRatioDataMapping$new(x = "x", y = "y"),
  ratioLimits = seq(1.5, 5, 0.5)
)

getSameLimits

Description

Get same limits from multiple sets of values

Usage

getSameLimits(...)

Arguments

...

numeric values

Value

An array of 2 values

Examples

getSameLimits(seq(-3, 8), seq(-12, 4))

getSqrtTickLabels

Description

Get ticklabels expressions for sqrt scale plots

Usage

getSqrtTickLabels(ticks)

Arguments

ticks

numeric values of the ticks

Value

Expressions to use in ticklabels input parameter of setXAxis and setYAxis functions

Examples

ticks <- sqrt(c(1, 5, 10, 50, 100, 500))
getSqrtTickLabels(ticks)

getSymmetricLimits

Description

Get symmetric limits from a set of values

Usage

getSymmetricLimits(values)

Arguments

values

numeric values

Value

An array of 2 symmetric values equally distant from 0

Examples

getSymmetricLimits(seq(-3, 8))

getTLFSettings

Description

Get Names of the default/global settings stored in tlfEnv. Can be used with getTLFSettings()

Usage

getTLFSettings(settingName)

Arguments

settingName

setting name as defined in enum tlfSettingsNames

Grouping

Description

R6 class for mapping a group of variable(s) and their label to data

Public fields

group

data.frame or character defining the groups or group variables to group by

label

character printed name of the grouping

Methods

Public methods

Method new()

Create a new Grouping object

Usage
Grouping$new(group, label = NULL)
Arguments
group

data.frame or character vector of groups

label

character name of the group

Returns

A new Grouping object

Method getCaptions()

Get the caption associated to each group

Usage
Grouping$getCaptions(data, metaData = NULL)
Arguments
data

data.frame to map

metaData

list of information on the data

Returns

A vector of characters containing the captions associated to each group of data

Method clone()

The objects of this class are cloneable with this method.

Usage
Grouping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

GroupMapping

Description

R6 class for mapping Grouping variables to data

Public fields

color

R6 class Grouping object

fill

R6 class Grouping object

linetype

R6 class Grouping object

shape

R6 class Grouping object

size

R6 class Grouping object

Methods

Public methods

Method new()

Create a new GroupMapping object

Usage
GroupMapping$new(
  color = NULL,
  fill = NULL,
  linetype = NULL,
  shape = NULL,
  size = NULL
)
Arguments
color

R6 class Grouping object or its input

fill

R6 class Grouping object or its input

linetype

R6 class Grouping object or its input

shape

R6 class Grouping object or its input

size

R6 class Grouping object or its input

Returns

A new GroupMapping object

Method clone()

The objects of this class are cloneable with this method.

Usage
GroupMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

HistogramDataMapping

Description

R6 class for mapping x, bins, binwidth,stack and distribution to data

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> HistogramDataMapping

Public fields

frequency

logical defining if histogram displays a frequency in y axis

stack

logical defining if histogram bars should be stacked

bins

number of bins or binning values/methods passed on ggplot2::geom_histogram

binwidth

width of bins passed on ggplot2::geom_histogram. Overwrites bins

distribution

Name of distribution to fit to the data. Only 2 distributions are currently available: "normal" and "logNormal"

Methods

Public methods

Inherited methods

Method new()

Create a new HistogramDataMapping object

Usage
HistogramDataMapping$new(
  frequency = FALSE,
  stack = FALSE,
  bins = NULL,
  binwidth = NULL,
  distribution = NULL,
  ...
)
Arguments
frequency

logical defining if histogram displays a frequency in y axis

stack

logical defining if histogram bars should be stacked

bins

argument passed on ggplot2::geom_histogram

binwidth

width of bins passed on ggplot2::geom_histogram. Overwrites bins

distribution

Name of distribution to fit to the data. Only 2 distributions are currently available: "normal" and "logNormal"

...

parameters inherited from XYGDataMapping

Returns

A new HistogramDataMapping object

Method clone()

The objects of this class are cloneable with this method.

Usage
HistogramDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

HistogramPlotConfiguration

Description

R6 class defining the configuration of a ggplot object for histograms

Super class

tlf::PlotConfiguration -> HistogramPlotConfiguration

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
HistogramPlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

HorizontalJustification

Description

List of all available horizontal justifications for plot annotation text.

Usage

HorizontalJustification

Format

An object of class list of length 3.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

initializePlot

Description

Initialize a ggplot object and set its labels, grid, background and watermark

Usage

initializePlot(plotConfiguration = NULL)

Arguments

plotConfiguration

An optional PlotConfiguration object defining labels, grid, background and watermark

Value

A ggplot graphical object

References

For examples, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/atom-plots.html

See Also

Other atom plots: addErrorbar(), addLine(), addRibbon(), addScatter()

Examples

# Initialize an empty plot
p <- initializePlot()

# Implement a customized configuration using PlotConfiguration
config <- PlotConfiguration$new(title = "My Plot", xlabel = "x variable", ylabel = "y variable")
p <- initializePlot(config)

isBetween

Description

Assess if x is between left and right bounds. Shortcut for x >= left & x <= right if strict=FALSE (default). Shortcut for x > left & x < right if strict=TRUE.

Usage

isBetween(x, left, right, strict = FALSE)

Arguments

x

Numeric values to assess
left

Numeric value(s) used as lower bound
right

Numeric value(s) used as upper bound
strict

Logical value defining if x is strictly between left and right. Default value is FALSE.

Value

Logical values

Examples

isBetween(1:12, 7, 9)

x <- rnorm(1e2)
x[isBetween(x, -1, 1)]

isBetween(x, cos(x) + 1, cos(x) - 1)

Label

Description

R6 class defining text and font of labels

Active bindings

text

character text of the label

font

Font object

Methods

Public methods

Method new()

Create a new Label object.

Usage
Label$new(
  text = "",
  font = NULL,
  color = NULL,
  size = NULL,
  fontFace = NULL,
  fontFamily = NULL,
  angle = NULL,
  align = NULL,
  maxWidth = NULL,
  margin = NULL
)
Arguments
text

character text of the label

font

Font object defining the font of the label

color

character defining the color of the label

size

numeric defining the size of the label

fontFace

character defining the font face of the label as defined in helper enum FontFaces.

fontFamily

character defining the font family of the label

angle

numeric defining the angle of the label.

align

character defining the alignment of the label as defined in helper enum Alignments.

maxWidth

numeric that will be converted to a ggplot2::unit object (in "pt" unit) defining the maximum width of text box.

margin

a numeric vector of length 4 defining the size of the area (in pt) around the text in the followin order: top, right, bottom, left.

Returns

A new Label object

Method createPlotTextBoxFont()

Create a ggtext::element_textbox directly convertible by ggplot2::theme().

Usage
Label$createPlotTextBoxFont(
  color = NULL,
  size = NULL,
  fontFace = NULL,
  fontFamily = NULL,
  angle = NULL,
  align = NULL,
  maxWidth = NULL,
  margin = NULL
)
Arguments
color

character defining the color of the label

size

numeric defining the size of the label

fontFace

character defining the font face of the label as defined in helper enum FontFaces.

fontFamily

character defining the font family of the label

angle

numeric defining the angle of the label.

align

character defining the alignment of the label as defined in helper enum Alignments.

maxWidth

numeric that will be converted to a ggplot2::unit object (in "pt" unit) defining the maximum width of text box.

margin

a numeric vector of length 4 defining the size of the area (in pt) around the text in the followin order: top, right, bottom, left.

Returns

An element_text or element_blankobject.

Method createPlotTextFont()

Create a ggplot2::element_text() directly convertible by ggplot2::theme().

Usage
Label$createPlotTextFont(
  color = NULL,
  size = NULL,
  fontFace = NULL,
  fontFamily = NULL,
  angle = NULL,
  align = NULL,
  margin = NULL
)
Arguments
color

character defining the color of the label

size

numeric defining the size of the label

fontFace

character defining the font face of the label as defined in helper enum FontFaces.

fontFamily

character defining the font family of the label

angle

numeric defining the angle of the label.

align

character defining the alignment of the label as defined in helper enum Alignments.

margin

a numeric vector of length 4 defining the size of the area (in pt) around the text in the followin order: top, right, bottom, left.

Returns

An element_text or element_blankobject.

Method clone()

The objects of this class are cloneable with this method.

Usage
Label$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

LabelConfiguration

Description

R6 class defining the configuration of the labels of a ggplot object

Active bindings

title

Label object defining the title of the plot

subtitle

Label object defining the subtitle of the plot

xlabel

Label object defining the xlabel of the plot

ylabel

Label object defining the ylabel of the plot

caption

Label object defining the caption of the plot

y2label

Label object defining the y2label of the plot

Methods

Public methods

Method new()

Create a new LabelConfiguration object

Usage
LabelConfiguration$new(
  title = NULL,
  subtitle = NULL,
  xlabel = NULL,
  ylabel = NULL,
  caption = NULL
)
Arguments
title

character or Label object defining title

subtitle

character or Label object defining subtitle

xlabel

character or Label object defining xlabel

ylabel

character or Label object defining ylabel

caption

character or Label object defining caption

Returns

A new LabelConfiguration object

Method updatePlot()

Update labels of a ggplot object and their properties

Usage
LabelConfiguration$updatePlot(plotObject)
Arguments
plotObject

a ggplot object

Returns

A ggplot object

Method clone()

The objects of this class are cloneable with this method.

Usage
LabelConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

LegendConfiguration

Description

R6 class defining the legend configuration of a ggplot object

Active bindings

caption

of legend defined as data.frame with caption properties

position

of legend as defined in Enum LegendPositions

font

Font object defining the font of the legend

background

Background object defining the background of the legend

title

character defining title of the legend

Methods

Public methods

Method new()

Create a new LegendConfiguration object

Usage
LegendConfiguration$new(
  position = NULL,
  caption = NULL,
  title = NULL,
  font = NULL,
  background = NULL
)
Arguments
position

position of the legend as defined by enum LegendPositions

caption

data.frame containing the properties of the legend caption

title

character or Label object defining the title of the legend. A value of NULL removes the title.

font

Font object defining the font of the legend caption

background

BackgroundElement object defining the background of the legend

Returns

A new LegendConfiguration object

Method updatePlot()

Update legend configuration on a ggplot object

Usage
LegendConfiguration$updatePlot(plotObject)
Arguments
plotObject

ggplot object

Returns

A ggplot object with updated axis properties

Method clone()

The objects of this class are cloneable with this method.

Usage
LegendConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

LegendPositions

Description

List of all available legend positions

Usage

LegendPositions

Format

An object of class list of length 17.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

LegendTypes

Description

List of all available legend types

Usage

LegendTypes

Format

An object of class list of length 5.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

LineElement

Description

R6 class defining the properties of background line elements

Super class

tlf::BackgroundElement -> LineElement

Methods

Public methods

Inherited methods

Method createPlotElement()

Create a ggplot2::element_line directly usable by ggplot2::theme.

Usage
LineElement$createPlotElement(color = NULL, size = NULL, linetype = NULL)
Arguments
color

character color of the frame of the background element

size

character size of the frame of the background element

linetype

character linetype of the frame of the background element

Returns

An element_line object.

Method clone()

The objects of this class are cloneable with this method.

Usage
LineElement$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

Linetypes

Description

Enum of ggplot2 linetypes

Usage

Linetypes

Format

An object of class list of length 7.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

Examples

# Use ggplot2 to plot and label Linetypes
linesData <- data.frame(
  x = 0,
  y = seq_along(Linetypes),
  linetype = factor(names(Linetypes), levels = names(Linetypes))
)

ggplot2::ggplot(data = linesData) +
  ggplot2::theme_void() +
  ggplot2::geom_hline(ggplot2::aes(yintercept = y, linetype = linetype)) +
  # Add linetype names from enum below the displayed linetype
  ggplot2::geom_text(ggplot2::aes(x = x, y = y, label = linetype), nudge_y = -0.2, size = 4) +
  # Use scale to display the actual linetype
  ggplot2::scale_linetype_manual(values = as.character(unlist(Linetypes))) +
  # Remove the legend as the linetype name is labelled below the linetype
  ggplot2::guides(linetype = "none")

# Perform a line plot with blue long dashes as linetype
addLine(
  x = 1:10,
  y = rlnorm(10),
  linetype = Linetypes$longdash,
  color = "blue",
  size = 1
)

loadThemeFromJson

Description

Load theme object from json file. A template of a json theme is available at system.file(package= "tlf", "theme-maker","theme-template.json")

Usage

loadThemeFromJson(jsonFile)

Arguments

jsonFile

path of json file

Value

A Theme object

loadTLFSettings

Description

Load TLF global settings from a file

Usage

loadTLFSettings(file)

Arguments

file

.RData file containing the settings

mean-1.96sd

Description

Calculate ⁠mean-1.96SD⁠

Usage

`mean-1.96sd`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to mean(x)-1.96*sd(x)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate mean-1.96SD
`mean-1.96sd`(rnorm(1000))

mean-sd

Description

Calculate mean-SD

Usage

`mean-sd`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to mean(x)-sd(x)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate mean-SD
`mean-sd`(rnorm(1000))

mean+1.96sd

Description

Calculate ⁠mean+1.96SD⁠

Usage

`mean+1.96sd`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to mean(x)+1.96*sd(x)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate mean+1.96SD
`mean+1.96sd`(rnorm(1000))

mean+sd

Description

Calculate mean+SD

Usage

`mean+sd`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to mean(x)+sd(x)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate mean-SD
`mean+sd`(rnorm(1000))

median-1.5IQR

Description

Calculate ⁠median-1.5IQR⁠

Usage

`median-1.5IQR`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to median(x)-1.5*iqr(x)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-IQR()

Examples

# Calculate median-1.5IQR
`median-1.5IQR`(rnorm(1000))

median-IQR

Description

Calculate median-IQR

Usage

`median-IQR`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to median(x)-iqr(x)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR()

Examples

# Calculate median-IQR
`median-IQR`(rnorm(1000))

median+1.5IQR

Description

Calculate ⁠median+1.5IQR⁠

Usage

`median+1.5IQR`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to median(x)+1.5*iqr(x)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate median+1.5IQR
`median+1.5IQR`(rnorm(1000))

median+IQR

Description

Calculate median+IQR

Usage

`median+IQR`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to median(x)+iqr(x)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate median+IQR
`median+IQR`(rnorm(1000))

MoleculePlots

Description

List of all available molecule plots

Usage

MoleculePlots

Format

An object of class list of length 15.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

ObservedDataMapping

Description

R6 class for mapping x, y, of observed data for a time profile plot

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> ObservedDataMapping

Public fields

error

mapping error bars around scatter points

mdv

mapping missing dependent variable

ymin

mapping error bars around scatter points

ymax

mapping error bars around scatter points

y2Axis

Name of y2Axis variable to map

lloq

mapping lloq lines

Methods

Public methods

Method new()

Create a new ObservedDataMapping object

Usage
ObservedDataMapping$new(
  x,
  y,
  ymin = NULL,
  ymax = NULL,
  y2Axis = NULL,
  group = NULL,
  color = NULL,
  shape = NULL,
  error = NULL,
  uncertainty = lifecycle::deprecated(),
  mdv = NULL,
  data = NULL,
  lloq = NULL
)
Arguments
x

Name of x variable to map

y

Name of y variable to map

ymin

mapping lower end of error bars around scatter points

ymax

mapping upper end of error bars around scatter points

y2Axis

Name of y2Axis variable to map

group

R6 class Grouping object or its input

color

R6 class Grouping object or its input

shape

R6 class Grouping object or its input

error

mapping error bars around scatter points

uncertainty

[Deprecated] uncertainty were replaced by error argument. Mapping error bars around scatter points.

mdv

mapping missing dependent variable

data

data.frame to map used by .smartMapping

lloq

mapping lloq lines

Returns

A new ObservedDataMapping object

Method checkMapData()

Check that data variables include map variables

Usage
ObservedDataMapping$checkMapData(data, metaData = NULL)
Arguments
data

data.frame to check

metaData

list containing information on data

Returns

A data.frame with map and defaultAes variables. Dummy variable defaultAes is necessary to allow further modification of plots.

Method requireDualAxis()

Assess if data require a dual axis plot

Usage
ObservedDataMapping$requireDualAxis(data)
Arguments
data

data.frame to check

Returns

A logical

Method getLeftAxis()

Render NA values for all right axis data

Usage
ObservedDataMapping$getLeftAxis(data)
Arguments
data

A data.frame

Returns

A data.frame to be plotted in left axis

Method getRightAxis()

Render NA values for all left axis data

Usage
ObservedDataMapping$getRightAxis(data)
Arguments
data

A data.frame

Returns

A data.frame to be plotted in right axis

Method clone()

The objects of this class are cloneable with this method.

Usage
ObservedDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

ObsVsPredDataMapping

Description

Class for mapping variables in observations vs predictions plot

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> ObsVsPredDataMapping

Public fields

lines

list of ratio limits to plot as horizontal lines

xmin

mapping of upper value of error bars around scatter points

xmax

mapping of lower value of error bars around scatter points

smoother

regression function name

lloq

mapping lloq lines

Methods

Public methods

Method new()

Create a new ObsVsPredDataMapping object

Usage
ObsVsPredDataMapping$new(
  x = NULL,
  y = NULL,
  xmin = NULL,
  xmax = NULL,
  lines = DefaultDataMappingValues$obsVsPred,
  smoother = NULL,
  lloq = NULL,
  ...
)
Arguments
x

Name of x variable to map

y

Name of y variable to map

xmin

mapping of upper value of error bars around scatter points

xmax

mapping of lower value of error bars around scatter points

lines

list of lines to plot

smoother

smoother function or parameter

lloq

mapping lloq lines To map a loess smoother to the plot, use smoother="loess"

...

parameters inherited from XYGDataMapping

Returns

A new ObsVsPredDataMapping object

Method checkMapData()

Check that data variables include map variables

Usage
ObsVsPredDataMapping$checkMapData(data, metaData = NULL)
Arguments
data

data.frame to check

metaData

list containing information on data

Returns

A data.frame with map and defaultAes variables. Dummy variable defaultAes is necessary to allow further modification of plots.

Method clone()

The objects of this class are cloneable with this method.

Usage
ObsVsPredDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

ObsVsPredPlotConfiguration

Description

R6 class defining the configuration of a ggplot object for Obs vs Pred plots

Super class

tlf::PlotConfiguration -> ObsVsPredPlotConfiguration

Public fields

defaultSymmetricAxes

Default option setting symmetric xAxis and/or yAxis limits when creating a ObsVsPredPlotConfiguration object

lloqDirection

Whether to draw LLOQ lines for x (vertical), y (horizontal) or x and y (both).

foldLinesLegend

Whether to draw fold lines in legend. default to FALSE.

foldLinesLegendDiagonal

Whether to draw diagonal lines in legend for fold lines. default to FALSE.

Active bindings

foldLineslegendType

translation of foldLinesLegendDiagonal in geom type.

Methods

Public methods

Method new()

Create a new ObsVsPredPlotConfiguration object

Usage
ObsVsPredPlotConfiguration$new(
  lloqDirection = "vertical",
  foldLinesLegend = FALSE,
  foldLinesLegendDiagonal = FALSE,
  ...
)
Arguments
lloqDirection

Whether to draw LLOQ lines for x (vertical), y (horizontal) or x and y (both).

foldLinesLegend

Whether to draw fold lines in legend. default to FALSE.

foldLinesLegendDiagonal

Whether to draw diagonal lines in legend for fold lines. default to FALSE.

...

parameters inherited from PlotConfiguration

Returns

A new CumulativeTimeProfilePlotConfiguration object

Method clone()

The objects of this class are cloneable with this method.

Usage
ObsVsPredPlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

Percentile0%

Description

Calculate ⁠Percentile0%⁠ i.e. min value

Usage

`Percentile0%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 0)

See Also

Other stat functions: Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile0%
`Percentile0%`(rnorm(1000))

Percentile1%

Description

Calculate ⁠Percentile1%⁠

Usage

`Percentile1%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 1/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile1%
`Percentile1%`(rnorm(1000))

Percentile10%

Description

Calculate ⁠Percentile10%⁠

Usage

`Percentile10%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 10/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile10%
`Percentile10%`(rnorm(1000))

Percentile100%

Description

Calculate ⁠Percentile100%⁠ i.e. max value

Usage

`Percentile100%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 1)

See Also

Other stat functions: Percentile0%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile100%
`Percentile100%`(rnorm(1000))

Percentile15%

Description

Calculate ⁠Percentile15%⁠

Usage

`Percentile15%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 15/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile15%
`Percentile15%`(rnorm(1000))

Percentile2.5%

Description

Calculate ⁠Percentile2.5%⁠

Usage

`Percentile2.5%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 2.5/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile2.5%
`Percentile2.5%`(rnorm(1000))

Percentile20%

Description

Calculate ⁠Percentile20%⁠

Usage

`Percentile20%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 20/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile20%
`Percentile20%`(rnorm(1000))

Percentile25%

Description

Calculate ⁠Percentile25%⁠ i.e. 1st quartile value

Usage

`Percentile25%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 25/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile25%
`Percentile25%`(rnorm(1000))

Percentile25%-1.5IQR

Description

Calculate ⁠Percentile25%-1.5IQR⁠

Usage

`Percentile25%-1.5IQR`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 0.25)-1.5*iqr(x)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile25%-1.5IQR
`Percentile25%-1.5IQR`(rnorm(1000))

Percentile5%

Description

Calculate ⁠Percentile5%⁠

Usage

`Percentile5%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 5/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile5%
`Percentile5%`(rnorm(1000))

Percentile50%

Description

Calculate ⁠Percentile50%⁠ i.e. median value

Usage

`Percentile50%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 50/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile50%
`Percentile50%`(rnorm(1000))

Percentile75%

Description

Calculate ⁠Percentile75%⁠ i.e. 3rd quartile value

Usage

`Percentile75%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 75/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile75%
`Percentile75%`(rnorm(1000))

Percentile75%+1.5IQR

Description

Calculate ⁠Percentile75%+1.5IQR⁠

Usage

`Percentile75%+1.5IQR`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 0.75)+1.5*iqr(x)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile75%+1.5IQR
`Percentile75%+1.5IQR`(rnorm(1000))

Percentile80%

Description

Calculate ⁠Percentile80%⁠

Usage

`Percentile80%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 80/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile80%
`Percentile80%`(rnorm(1000))

Percentile85%

Description

Calculate ⁠Percentile85%⁠

Usage

`Percentile85%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 85/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile90%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile85%
`Percentile85%`(rnorm(1000))

Percentile90%

Description

Calculate ⁠Percentile90%⁠

Usage

`Percentile90%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 90/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile95%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile90%
`Percentile90%`(rnorm(1000))

Percentile95%

Description

Calculate ⁠Percentile95%⁠

Usage

`Percentile95%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 95/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile97.5%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile95%
`Percentile95%`(rnorm(1000))

Percentile97.5%

Description

Calculate ⁠Percentile97.5%⁠

Usage

`Percentile97.5%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 97.5/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile99%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile97.5%
`Percentile97.5%`(rnorm(1000))

Percentile99%

Description

Calculate ⁠Percentile99%⁠

Usage

`Percentile99%`(x)

Arguments

x

Numeric values

Value

Numeric value corresponding to quantile(x, 99/100)

See Also

Other stat functions: Percentile0%(), Percentile100%(), Percentile10%(), Percentile15%(), Percentile1%(), Percentile2.5%(), Percentile20%(), Percentile25%(), Percentile25%-1.5IQR(), Percentile50%(), Percentile5%(), Percentile75%(), Percentile75%+1.5IQR(), Percentile80%(), Percentile85%(), Percentile90%(), Percentile95%(), Percentile97.5%(), mean+1.96sd(), mean+sd(), mean-1.96sd(), mean-sd(), median+1.5IQR(), median+IQR(), median-1.5IQR(), median-IQR()

Examples

# Calculate Percentile99%
`Percentile99%`(rnorm(1000))

PieChartDataMapping

Description

R6 class for mapping x, y, and group to data

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> PieChartDataMapping

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
PieChartDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

PieChartPlotConfiguration

Description

R6 class defining the configuration of a ggplot object for pie charts

Super class

tlf::PlotConfiguration -> PieChartPlotConfiguration

Public fields

colorPalette

color palette property from ggplot2

chartFont

Font object defining properties of text within pie chart

start

Offset of starting point from 12 o'clock in radians. Offset is applied clockwise or anticlockwise depending on value of direction

clockwiseDirection

logical defining if values are displayed in clockwise order

Methods

Public methods

Method new()

Create a new PieChartPlotConfiguration object

Usage
PieChartPlotConfiguration$new(
  colorPalette = NULL,
  chartFont = NULL,
  start = 0,
  clockwiseDirection = TRUE,
  ...
)
Arguments
colorPalette

color palette property from ggplot2

chartFont

Font object defining properties of text within pie chart

start

Offset of starting point from 12 o'clock in radians. Offset is applied clockwise or anticlockwise depending on value of direction

clockwiseDirection

logical defining if values are displayed in clockwise order

...

parameters inherited from PlotConfiguration

Returns

A new PieChartPlotConfiguration object

Method clone()

The objects of this class are cloneable with this method.

Usage
PieChartPlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

PKRatioDataMapping

Description

R6 class for mapping x, y, GroupMapping and pkRatio lines variables to data

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> PKRatioDataMapping

Public fields

lines

list of ratio limits to plot as horizontal lines

ymin

mapping of upper value of error bars around scatter points

ymax

mapping of lower value of error bars around scatter points

Methods

Public methods

Method new()

Create a new PKRatioDataMapping object

Usage
PKRatioDataMapping$new(
  x = NULL,
  y = NULL,
  ymin = NULL,
  ymax = NULL,
  lines = DefaultDataMappingValues$pkRatio,
  ...
)
Arguments
x

Name of x variable to map

y

Name of y variable to map

ymin

mapping of upper value of error bars around scatter points

ymax

mapping of lower value of error bars around scatter points

lines

List of ratio limits to display as horizontal lines

...

parameters inherited from XYGDataMapping

Returns

A new PKRatioDataMapping object

Method checkMapData()

Check that data variables include map variables

Usage
PKRatioDataMapping$checkMapData(data, metaData = NULL)
Arguments
data

data.frame to check

metaData

list containing information on data

Returns

A data.frame with map and defaultAes variables. Dummy variable defaultAes is necessary to allow further modification of plots.

Method clone()

The objects of this class are cloneable with this method.

Usage
PKRatioDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

PKRatioPlotConfiguration

Description

R6 class defining the configuration of a ggplot object for PK ratio plots

Super class

tlf::PlotConfiguration -> PKRatioPlotConfiguration

Public fields

defaultYScale

Default yAxis scale value when creating a PKRatioPlotConfiguration object

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
PKRatioPlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

PlotAnnotationTextSize

Description

List of default text sizes for plot annotations.

Usage

PlotAnnotationTextSize

Format

An object of class list of length 12.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

plotBoxWhisker

Description

Producing box-and-whisker plots

Usage

plotBoxWhisker(
  data,
  metaData = NULL,
  outliers = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
outliers

Logical defining if outliers should be included in boxplot
dataMapping

A BoxWhiskerDataMapping object mapping x, y and aesthetic groups to their variable names of data.
plotConfiguration

An optional BoxWhiskerConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

References

For examples, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/box-whisker-vignette.html

See Also

Other molecule plots: plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

# Produce box-and-whisker plots of log-normal distributed data
boxData <- data.frame(x = c(rep("A", 500), rep("B", 500)), y = rlnorm(1000))

plotBoxWhisker(data = boxData, dataMapping = BoxWhiskerDataMapping$new(x = "x", y = "y"))

# Remove outliers from boxplot
plotBoxWhisker(
  data = boxData,
  dataMapping = BoxWhiskerDataMapping$new(x = "x", y = "y"),
  outliers = FALSE
)

PlotConfiguration

Description

R6 class defining the configuration of a ggplot object

Public fields

export

R6 class ExportConfiguration defining properties for saving/exporting plot

defaultXScale

Default xAxis scale value when creating a PlotConfiguration object

defaultYScale

Default yAxis scale value when creating a PlotConfiguration object

defaultExpand

Default expand value when creating a PlotConfiguration object

defaultSymmetricAxes

Default option setting symmetric xAxis and/or yAxis limits when creating a PlotConfiguration object

Active bindings

labels

LabelConfiguration object defining properties of labels

legend

LegendConfiguration object defining properties of legend

xAxis

XAxisConfiguration object defining properties of x-axis

yAxis

YAxisConfiguration object defining properties of x-axis

background

BackgroundConfiguration object defining properties of x-axis

lines

ThemeAestheticSelections defining properties of lines

ribbons

ThemeAestheticSelections defining properties of ribbons

points

ThemeAestheticSelections defining properties of points

errorbars

ThemeAestheticSelections defining properties of error bars

Methods

Public methods

Method new()

Create a new PlotConfiguration object

Usage
PlotConfiguration$new(
  title = NULL,
  subtitle = NULL,
  xlabel = NULL,
  ylabel = NULL,
  caption = NULL,
  legend = NULL,
  legendTitle = NULL,
  legendPosition = NULL,
  xAxis = NULL,
  xScale = NULL,
  xValuesLimits = NULL,
  xAxisLimits = NULL,
  xLimits = lifecycle::deprecated(),
  yAxis = NULL,
  yScale = NULL,
  yValuesLimits = NULL,
  yAxisLimits = NULL,
  yLimits = lifecycle::deprecated(),
  background = NULL,
  plotArea = NULL,
  panelArea = NULL,
  xGrid = NULL,
  yGrid = NULL,
  watermark = NULL,
  lines = NULL,
  points = NULL,
  ribbons = NULL,
  errorbars = NULL,
  export = NULL,
  name = NULL,
  format = NULL,
  width = NULL,
  height = NULL,
  units = NULL,
  dpi = NULL,
  data = NULL,
  metaData = NULL,
  dataMapping = NULL
)
Arguments
title

character or Label object defining plot title

subtitle

character or Label object defining plot subtitle

xlabel

character or Label object defining plot xlabel

ylabel

character or Label object defining plot ylabel

caption

character or Label object defining plot caption

legend

LegendConfiguration object defining legend properties

legendTitle

character or Label object defining legend title

legendPosition

character defining legend position. Use Enum LegendPositions to get a list of available to legend positions.

xAxis

XAxisConfiguration object defining x-axis properties

xScale

name of X-axis scale. Use enum Scaling to access predefined scales.

xValuesLimits

numeric vector of length 2 defining x values limits

xAxisLimits

numeric vector of length 2 defining x-axis limits

xLimits

[Deprecated]. Replaced by xAxisLimits argument.

yAxis

YAxisConfiguration object defining y-axis properties

yScale

name of y-axis scale. Use enum Scaling to access predefined scales.

yValuesLimits

numeric vector of length 2 defining x values limits

yAxisLimits

numeric vector of length 2 defining x-axis limits

yLimits

[Deprecated]. Replaced by yAxisLimits argument.

background

BackgroundConfiguration object defining background properties

plotArea

BackgroundElement object defining properties of plot area

panelArea

BackgroundElement object defining properties of panel area

xGrid

LineElement object defining properties of x-grid background

yGrid

LineElement object defining properties of y-grid background

watermark

character or Label object defining watermark

lines

ThemeAestheticSelections object or list defining how lines are plotted

points

ThemeAestheticSelections object or list defining how points are plotted

ribbons

ThemeAestheticSelections object or list defining how ribbons are plotted

errorbars

ThemeAestheticSelections object or list defining how errorbars are plotted

export

R6 class ExportConfiguration defining properties for saving/exporting plot

name

character defining the name of the file to be saved (without extension)

format

character defining the format of the file to be saved.

width

numeric values defining the width in units of the plot dimensions after saving

height

numeric values defining the height in units of the plot dimensions after saving

units

character defining the unit of the saving dimension

dpi

numeric value defining plot resolution (dots per inch)

data

data.frame used by .smartMapping

metaData

list of information on data

dataMapping

R6 class or subclass XYDataMapping

Returns

A new PlotConfiguration object

Method clone()

The objects of this class are cloneable with this method.

Usage
PlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

References

For examples, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/plot-configuration.html

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

PlotConfigurations

Description

List of all available molecule plots

Usage

PlotConfigurations

Format

An object of class list of length 23.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

plotCumulativeTimeProfile

Description

Producing Cumulative Time Profile plots

Usage

plotCumulativeTimeProfile(
  data = NULL,
  metaData = NULL,
  dataMapping = NULL,
  colorPalette = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
dataMapping

A CumulativeTimeProfileDataMapping object mapping x and aesthetic groups to their variable names of data.
colorPalette

Optional character values defining a ggplot2 colorPalette (e.g. "Set1" or "Spectral")
plotConfiguration

An optional CumulativeTimeProfilePlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

See Also

Other molecule plots: plotBoxWhisker(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

# Define data to be plotted as cumulative time profile
time <- seq(1, 10)
data <- data.frame(
  x = rep(time),
  y = c(exp(-time / 10), 1 - exp(-time / 10)),
  legend = rep(c("decreasing area", "increasing area"), each = 10)
)

# Produce a Cumulative Time Profile plot
plotCumulativeTimeProfile(
  data = data,
  dataMapping = CumulativeTimeProfileDataMapping$new(x = "x", y = "y", fill = "legend")
)

# Produce a Cumulative Time Profile plot with a ggplot2 color palette
plotCumulativeTimeProfile(
  data = data,
  dataMapping = CumulativeTimeProfileDataMapping$new(
    x = "x",
    y = "y",
    fill = "legend"
  ),
  colorPalette = "Set1"
)

plotDDIRatio

Description

Producing DDI Ratio plots

Usage

plotDDIRatio(
  data,
  metaData = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  residualsVsObserved = NULL,
  foldDistance = NULL,
  deltaGuest = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
dataMapping

A DDIRatioDataMapping object mapping x, y and aesthetic groups to their variable names of data.
plotConfiguration

An optional DDIRatioPlotConfiguration object defining labels, grid, background and watermark.
residualsVsObserved

Optional logical value defining if DDI Ratio plot is drawn as residuals vs observed, instead of predicted vs observed.
foldDistance

Numeric values of fold distance lines to display in log plots. This argument is internally translated into lines field of dataMapping. Caution: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive. In particular, line of identity corresponds to a foldDistance of 1.
deltaGuest

Numeric value parameter of Guest function
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

References

For examples, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/pk-ratio-vignette.html

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

# Produce DDI Ratio plot
ddiData <- data.frame(x = c(1, 2, 1, 2, 3), y = c(5, 0.2, 2, 3, 4))

plotDDIRatio(data = ddiData, dataMapping = DDIRatioDataMapping$new(x = "x", y = "y"))

# Produce DDI Ratio plot with user-defined horizontal lines
plotDDIRatio(
  data = ddiData,
  dataMapping = DDIRatioDataMapping$new(x = "x", y = "y"),
  foldDistance = c(1, 10),
  deltaGuest = 1.25,
  residualsVsObserved = TRUE
)

Create a plot grid

Description

Create a plot grid using the patchwork::wrap_plots() function. The required arguments are supplied through the PlotGridConfiguration object.

Usage

plotGrid(plotGridConfiguration)

Arguments

plotGridConfiguration

A PlotGridConfiguration object, which is an R6 class object that defines properties of a plot grid (like number of rows, columns, labels, etc.).

References

For more, see: https://patchwork.data-imaginist.com/articles/patchwork.html

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

library(ggplot2)
library(tlf)

# only `{tlf}` ---------------------

# plots to be arranged in a grid
set.seed(123)
ls_plots <- list(
  plotHistogram(x = rnorm(100)),
  plotHistogram(x = rnorm(100, mean = 3)),
  plotHistogram(x = rnorm(100, mean = 10))
)

# create an instance of plot configuration class
plotGridObj <- PlotGridConfiguration$new(plotList = ls_plots)

# specify further customizations for the plot grid
plotGridObj$title <- "my combined plot"
plotGridObj$subtitle <- "something clever"
plotGridObj$caption <- "my sources"
plotGridObj$nColumns <- 2L
plotGridObj$tagLevels <- "A"
plotGridObj$tagPrefix <- "Plot ("
plotGridObj$tagSuffix <- ")"
plotGridObj$tagColor <- "blue"
plotGridObj$tagSize <- 15
plotGridObj$tagAngle <- 45
plotGridObj$tagPosition <- TagPositions$top
plotGridObj$titleHorizontalJustification <- HorizontalJustification$middle
plotGridObj$subtitleHorizontalJustification <- HorizontalJustification$middle

# plot the grid
plotGrid(plotGridObj)

#  `{tlf}` and `{ggplot2}` ---------------------

# `{tlf}` plot
set.seed(123)
p1 <- plotBoxWhisker(mtcars,
  dataMapping = BoxWhiskerDataMapping$new(x = "am", y = "wt"), outliers = FALSE
)

# custom `{ggplot2}` plot
set.seed(123)
p2 <- ggplot(mtcars, aes(wt, mpg)) +
  geom_point()

# create an instance of plot configuration class
plotGridObj2 <- PlotGridConfiguration$new(list(p1, p2))

# specify further customizations for the plot grid
plotGridObj2$nColumns <- 1L
plotGridObj2$tagLevels <- "i"

# plot the grid
plotGrid(plotGridObj2)

Class for creating a plot grid

Description

An R6 class defining the configuration for {patchwork} plot grid used to create a grid of plots from {tlf}. It holds values for all relevant plot properties.

Value

A PlotGridConfiguration object.

Customizing

You can change the default values present in public fields.

For example, if you want to specify a new position for tags, you will have to do the following: 

myPlotGridConfiguration <- PlotGridConfiguration$new()
myPlotGridConfiguration$tagPosition <- TagPositions$right

For more, see examples.

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 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()

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

Super class

ospsuite.utils::Printable -> PlotGridConfiguration

Public fields

plotList

A list containing ggplot objects.

title, subtitle, caption

Text strings to use for the various plot annotations, where plot refers to the grid of plots as a whole.

titleColor, titleSize, titleFontFace, titleFontFamily, titleHorizontalJustification, titleVerticalJustification, titleAngle, titleMargin

Aesthetic properties for the plot title.

subtitleColor, subtitleSize, subtitleFontFace, subtitleFontFamily, subtitleHorizontalJustification, subtitleVerticalJustification, subtitleAngle, subtitleMargin

Aesthetic properties for the plot subtitle.

captionColor, captionSize, captionFontFace, captionFontFamily, captionHorizontalJustification, captionVerticalJustification, captionAngle, captionMargin

Aesthetic properties for the plot caption.

tagLevels

A character vector defining the enumeration format to use at each level. Possible values are 'a' for lowercase letters, 'A' for uppercase letters, '1' for numbers, 'i' for lowercase Roman numerals, and 'I' for uppercase Roman numerals. It can also be a list containing character vectors defining arbitrary tag sequences. If any element in the list is a scalar and one of 'a', 'A', '1', ⁠'i⁠, or 'I', this level will be expanded to the expected sequence.

tagPrefix, tagSuffix

Strings that should appear before or after the tag.

tagSeparator

A separator between different tag levels.

tagPosition

Position of the tag for an individual plot with respect to that plot. Default is topleft. For all available options, see TagPositions.

tagColor, tagSize, tagFontFamily, tagFontFace, tagHorizontalJustification, tagVerticalJustification, tagAngle, tagLineHeight, tagMargin

Aesthetic properties of individual plot tag text. For more detailed description of each aesthetic property, see docs for element_text().

nColumns, nRows

The dimensions of the grid to create - if both are NULL it will use the same logic as facet_wrap() to set the dimensions

byRow

Analogous to byrow in matrix(). If FALSE the plots will be filled in in column-major order.

widths, heights

The relative widths and heights of each column and row in the grid. Will get repeated to match the dimensions of the grid.

guides

A string specifying how guides should be treated in the layout. 'collect' will collect guides below to the given nesting level, removing duplicates. 'keep' will stop collection at this level and let guides be placed alongside their plot. auto will allow guides to be collected if a upper level tries, but place them alongside the plot if not. If you modify default guide "position" with theme(legend.position=...) while also collecting guides you must apply that change to the overall patchwork.

design

Specification of the location of areas in the layout. Can either be specified as a text string or by concatenating calls to patchwork::area() together. See the examples in wrap_plots() for further information on use.

Active bindings

title, subtitle, caption

Text strings to use for the various plot annotations, where plot refers to the grid of plots as a whole.

titleColor, titleSize, titleFontFace, titleFontFamily, titleHorizontalJustification, titleVerticalJustification, titleAngle, titleMargin

Aesthetic properties for the plot title.

subtitleColor, subtitleSize, subtitleFontFace, subtitleFontFamily, subtitleHorizontalJustification, subtitleVerticalJustification, subtitleAngle, subtitleMargin

Aesthetic properties for the plot subtitle.

captionColor, captionSize, captionFontFace, captionFontFamily, captionHorizontalJustification, captionVerticalJustification, captionAngle, captionMargin

Aesthetic properties for the plot caption.

tagPrefix, tagSuffix

Strings that should appear before or after the tag.

tagColor, tagSize, tagFontFamily, tagFontFace, tagHorizontalJustification, tagVerticalJustification, tagAngle, tagLineHeight, tagMargin

Aesthetic properties of individual plot tag text. For more detailed description of each aesthetic property, see docs for element_text().

nColumns, nRows

The dimensions of the grid to create - if both are NULL it will use the same logic as facet_wrap() to set the dimensions

widths, heights

The relative widths and heights of each column and row in the grid. Will get repeated to match the dimensions of the grid.

Methods

Public methods

Method new()

Create an instance of PlotGridConfiguration class.

Usage
PlotGridConfiguration$new(plotList = NULL)
Arguments
plotList

A list containing ggplot objects.

Returns

A PlotGridConfiguration object.

Method addPlots()

Add a plot object.

Usage
PlotGridConfiguration$addPlots(plots = NULL)
Arguments
plots

A single or a list containing ggplot object(s).

Returns

PlotGridConfiguration object with ⁠$plotList⁠ field updated to store entered plots.

Examples
library(ggplot2)

myPlotGrid <- PlotGridConfiguration$new()

# You can add a single ggplot object
p <- ggplot(mtcars, aes(wt, mpg)) + geom_point()
myPlotGrid$addPlots(p)

# Or you can also pass a list
myPlotGrid$addPlots(list("p1" = ggplot(), "p2" = ggplot()))

# Since we added three plots, the `plotList` field should
# now be a list of length `3`
length(myPlotGrid$plotList)

Method print()

Print the object to the console.

Usage
PlotGridConfiguration$print()

Method clone()

The objects of this class are cloneable with this method.

Usage
PlotGridConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

Examples

library(tlf)

# create a list of plots
ls_plots <- list(
  # first plot
  plotBoxWhisker(mtcars,
    dataMapping = BoxWhiskerDataMapping$new(x = "am", y = "wt"), outliers = FALSE
  ),
  # second plot
  plotBoxWhisker(ToothGrowth,
    dataMapping = BoxWhiskerDataMapping$new(x = "supp", y = "len")
  )
)

plotGridObj <- PlotGridConfiguration$new(ls_plots)

# specify further customizations for the plot grid
plotGridObj$title <- "my combined plot"
plotGridObj$subtitle <- "something clever"
plotGridObj$caption <- "my sources"
plotGridObj$nColumns <- 2L
plotGridObj$tagLevels <- "A"
plotGridObj$tagPrefix <- "Plot ("
plotGridObj$tagSuffix <- ")"
plotGridObj$tagColor <- "blue"
plotGridObj$tagSize <- 15
plotGridObj$tagAngle <- 45
plotGridObj$tagPosition <- TagPositions$top
plotGridObj$titleHorizontalJustification <- HorizontalJustification$middle
plotGridObj$subtitleHorizontalJustification <- HorizontalJustification$middle

# print the object to see its properties
plotGridObj


## ------------------------------------------------
## Method `PlotGridConfiguration$addPlots`
## ------------------------------------------------


library(ggplot2)

myPlotGrid <- PlotGridConfiguration$new()

# You can add a single ggplot object
p <- ggplot(mtcars, aes(wt, mpg)) + geom_point()
myPlotGrid$addPlots(p)

# Or you can also pass a list
myPlotGrid$addPlots(list("p1" = ggplot(), "p2" = ggplot()))

# Since we added three plots, the `plotList` field should
# now be a list of length `3`
length(myPlotGrid$plotList)

plotHistogram

Description

Producing Histograms

Usage

plotHistogram(
  data = NULL,
  metaData = NULL,
  x = NULL,
  dataMapping = NULL,
  frequency = NULL,
  bins = NULL,
  binwidth = NULL,
  stack = NULL,
  distribution = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
x

Numeric values to plot along the x axis. Only used instead of data if data is NULL.
dataMapping

A HistogramDataMapping object mapping x and aesthetic groups to their variable names of data.
frequency

logical defining if histogram displays a frequency in y axis
bins

Number or edges of bins. If bins is provided as a single numeric values, bin corresponds to number of bins. The bin edges are then equally spaced within the range of data. If bins is provided as an array of numeric values, bin corresponds to their edges. Default value, bins=NULL, uses the value defined by dataMapping
binwidth

Numerical value of defining the width of each bin. If defined, binwidth can overwrite bins if bins was not provided or simply provided as a single value. Default value, binwidth=NULL, uses the value defined by dataMapping
stack

Logical defining for multiple histograms if their bars are stacked Default value, stack=NULL, uses the value defined by dataMapping
distribution

Name of distribution to fit to the data. Only 2 distributions are currently available: "normal" and "logNormal" Use distribution="none" to prevent fit of distribution Default value, distribution=NULL, uses the value defined by dataMapping
plotConfiguration

An optional HistogramPlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

References

For examples, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/histogram.html

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

# Produce histogram of normally distributed data
plotHistogram(x = rnorm(100))

# Produce histogram of normally distributed data normalized in y axis
plotHistogram(x = rnorm(100), frequency = TRUE)

# Produce histogram of normally distributed data with many bins
plotHistogram(x = rlnorm(100), bins = 21)

# Produce histogram of fitted normally distributed data
plotHistogram(x = rlnorm(100), distribution = "normal")


# Produce histogram of fitted normally distributed data
plotHistogram(x = rlnorm(100), distribution = "normal", frequency = TRUE, stack = TRUE)

plotObservedTimeProfile

Description

Producing Time Profile plots for observed data

Usage

plotObservedTimeProfile(
  data,
  metaData = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
dataMapping

An ObservedDataMapping object mapping x, y, ymin, ymax and aesthetic groups to their variable names of observedData.
plotConfiguration

An optional TimeProfilePlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

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")
)

plotObsVsPred

Description

Producing observed vs predicted plots

Usage

plotObsVsPred(
  data,
  metaData = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  foldDistance = NULL,
  smoother = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
dataMapping

A ObsVsPredDataMapping object mapping x, y and aesthetic groups to their variable names of data.
plotConfiguration

An optional ObsVsPredConfiguration object defining labels, grid, background and watermark.
foldDistance

Numeric values of fold distance lines to display in log plots. This argument is internally translated into lines field of dataMapping. Caution: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive. In particular, line of identity corresponds to a foldDistance of 1.
smoother

Optional name of smoother function:

  • "loess" for loess regression

  • "lm" for linear regression

plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

# Produce Obs vs Pred plot
obsVsPredData <- data.frame(x = c(1, 2, 1, 2, 3), y = c(5, 0.2, 2, 3, 4))

plotObsVsPred(data = obsVsPredData, dataMapping = ObsVsPredDataMapping$new(x = "x", y = "y"))

# Produce Obs vs Pred plot with linear regression
plotObsVsPred(
  data = obsVsPredData,
  dataMapping = ObsVsPredDataMapping$new(x = "x", y = "y"),
  smoother = "lm"
)

# Produce Obs vs Pred plot with user-defined fold distance lines
plotObsVsPred(
  data = obsVsPredData,
  dataMapping = ObsVsPredDataMapping$new(x = "x", y = "y"),
  plotConfiguration = ObsVsPredPlotConfiguration$new(
    xScale = Scaling$log, xAxisLimits = c(0.05, 50),
    yScale = Scaling$log, yAxisLimits = c(0.05, 50)
  ),
  foldDistance = c(1, 10)
)

plotPieChart

Description

Producing a Pie Chart

Usage

plotPieChart(
  data = NULL,
  metaData = NULL,
  dataMapping = NULL,
  colorPalette = NULL,
  start = NULL,
  clockwiseDirection = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
dataMapping

A PieChartDataMapping object mapping x and fill aesthetic groups to their variable names of data. Values mapped to y variable will be displayed as text within the pie chart
colorPalette

color palette property from ggplot2
start

Offset of starting point from 12 o'clock in radians. Offset is applied clockwise or anticlockwise depending on value of direction
clockwiseDirection

logical defining if values are displayed in clockwise order
plotConfiguration

An optional PieChartPlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

# Data for the pie chart
values <- runif(5)
data <- data.frame(
  values = values,
  text = paste0(round(100 * values / sum(values)), "%"),
  legend = letters[1:5]
)

# Plot pie chart with its legend
plotPieChart(
  data = data,
  dataMapping = PieChartDataMapping$new(x = "values", fill = "legend")
)

# Plot pie chart with text within pie
plotPieChart(
  data = data,
  dataMapping = PieChartDataMapping$new(x = "values", y = "text", fill = "legend")
)

# Reverse direction of pie chart
plotPieChart(
  data = data,
  dataMapping = PieChartDataMapping$new(x = "values", y = "text", fill = "legend"),
  clockwiseDirection = FALSE
)

# Start first slice of pie at 90 degrees
plotPieChart(
  data = data,
  dataMapping = PieChartDataMapping$new(x = "values", y = "text", fill = "legend"),
  start = pi / 2
)

# Leverages ggplot color palettes
plotPieChart(
  data = data,
  dataMapping = PieChartDataMapping$new(x = "values", y = "text", fill = "legend"),
  colorPalette = ColorPalettes$Set1
)

plotPKRatio

Description

Producing PK Ratio plots

Usage

plotPKRatio(
  data,
  metaData = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  foldDistance = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
dataMapping

A PKRatioDataMapping object mapping x, y and aesthetic groups to their variable names of data.
plotConfiguration

An optional PKRatioPlotConfiguration object defining labels, grid, background and watermark.
foldDistance

Numeric values of fold distance lines to display in log plots. This argument is internally translated into lines field of dataMapping. Caution: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive. In particular, line of identity corresponds to a foldDistance of 1.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

References

For examples, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/pk-ratio-vignette.html

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

# Produce PK Ratio plot
pkData <- data.frame(x = c(1, 2, 1, 2, 3), y = c(5, 0.2, 2, 3, 4))

plotPKRatio(data = pkData, dataMapping = PKRatioDataMapping$new(x = "x", y = "y"))

# Produce PK Ratio plot with user-defined horizontal lines
plotPKRatio(
  data = pkData,
  dataMapping = PKRatioDataMapping$new(x = "x", y = "y"),
  foldDistance = c(1, 10)
)

plotQQ

Description

Producing Histograms

Usage

plotQQ(
  data = NULL,
  metaData = NULL,
  y = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
y

Numeric values to plot along the y axis. Only used instead of data if data is NULL.
dataMapping

A QQDataMapping object mapping y and aesthetic groups to their variable names of data.
plotConfiguration

An optional QQPlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

# Produce QQ plot of normally distributed data
plotQQ(y = rnorm(100))

# Produce QQ plot of normally distributed data split by group
qqData <- data.frame(
  residuals = c(rnorm(100), rnorm(100)),
  groups = c(rep("Group A", 100), rep("Group B", 100))
)
plotQQ(
  data = qqData,
  dataMapping = QQDataMapping$new(y = "residuals", group = "groups")
)

plotResVsPred

Description

Producing residuals vs predicted plots

Usage

plotResVsPred(
  data,
  metaData = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  smoother = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
dataMapping

A ResVsPredDataMapping object mapping x, y and aesthetic groups to their variable names of data.
plotConfiguration

An optional ResVsPredConfiguration object defining labels, grid, background and watermark.
smoother

Optional name of smoother function:

  • "loess" for loess regression

  • "lm" for linear regression

plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

# Produce Obs vs Pred plot
resVsPredData <- data.frame(x = c(1, 2, 1, 2, 3), y = c(5, 0.2, 2, 3, 4))

plotResVsPred(data = resVsPredData, dataMapping = ResVsPredDataMapping$new(x = "x", y = "y"))

# Produce Res vs Pred plot with linear regression
plotResVsPred(
  data = resVsPredData,
  dataMapping = ResVsPredDataMapping$new(x = "x", y = "y"),
  smoother = "lm"
)

plotResVsTime

Description

Producing residuals vs time plots

Usage

plotResVsTime(
  data,
  metaData = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  smoother = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
dataMapping

A ResVsTimeDataMapping object mapping x, y and aesthetic groups to their variable names of data.
plotConfiguration

An optional ResVsTimeConfiguration object defining labels, grid, background and watermark.
smoother

Optional name of smoother function:

  • "loess" for loess regression

  • "lm" for linear regression

plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotSimulatedTimeProfile(), plotTimeProfile(), plotTornado()

Examples

# Produce Obs vs Pred plot
resVsTimeData <- data.frame(x = c(1, 2, 1, 2, 3), y = c(5, 0.2, 2, 3, 4))

plotResVsTime(data = resVsTimeData, dataMapping = ResVsTimeDataMapping$new(x = "x", y = "y"))

# Produce Res vs Time plot with linear regression
plotResVsTime(
  data = resVsTimeData,
  dataMapping = ResVsTimeDataMapping$new(x = "x", y = "y"),
  smoother = "lm"
)

plotSimulatedTimeProfile

Description

Producing Time Profile plots

Usage

plotSimulatedTimeProfile(
  data = NULL,
  metaData = NULL,
  dataMapping = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
dataMapping

A TimeProfileDataMapping object mapping x, y, ymin, ymax and aesthetic groups to their variable names of data.
plotConfiguration

An optional TimeProfilePlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotTimeProfile(), plotTornado()

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")
)

plotTimeProfile

Description

Producing Time Profile plots

Usage

plotTimeProfile(
  data = NULL,
  metaData = NULL,
  dataMapping = NULL,
  observedData = NULL,
  observedDataMapping = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
dataMapping

A TimeProfileDataMapping object mapping x, y, ymin, ymax and aesthetic groups to their variable names of data.
observedData

A data.frame to use for plot. Unlike data, meant for simulated data, plotted as lines and ribbons; observedData is plotted as scatter points and errorbars.
observedDataMapping

An ObservedDataMapping object mapping x, y, ymin, ymax and aesthetic groups to their variable names of observedData.
plotConfiguration

An optional TimeProfilePlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTornado()

Examples

# Produce a Time profile plot with observed and simulated data
obsData <- data.frame(x = c(1, 2, 1, 2, 3), y = c(5, 0.2, 2, 3, 4))
simTime <- seq(1, 10, 0.1)
simData <- data.frame(
  x = simTime,
  y = 10 * exp(-simTime),
  ymin = 8 * exp(-simTime),
  ymax = 12 * exp(-simTime)
)

plotTimeProfile(
  data = simData,
  observedData = obsData,
  dataMapping = TimeProfileDataMapping$new(x = "x", y = "y", ymin = "ymin", ymax = "ymax"),
  observedDataMapping = ObservedDataMapping$new(x = "x", y = "y")
)

plotTornado

Description

Producing tornado plots

Usage

plotTornado(
  data = NULL,
  metaData = NULL,
  x = NULL,
  y = NULL,
  sorted = NULL,
  colorPalette = NULL,
  bar = TRUE,
  dataMapping = NULL,
  plotConfiguration = NULL,
  plotObject = NULL
)

Arguments

data

A data.frame to use for plot.
metaData

A named list of information about data such as the dimension and unit of its variables.
x

Numeric values to plot along the x axis. Only used instead of data if data is NULL.
y

Character values to plot along the y axis. Only used instead of data if data is NULL.
sorted

Optional logical value defining if y values are sorted by absolute values of x.
colorPalette

Optional character values defining a ggplot2 colorPalette (e.g. "Spectral")
bar

Optional logical value setting tornado plot as bar plot instead of scatter plot.
dataMapping

A TornadoDataMapping object mapping x, y and aesthetic groups to their variable names of data.
plotConfiguration

An optional TornadoPlotConfiguration object defining labels, grid, background and watermark.
plotObject

An optional ggplot object on which to add the plot layer

Value

A ggplot object

See Also

Other molecule plots: plotBoxWhisker(), plotCumulativeTimeProfile(), plotDDIRatio(), plotGrid(), plotHistogram(), plotObsVsPred(), plotObservedTimeProfile(), plotPKRatio(), plotPieChart(), plotQQ(), plotResVsPred(), plotResVsTime(), plotSimulatedTimeProfile(), plotTimeProfile()

Examples

# Produce a tornado plot
plotTornado(x = c(2, -1, 3), y = c("A", "B", "C"))

# Produce a tornado plot as scatter plot
plotTornado(x = c(2, -1, 3), y = c("A", "B", "C"), bar = FALSE)

# Produce a tornado plot as is (no sorting)
plotTornado(x = c(2, -1, 3), y = c("A", "B", "C"), sorted = FALSE)

QQDataMapping

Description

R6 class for mapping x, y and GroupMapping variables to data

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> QQDataMapping

Methods

Public methods

Inherited methods

Method checkMapData()

Check that data variables include map variables

Usage
QQDataMapping$checkMapData(data, metaData = NULL)
Arguments
data

data.frame to check

metaData

list containing information on data

Returns

A data.frame with map and defaultAes variables. Dummy variable defaultAes is necessary to allow further modification of plots.

Method clone()

The objects of this class are cloneable with this method.

Usage
QQDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

QQPlotConfiguration

Description

R6 class defining the configuration of a ggplot object for Quantile-Quantile plots

Super class

tlf::PlotConfiguration -> QQPlotConfiguration

Methods

Public methods

Method new()

Create a new QQPlotConfiguration object

Usage
QQPlotConfiguration$new(xlabel = "Standard Normal Quantiles", ...)
Arguments
xlabel

QQ-plot default display is "Standard Normal Quantiles"

...

parameters inherited from PlotConfiguration

Returns

A new QQPlotConfiguration object

Method clone()

The objects of this class are cloneable with this method.

Usage
QQPlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

RangeDataMapping

Description

R6 class for mapping x, ymin and ymax variable to data

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> RangeDataMapping

Public fields

ymin

Name of ymin variable to map

ymax

Name of ymax variable to map

Methods

Public methods

Method new()

Create a new RangeDataMapping object

Usage
RangeDataMapping$new(
  x = NULL,
  ymin = NULL,
  ymax = NULL,
  groupMapping = NULL,
  color = NULL,
  fill = NULL,
  linetype = NULL,
  shape = NULL,
  size = NULL,
  group = NULL,
  data = NULL
)
Arguments
x

Name of x variable to map

ymin

Name of ymin variable to map

ymax

Name of ymax variable to map

groupMapping

R6 class GroupMapping object

color

R6 class Grouping object or its input

fill

R6 class Grouping object or its input

linetype

R6 class Grouping object or its input

shape

R6 class Grouping object or its input

size

R6 class Grouping object or its input

group

R6 class Grouping object or its input

data

data.frame to map used by .smartMapping

Returns

A new RangeDataMapping object

Method checkMapData()

Check that data variables include map variables

Usage
RangeDataMapping$checkMapData(data, metaData = NULL)
Arguments
data

data.frame to check

metaData

list containing information on data

Returns

A data.frame with map and legendLabels variables. Dummy variable legendLabels is necessary to allow further modification of plots.

Method clone()

The objects of this class are cloneable with this method.

Usage
RangeDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

resetTLFSettingsToDefault

Description

Reset the global settings stored in tlfEnv to default values defined by the package.

Usage

resetTLFSettingsToDefault()

ResVsPredDataMapping

Description

Class for mapping variables in residuals vs predictions/time plot

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> tlf::ObsVsPredDataMapping -> ResVsPredDataMapping

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
ResVsPredDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

ResVsPredPlotConfiguration

Description

R6 class defining the configuration of a ggplot object for Res vs Pred/Time plots

Super class

tlf::PlotConfiguration -> ResVsPredPlotConfiguration

Public fields

defaultSymmetricAxes

Default option setting symmetric xAxis and/or yAxis limits when creating a ResVsPredPlotConfiguration object

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
ResVsPredPlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

ResVsTimeDataMapping

Description

Class for mapping variables in residuals vs predictions/time plot

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> tlf::ObsVsPredDataMapping -> tlf::ResVsPredDataMapping -> ResVsTimeDataMapping

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
ResVsTimeDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

ResVsTimePlotConfiguration

Description

R6 class defining the configuration of a ggplot object for Res vs Pred/Time plots

Super classes

tlf::PlotConfiguration -> tlf::ResVsPredPlotConfiguration -> ResVsTimePlotConfiguration

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
ResVsTimePlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

runPlotMaker

Description

Run shiny app that allows to easily make plots from user interface.

Usage

runPlotMaker()

References

For tutorial, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/plot-maker.html

See Also

Other shiny apps: runThemeMaker()

runThemeMaker

Description

Run shiny app that allows easy setting of Theme objects. Theme objects drive default properties of plots

Usage

runThemeMaker()

References

For tutorial, see: https://www.open-systems-pharmacology.org/TLF-Library/articles/theme-maker.html

See Also

Other shiny apps: runPlotMaker()

saveThemeToJson

Description

Save theme object to a json file.

Usage

saveThemeToJson(jsonFile, theme = NULL)

Arguments

jsonFile

path of json file
theme

Theme object path of json file

saveTLFSettings Save the current TLF global settings in a .RData file

Description

saveTLFSettings Save the current TLF global settings in a .RData file

Usage

saveTLFSettings(file)

Arguments

file

.RData file containing the settings

Scaling

Description

Helper enum of predefined transformations of axes Note that the transformations will be translated internally into ggplot2 transformations. ggplot2 includes more transformations than what is available in this enum.

Usage

Scaling

Format

An object of class list of length 9.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

Examples

# Continuous linear/identity scale
Scaling$identity
Scaling$lin

# Continuous log10 scale
Scaling$log

# Continuous natural logarithm (ln) scale (base is *e*)
Scaling$ln

# Discrete scale for categrical data such as boxplot and tornado plot data
Scaling$discrete

# Reverse continuous linear scale to switch end and beginning of linear scale
Scaling$reverse

# Continusous square root scale
Scaling$sqrt

# Time scale for POSIXlt or POSIXct data
Scaling$time

# Date scale for POSIXlt or POSIXct data
Scaling$date

setBackground

Description

Set background properties of a ggplot object

Usage

setBackground(
  plotObject,
  fill = NULL,
  color = NULL,
  linetype = NULL,
  size = NULL
)

Arguments

plotObject

A ggplot object
fill

Optional character values defining the color of the background. See grDevices::colors() to get names of colors
color

Optional character values defining the color of the background frame. See grDevices::colors() to get names of colors
linetype

Optional character values defining the linetype of the background frame. See enum Linetypes to get names of linetype.
size

Optional numeric values defining the size of the background frame.

Value

A ggplot object

Examples

# Set background of a scatter plot
p <- addScatter(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

setBackground(p, fill = "yellowgreen", color = "red", linetype = "dotted")

setBackgroundPanelArea

Description

Set background panel area properties of a ggplot object

Usage

setBackgroundPanelArea(
  plotObject,
  fill = NULL,
  color = NULL,
  linetype = NULL,
  size = NULL
)

Arguments

plotObject

A ggplot object
fill

Optional character values defining the color of the background. See grDevices::colors() to get names of colors
color

Optional character values defining the color of the background frame. See grDevices::colors() to get names of colors
linetype

Optional character values defining the linetype of the background frame. See enum Linetypes to get names of linetype.
size

Optional numeric values defining the size of the background frame.

Value

A ggplot object

Examples

# Set background of a scatter plot
p <- addScatter(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

setBackgroundPanelArea(p, fill = "yellowgreen", color = "red", linetype = "dotted")

setBackgroundPlotArea

Description

Set background plot area properties of a ggplot object

Usage

setBackgroundPlotArea(
  plotObject,
  fill = NULL,
  color = NULL,
  linetype = NULL,
  size = NULL
)

Arguments

plotObject

A ggplot object
fill

Optional character values defining the color of the background. See grDevices::colors() to get names of colors
color

Optional character values defining the color of the background frame. See grDevices::colors() to get names of colors
linetype

Optional character values defining the linetype of the background frame. See enum Linetypes to get names of linetype.
size

Optional numeric values defining the size of the background frame.

Value

A ggplot object

Examples

# Set background of a scatter plot
p <- addScatter(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

setBackgroundPlotArea(p, fill = "yellowgreen", color = "red", linetype = "dotted")

setCaptionColor

Description

Set the colors of the data in plot and legend caption

Usage

setCaptionColor(plotObject, color, name = NULL)

Arguments

plotObject

ggplot graphical object
color

colors of the data in plot and legend caption
name

reference names in caption$name identifying the legend caption lines

Value

A ggplot graphical object

setCaptionFill

Description

Set the fills of the data in plot and legend caption

Usage

setCaptionFill(plotObject, fill, name = NULL)

Arguments

plotObject

ggplot graphical object
fill

fills of the data in plot and legend caption
name

reference names in caption$name identifying the legend caption lines

Value

A ggplot graphical object

setCaptionLabel

Description

Set the legend caption labels

Usage

setCaptionLabels(plotObject, label, name = NULL)

Arguments

plotObject

ggplot graphical object
label

new labels of the legend caption
name

reference names in caption$name identifying the legend caption lines

Value

A ggplot graphical object

setCaptionLinetype

Description

Set the linetypes of the data in plot and legend caption

Usage

setCaptionLinetype(plotObject, linetype, name = NULL)

Arguments

plotObject

ggplot graphical object
linetype

linetypes of the data in plot and legend caption
name

reference names in caption$name identifying the legend caption lines

Value

A ggplot graphical object

setCaptionOrder

Description

Set the order of the legend caption labels

Usage

setCaptionOrder(plotObject, order, name = NULL)

Arguments

plotObject

ggplot graphical object
order

numeric order of the legend caption labels
name

reference names in caption$name identifying the legend caption lines

Value

A ggplot graphical object

setCaptionShape

Description

Set the shapes of the data in plot and legend caption

Usage

setCaptionShape(plotObject, shape, name = NULL)

Arguments

plotObject

ggplot graphical object
shape

shapes of the data in plot and legend caption
name

reference names in caption$name identifying the legend caption lines

Value

A ggplot graphical object

setCaptionSize

Description

Set the sizes of the data in plot and legend caption

Usage

setCaptionSize(plotObject, size, name = NULL)

Arguments

plotObject

ggplot graphical object
size

sizes of the data in plot and legend caption
name

reference names in caption$name identifying the legend caption lines

Value

A ggplot graphical object

setCaptionVisibility

Description

Set the visibility of the legend caption labels

Usage

setCaptionVisibility(plotObject, visibility, name = NULL)

Arguments

plotObject

ggplot graphical object
visibility

logical visibility of the legend caption labels
name

reference names in caption$name identifying the legend caption lines

Value

A ggplot graphical object

setDefaultAggregationBins

Description

Set default aggregation bins of tlf environment

Usage

setDefaultAggregationBins(bins = NULL)

Arguments

bins

Number of bins if value, edges if vector or binning function if function

Examples

# Set default number of bins
plotHistogram(x = rnorm(1000))

setDefaultAggregationBins(21)
plotHistogram(x = rnorm(1000))

setDefaultAggregationFunctions

Description

Set default aggregation functions of tlf environment

Usage

setDefaultAggregationFunctions(y = NULL, ymin = NULL, ymax = NULL)

Arguments

y

function or its name as median aggregation
ymin

function or its name as min aggregation
ymax

function or its name as max aggregation

setDefaultAggregationLabels

Description

Set default aggregation labels of tlf environment

Usage

setDefaultAggregationLabels(y = NULL, range = NULL)

Arguments

y

label for median aggregation
range

label for range aggregation

setDefaultAlphaRatio

Description

Set the default alpha (transparency) difference ratio between points above and bellow lloq

Usage

setDefaultAlphaRatio(alphaRatio)

Arguments

alphaRatio

alpha ratio to set as default. Must be between 0 and 1.

setDefaultErrorbarCapSize

Description

Set default cap size of error bars

Usage

setDefaultErrorbarCapSize(size)

Arguments

size

A numeric defining the size of the error bar caps in pts

setDefaultExportParameters

Description

Set default tlf properties for exporting/saving plots

Usage

setDefaultExportParameters(
  format = NULL,
  width = NULL,
  height = NULL,
  units = NULL,
  dpi = NULL,
  name = NULL
)

Arguments

format

file format of the exported plots
width

plot width in unit
height

plot height in unit
units

units of width and height
dpi

units of width and height
name

base file name of the exported plots

setDefaultLegendPosition

Description

Set default legend position of tlf environment

Usage

setDefaultLegendPosition(position)

Arguments

position

legend position. Use Enum LegendPositions to assess available legend positions

setDefaultLegendTitle

Description

Set default legend title of tlf environment

Usage

setDefaultLegendTitle(title)

Arguments

title

Character or Label object

setDefaultLLOQLinetype

Description

Set default cap linetype for lloq lines

Usage

setDefaultLLOQLinetype(linetype)

Arguments

linetype

linetype to set as default

setDefaultLogTicks

Description

Set default values for log ticks

Usage

setDefaultLogTicks(ticks)

Arguments

ticks

numeric values where ticks are placed. Ensure that the values are positive (they are meant for log scale)

setDefaultMaxCharacterWidth

Description

Set the maximum number of characters per row for axis ticks labels and legend. Long strings will be wraped on spaces or non-word characters.

Usage

setDefaultMaxCharacterWidth(maxCharacterWidth)

Arguments

maxCharacterWidth

the maximum number of characters per row

setDefaultWatermark

Description

Set default watermark value for current theme

Usage

setDefaultWatermark(watermark = NULL)

Arguments

watermark

A character value or Label object

Examples

# Set default watermark using a character
setDefaultWatermark("Confidential")
addScatter(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

# Set default watermark using a `Label` object
setDefaultWatermark(Label$new(text = "Confidential", color = "red", angle = 30))
addScatter(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

setGrid

Description

Set x and y grid properties of a ggplot object

Usage

setGrid(plotObject, color = NULL, linetype = NULL, size = NULL)

Arguments

plotObject

A ggplot object
color

Optional character values defining the color of the grid. See grDevices::colors() to get names of colors
linetype

Optional character values defining the linetype of the grid. See enum Linetypes to get names of linetype.
size

Optional numeric values defining the size of the grid.

Value

A ggplot object

Examples

# Set grid of a scatter plot
p <- addScatter(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

setGrid(p, color = "red", linetype = "dotted")

setLegend

Description

Set legend position, title, font and/or caption

Usage

setLegend(
  plotObject,
  position = NULL,
  title = NULL,
  font = NULL,
  caption = NULL
)

Arguments

plotObject

Graphical object created from ggplot
position

legend position. Use enum LegendPositions to access the list of legend positions.
title

character or Label object
font

Font object defining legend font
caption

data.frame containing the caption properties of the legend

Value

A ggplot object

setLegendCaption

Description

Set the legend caption

Usage

setLegendCaption(plotObject, caption = NULL)

Arguments

plotObject

ggplot graphical object
caption

data.frame containing the caption properties of the legend

Value

A ggplot graphical object

setLegendFont

Description

Set legend font properties

Usage

setLegendFont(
  plotObject,
  color = NULL,
  size = NULL,
  fontFamily = NULL,
  fontFace = NULL,
  angle = NULL,
  align = NULL
)

Arguments

plotObject

ggplot object
color

character defining the color of legend font
size

numeric defining the size of legend font
fontFamily

character defining the family of legend font
fontFace

character defining the legend font face as defined in helper enum FontFaces.
angle

numeric defining the angle of legend font
align

character defining the alignment of legend font as defined in helper enum Alignments.

Value

A ggplot object

setLegendPosition

Description

Set the legend position

Usage

setLegendPosition(plotObject, position = NULL)

Arguments

plotObject

ggplot graphical object
position

legend position as defined in helper enum LegendPositions

Value

A ggplot graphical object

See Also

LegendPositions

setLegendTitle

Description

Set legend title

Usage

setLegendTitle(plotObject, title = NULL)

Arguments

plotObject

ggplot object
title

character or Label object

Value

A ggplot object

setPlotExport

Description

Set plot export properties

Usage

setPlotExport(
  plotObject,
  name = NULL,
  format = NULL,
  width = NULL,
  height = NULL,
  units = NULL,
  dpi = NULL
)

Arguments

plotObject

Graphical object created from ggplot
name

character defining the name of the file to be saved (without extension)
format

character defining the format of the file to be saved.
width

numeric values defining the width in units of the plot dimensions after saving
height

numeric values defining the height in units of the plot dimensions after saving
units

character defining the unit of the saving dimension
dpi

numeric value defining plot resolution (dots per inch)

Value

ggplot object with updated saving properties

setPlotExportDimensions

Description

Set plot export properties

Usage

setPlotExportDimensions(
  plotObject,
  width = NULL,
  height = NULL,
  units = NULL,
  dpi = NULL
)

Arguments

plotObject

Graphical object created from ggplot
width

plot width in unit
height

plot height in unit
units

units of width and height
dpi

numeric value defining plot resolution (dots per inch)

Value

ggplot object with updated labels

setPlotExportFormat

Description

Set plot export properties

Usage

setPlotExportFormat(plotObject, format = NULL)

Arguments

plotObject

Graphical object created from ggplot
format

file format of the exported plot

Value

ggplot object with updated labels

setPlotExportSize

Description

Set plot export properties

Usage

setPlotExportSize(
  plotObject,
  width = NULL,
  height = NULL,
  units = NULL,
  dpi = NULL
)

Arguments

plotObject

Graphical object created from ggplot
width

plot width in unit
height

plot height in unit
units

units of width and height
dpi

numeric value defining plot resolution (dots per inch)

Value

ggplot object with updated labels

setPlotLabels

Description

Set labels properties on a ggplot object

Usage

setPlotLabels(
  plotObject,
  title = NULL,
  subtitle = NULL,
  xlabel = NULL,
  ylabel = NULL,
  caption = NULL
)

Arguments

plotObject

A ggplot object
title

A character value or Label object
subtitle

A character value or Label object
xlabel

A character value or Label object
ylabel

A character value or Label object
caption

A character value or Label object

Value

A ggplot object

Examples

# Set labels of a scatter plot
p <- addScatter(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

setPlotLabels(p, xlabel = "new x label", ylabel = "new y label")

# Set labels using Label object
setPlotLabels(p, ylabel = Label$new(text = "red y label", color = "red"))

setWatermark

Description

Set the watermark of a ggplot object. Unlike addWatermark, the watermark layer is overridden by setWatermark.

Usage

setWatermark(
  plotObject,
  watermark = NULL,
  color = NULL,
  size = NULL,
  angle = NULL,
  alpha = NULL
)

Arguments

plotObject

A ggplot object
watermark

A character value or a Label object
color

Color of the watermark.
size

Size of the watermark.
angle

Angle of the watermark (in degree).
alpha

Numeric value between 0 and 1 corresponding to transparency of the watermark The closer to 0, the more transparent the watermark is. The closer to 1, the more opaque the watermark is.

Value

A ggplot object

Examples

# Add a watermark to an empty plot
p <- initializePlot()
setWatermark(p, "watermark")

# Watermark with font properties
watermarkLabel <- Label$new(text = "watermark", color = "blue")
setWatermark(p, watermarkLabel)

# Horizontal watermark
setWatermark(p, watermarkLabel, angle = 0)

# Watermark totally opaque
setWatermark(p, watermarkLabel, alpha = 1)

setXAxis

Description

Set X-axis properties of a ggplot object

Usage

setXAxis(
  plotObject,
  scale = NULL,
  valuesLimits = NULL,
  axisLimits = NULL,
  limits = lifecycle::deprecated(),
  ticks = NULL,
  ticklabels = NULL,
  minorTicks = NULL,
  font = NULL,
  expand = NULL
)

Arguments

plotObject

A ggplot object to set X-axis properties
scale

Scale of axis. Use enum Scaling to access names of scales.
valuesLimits

Optional numeric values of values limits
axisLimits

Optional numeric values of axis limits
limits

[Deprecated]. Replaced by axisLimits argument.
ticks

Optional values or function for axis ticks
ticklabels

Optional values or function for axis ticklabels
minorTicks

Optional values or function for axis minor ticks
font

A Font object defining font of ticklabels
expand

Logical defining if data is expanded until axis

Value

A ggplot object

Examples

myPlot <- addLine(x = c(1, 2, 3), y = c(10, 50, 100))

# Set x-axis in log scale
setXAxis(myPlot, scale = Scaling$log)

# Set x-axis ticklabels to Greek letters
setXAxis(myPlot, ticks = c(1, 2, 3), ticklabels = parse(text = c("alpha", "beta", "gamma")))

# Set x-axis limits
setXAxis(myPlot, axisLimits = c(1, 2.5))

# Set x-axis fonts
setXAxis(myPlot, font = Font$new(color = "blue", size = 14))

setXGrid

Description

Set x grid properties of a ggplot object

Usage

setXGrid(plotObject, color = NULL, linetype = NULL, size = NULL)

Arguments

plotObject

A ggplot object
color

Optional character values defining the color of the grid. See grDevices::colors() to get names of colors
linetype

Optional character values defining the linetype of the grid. See enum Linetypes to get names of linetype.
size

Optional numeric values defining the size of the grid.

Value

A ggplot object

Examples

# Set x grid of a scatter plot
p <- addScatter(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

setXGrid(p, color = "red", linetype = "dotted")

setY2Axis

Description

Set right Y-axis properties of a ggplot object

Usage

setY2Axis(
  plotObject,
  scale = NULL,
  valuesLimits = NULL,
  axisLimits = NULL,
  limits = lifecycle::deprecated(),
  ticks = NULL,
  ticklabels = NULL,
  minorTicks = NULL,
  font = NULL,
  expand = NULL
)

Arguments

plotObject

A ggplot object to set X-axis properties
scale

Scale of axis. Use enum Scaling to access names of scales.
valuesLimits

Optional numeric values of values limits
axisLimits

Optional numeric values of axis limits
limits

[Deprecated]. Replaced by axisLimits argument.
ticks

Optional values or function for axis ticks
ticklabels

Optional values or function for axis ticklabels
minorTicks

Optional values or function for axis minor ticks
font

A Font object defining font of ticklabels
expand

Logical defining if data is expanded until axis

Value

A ggplot object

setYAxis

Description

Set Y-axis properties of a ggplot object

Usage

setYAxis(
  plotObject,
  scale = NULL,
  valuesLimits = NULL,
  axisLimits = NULL,
  limits = lifecycle::deprecated(),
  ticks = NULL,
  ticklabels = NULL,
  minorTicks = NULL,
  font = NULL,
  expand = NULL
)

Arguments

plotObject

A ggplot object to set X-axis properties
scale

Scale of axis. Use enum Scaling to access names of scales.
valuesLimits

Optional numeric values of values limits
axisLimits

Optional numeric values of axis limits
limits

[Deprecated]. Replaced by axisLimits argument.
ticks

Optional values or function for axis ticks
ticklabels

Optional values or function for axis ticklabels
minorTicks

Optional values or function for axis minor ticks
font

A Font object defining font of ticklabels
expand

Logical defining if data is expanded until axis

Value

A ggplot object

Examples

myPlot <- addLine(x = c(1, 2, 3), y = c(10, 50, 100))

# Set y-axis in log scale
setYAxis(myPlot, scale = Scaling$log)

# Set y-axis ticklabels to Greek letters
setYAxis(myPlot, ticks = c(10, 50, 100), ticklabels = parse(text = c("alpha", "beta", "gamma")))

# Set y-axis limits
setYAxis(myPlot, axisLimits = c(10, 75))

# Set y-axis fonts
setYAxis(myPlot, font = Font$new(color = "blue", size = 14))

setYGrid

Description

Set y grid properties of a ggplot object

Usage

setYGrid(plotObject, color = NULL, linetype = NULL, size = NULL)

Arguments

plotObject

A ggplot object
color

Optional character values defining the color of the grid. See grDevices::colors() to get names of colors
linetype

Optional character values defining the linetype of the grid. See enum Linetypes to get names of linetype.
size

Optional numeric values defining the size of the grid.

Value

A ggplot object

Examples

# Set y grid of a scatter
p <- addScatter(x = c(1, 2, 1, 2, 3), y = c(5, 0, 2, 3, 4))

setYGrid(p, color = "red", linetype = "dotted")

Shapes

Description

List of some ggplot2 shapes. The shapes from this enum/list are unicode characters corresponding to their appropriate shapes. Note that user-defined characters are also accepted by geomTLFPoint()

Usage

Shapes

Format

An object of class list of length 40.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

Examples

# Use ggplot2 to plot and label shapes
shapesData <- data.frame(
  x = (seq_along(Shapes) - 1) %% 6,
  y = floor((seq_along(Shapes) - 1) / 6),
  shape = factor(names(Shapes), levels = names(Shapes))
)
ggplot2::ggplot(data = shapesData, ggplot2::aes(x, y)) +
  ggplot2::theme_void() +
  # Define size and color of shapes
  geomTLFPoint(ggplot2::aes(shape = shape), size = 8, color = "red") +
  # Add shape names from enum below the displayed shape
  ggplot2::geom_text(ggplot2::aes(label = shape), nudge_y = -0.3, size = 3) +
  # Use scale to display the actual shape
  ggplot2::scale_shape_manual(values = as.character(unlist(Shapes))) +
  # Remove the legend as the shape name is labelled below the shape
  ggplot2::guides(shape = "none")

# Perform a scatter plot with blue pentagons as shape
addScatter(
  x = 1:10,
  y = rlnorm(10),
  shape = Shapes$pentagon,
  color = "blue",
  size = 3
)

TagPositions

Description

List of all available tag positions in a plot grid.

Usage

TagPositions

Format

An object of class list of length 8.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TickLabelTransforms, VerticalJustification, tlfSettingsNames, tlfStatFunctions

Theme

Description

R6 class defining theme properties

Active bindings

fonts

ThemeFont object

background

ThemeBackground object

aestheticMaps

ThemeAestheticMaps object

plotConfigurations

ThemePlotConfiguration object

Methods

Public methods

Method new()

Create a new Theme object

Usage
Theme$new(
  fonts = NULL,
  background = NULL,
  aestheticMaps = NULL,
  plotConfigurations = NULL
)
Arguments
fonts

ThemeFont object

background

ThemeBackground object

aestheticMaps

ThemeAestheticMaps object

plotConfigurations

ThemePlotConfiguration object

Returns

A new Theme object

Method save()

Save Theme as a json file

Usage
Theme$save(jsonFile)
Arguments
jsonFile

name of json file

Method clone()

The objects of this class are cloneable with this method.

Usage
Theme$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

ThemeAestheticMaps

Description

R6 class defining theme aesthetic maps

Public fields

color

color map as character or numeric vector

fill

fill map as character or numeric vector

size

size map as numeric vector

shape

shape map as numeric vector

linetype

linetype as character vector

alpha

map as numeric vector

Methods

Public methods

Method new()

Create a new ThemeAestheticMaps object

Usage
ThemeAestheticMaps$new(
  color = NULL,
  fill = NULL,
  shape = NULL,
  size = NULL,
  linetype = NULL,
  alpha = NULL
)
Arguments
color

color map as list, character or numeric vector

fill

fill map as list, character or numeric vector

shape

shape map as list, character or numeric vector

size

size map as list, character or numeric vector

linetype

linetype map as list, character or numeric vector

alpha

alpha map as list, character or numeric vector

Returns

A new ThemeAestheticMaps object

Method toJson()

Translate object into a json list

Usage
ThemeAestheticMaps$toJson()
Returns

A list that can be saved into a json file

Method clone()

The objects of this class are cloneable with this method.

Usage
ThemeAestheticMaps$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

ThemeAestheticSelections

Description

R6 class defining how plot configurations will use aesthetic maps

Super class

tlf::ThemeAestheticMaps -> ThemeAestheticSelections

Methods

Public methods

Method new()

Create a new ThemeAestheticSelections object

Usage
ThemeAestheticSelections$new(
  color = NULL,
  fill = NULL,
  shape = NULL,
  size = NULL,
  linetype = NULL,
  alpha = NULL
)
Arguments
color

selection key or values for choice of color

fill

selection key or values for choice of fill

shape

selection key or values for choice of shape

size

selection key or values for choice of size

linetype

selection key or values for choice of linetype

alpha

selection key or values for choice of alpha

Returns

A new ThemeAestheticSelections object

Method toJson()

Translate object into a json list

Usage
ThemeAestheticSelections$toJson()
Returns

A list that can be saved into a json file

Method clone()

The objects of this class are cloneable with this method.

Usage
ThemeAestheticSelections$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

ThemeBackground

Description

R6 class defining theme background properties

Public fields

watermark

character defining content of watermark

legendPosition

character defining where legend should usually be placed

legendTitle

character defining the content of legend title

plot

BackgroundElement object for plot area properties (outside of panel)

panel

BackgroundElement object for plot area properties (inside of panel)

xAxis

BackgroundElement object for x axis properties

yAxis

BackgroundElement object for y axis properties

y2Axis

BackgroundElement object for right y axis properties

xGrid

BackgroundElement object for x grid properties

yGrid

BackgroundElement object for y grid properties

y2Grid

BackgroundElement object for right y grid properties

legend

BackgroundElement object for legend area properties

Methods

Public methods

Method new()

Create a new ThemeBackground object

Usage
ThemeBackground$new(
  watermark = NULL,
  legendPosition = NULL,
  legendTitle = NULL,
  plot = NULL,
  panel = NULL,
  xAxis = NULL,
  yAxis = NULL,
  y2Axis = NULL,
  xGrid = NULL,
  yGrid = NULL,
  y2Grid = NULL,
  legend = NULL,
  baseFill = "white",
  baseColor = "black",
  baseSize = 0.5,
  baseLinetype = "solid"
)
Arguments
watermark

character defining content of watermark

legendPosition

character defining where legend should usually be placed

legendTitle

character defining the content of legend title

plot

BackgroundElement object or list for plot area properties (outside of panel)

panel

BackgroundElement object or list for plot area properties (inside of panel)

xAxis

BackgroundElement object or list for x axis properties

yAxis

BackgroundElement object or list for y axis properties

y2Axis

BackgroundElement object or list for right y axis properties

xGrid

BackgroundElement object or list for x grid properties

yGrid

BackgroundElement object or list for y grid properties

y2Grid

BackgroundElement object or list for right y grid properties

legend

BackgroundElement object or list for legend area properties

baseFill

name of base color fill of undefined background elements. Default is "white".

baseColor

name of base color of undefined background elements. Default is "black".

baseSize

name of base size of undefined background elements. Default is 0.5.

baseLinetype

name of base size of undefined background elements. Default is "solid".

Returns

A new ThemeBackground object

Method toJson()

Translate object into a json list

Usage
ThemeBackground$toJson()
Returns

A list that can be saved into a json file

Method clone()

The objects of this class are cloneable with this method.

Usage
ThemeBackground$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

ThemeFont

Description

R6 class defining theme font properties

Public fields

title

Font object for font properties title

subtitle

Font object for font properties of subtitle

xlabel

Font object for font properties of xlabel

ylabel

Font object for font properties of ylabel

y2label

Font object for font properties of y2label

caption

Font object for font properties of caption

watermark

Font object for font properties of watermark

legendTitle

Font object for font properties of legend title

legend

Font object for font properties of legend

xAxis

Font object for font properties of xAxis

yAxis

Font object for font properties of yAxis

y2Axis

Font object for font properties of y2Axis

Methods

Public methods

Method new()

Create a new ThemeFont object

Usage
ThemeFont$new(
  title = NULL,
  subtitle = NULL,
  xlabel = NULL,
  ylabel = NULL,
  y2label = NULL,
  caption = NULL,
  watermark = NULL,
  legendTitle = NULL,
  legend = NULL,
  xAxis = NULL,
  yAxis = NULL,
  y2Axis = NULL,
  baseColor = "black",
  baseSize = 12,
  baseFace = "plain",
  baseFamily = "",
  baseAngle = 0,
  baseAlign = "center",
  baseMaxWidth = NULL
)
Arguments
title

Font object or list for font properties title

subtitle

Font object or list for font properties of subtitle

xlabel

Font object or list for font properties of xlabel

ylabel

Font object or list for font properties of ylabel

y2label

Font object or list for font properties of y2label

caption

Font object or list for font properties of caption

watermark

Font object or list for font properties of watermark

legendTitle

Font object or list for font properties of legend title

legend

Font object or list for font properties of legend

xAxis

Font object or list for font properties of xAxis

yAxis

Font object or list for font properties of yAxis

y2Axis

Font object or list for font properties of y2Axis

baseColor

name of base color of undefined fonts. Default is "black".

baseSize

base size of undefined fonts. Default is 12.

baseFace

name of base face of undefined fonts. Default is "plain".

baseFamily

name of base family of undefined fonts. Default is "".

baseAngle

base angle of undefined fonts. Default is 0 degree.

baseAlign

base alignment of undefined fonts. Default is "center".

baseMaxWidth

base maximum ggplot2 "pt" unit in which text is drawn.

Returns

A new ThemeFont object

Method toJson()

Translate object into a json list

Usage
ThemeFont$toJson()
Returns

A list that can be saved into a json file

Method clone()

The objects of this class are cloneable with this method.

Usage
ThemeFont$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

ThemePlotConfigurations

Description

R6 class defining theme of plot configuration objects

Public fields

addScatter

theme properties for PlotConfiguration objects as used in function addScatter()

addLine

theme properties for PlotConfiguration objects as used in function addLine()

addRibbon

theme properties for PlotConfiguration objects as used in function addRibbon()

addErrorbar

theme properties for PlotConfiguration objects as used in function addErrorbar()

Methods

Public methods

Method new()

Create a new ThemePlotConfigurations object

Usage
ThemePlotConfigurations$new(
  addScatter = NULL,
  addLine = NULL,
  addRibbon = NULL,
  addErrorbar = NULL,
  ...
)
Arguments
addScatter

theme properties for PlotConfiguration objects as used in function addScatter()

addLine

theme properties for PlotConfiguration objects as used in function addLine()

addRibbon

theme properties for PlotConfiguration objects as used in function addRibbon()

addErrorbar

theme properties for PlotConfiguration objects as used in function addErrorbar()

...

theme properties for PlotConfiguration objects as used in molecule plots

Returns

A new ThemePlotConfigurations object

Method toJson()

Translate object into a json list

Usage
ThemePlotConfigurations$toJson()
Returns

A list that can be saved into a json file

Method clone()

The objects of this class are cloneable with this method.

Usage
ThemePlotConfigurations$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

TickLabelTransforms

Description

List of all available tick label transformation names

Usage

TickLabelTransforms

Format

An object of class list of length 9.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, VerticalJustification, tlfSettingsNames, tlfStatFunctions

TimeProfileDataMapping

Description

R6 class defining the configuration of a ggplot object for time profile plot

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> tlf::RangeDataMapping -> TimeProfileDataMapping

Public fields

y2Axis

Name of y2Axis variable to map

Methods

Public methods

Method new()

Create a new TimeProfileDataMapping object

Usage
TimeProfileDataMapping$new(
  x = NULL,
  y = NULL,
  ymin = NULL,
  ymax = NULL,
  group = NULL,
  y2Axis = NULL,
  color = NULL,
  fill = NULL,
  linetype = NULL,
  data = NULL
)
Arguments
x

Name of x variable to map

y

Name of y variable to map

ymin

Name of ymin variable to map

ymax

Name of ymax variable to map

group

R6 class Grouping object or its input

y2Axis

Name of y2Axis variable to map

color

R6 class Grouping object or its input

fill

R6 class Grouping object or its input

linetype

R6 class Grouping object or its input

data

data.frame to map used by .smartMapping

Returns

A new RangeDataMapping object

Method checkMapData()

Check that data variables include map variables

Usage
TimeProfileDataMapping$checkMapData(data, metaData = NULL)
Arguments
data

data.frame to check

metaData

list containing information on data

Returns

A data.frame with map and legendLabels variables. Dummy variable legendLabels is necessary to allow further modification of plots.

Method requireDualAxis()

Assess if data require a dual axis plot

Usage
TimeProfileDataMapping$requireDualAxis(data)
Arguments
data

data.frame to check

Returns

A logical

Method getLeftAxis()

Render NA values for all right axis data

Usage
TimeProfileDataMapping$getLeftAxis(data)
Arguments
data

A data.frame

Returns

A data.frame to be plotted in left axis

Method getRightAxis()

Render NA values for all left axis data

Usage
TimeProfileDataMapping$getRightAxis(data)
Arguments
data

A data.frame

Returns

A data.frame to be plotted in right axis

Method clone()

The objects of this class are cloneable with this method.

Usage
TimeProfileDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TornadoDataMapping, XYDataMapping, XYGDataMapping

TimeProfilePlotConfiguration

Description

R6 class defining the configuration of a ggplot object for time profile plots

Super class

tlf::PlotConfiguration -> TimeProfilePlotConfiguration

Public fields

lloqDirection

Whether to draw LLOQ lines for x (vertical), y (horizontal) or x and y (both).

Active bindings

y2Axis

YAxisConfiguration object defining properties of y2-axis

Methods

Public methods

Method new()

Create a new TimeProfilePlotConfiguration object

Usage
TimeProfilePlotConfiguration$new(
  ...,
  y2label = NULL,
  y2Axis = NULL,
  y2Scale = NULL,
  y2ValuesLimits = NULL,
  y2AxisLimits = NULL,
  y2Limits = lifecycle::deprecated(),
  lloqDirection = "horizontal",
  data = NULL,
  metaData = NULL,
  dataMapping = NULL
)
Arguments
...

parameters inherited from PlotConfiguration

y2label

character or Label object defining plot y2label

y2Axis

YAxisConfiguration object defining y-axis properties

y2Scale

name of y2-axis scale. Use enum Scaling to access predefined scales.

y2ValuesLimits

numeric vector of length 2 defining y values limits

y2AxisLimits

numeric vector of length 2 defining y axis limits

y2Limits

[Deprecated]. Replaced by y2AxisLimits argument.

lloqDirection

Whether to draw LLOQ lines for x (vertical), y (horizontal) or x and y (both).

data

data.frame used by .smartMapping

metaData

list of information on data

dataMapping

R6 class or subclass TimeProfileDataMapping

Returns

A new TimeProfilePlotConfiguration object

Method clone()

The objects of this class are cloneable with this method.

Usage
TimeProfilePlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration, YAxisConfiguration

tlfSettingsNames

Description

Names of the default/global settings stored in tlfEnv. Can be used with getTLFSettings()

Usage

tlfSettingsNames

Format

An object of class list of length 14.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfStatFunctions

tlfStatFunctions

Description

Bank of predefined functions ready to use by Aggregation methods. Bank defined as Enum. To access the function from its name, use match.fun: e.g. testFun <- match.fun("mean-1.96sd")

Usage

tlfStatFunctions

Format

An object of class list of length 31.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, VerticalJustification, tlfSettingsNames

TornadoDataMapping

Description

R6 class for mapping values, labels to data

Super classes

tlf::XYDataMapping -> tlf::XYGDataMapping -> TornadoDataMapping

Public fields

lines

numeric vector of limits to plot

sorted

logical indicating if values should be sorted

Methods

Public methods

Method new()

Create a new TornadoDataMapping object

Usage
TornadoDataMapping$new(
  lines = DefaultDataMappingValues$tornado,
  sorted = NULL,
  x = NULL,
  y = NULL,
  ...
)
Arguments
lines

numeric vector of limits to plot

sorted

logical indicating if values should be sorted

x

Variable including the values of tornado plot

y

Variable including the labels of tornado plot

...

parameters inherited from XYGDataMapping

Returns

A new TornadoDataMapping object

Method checkMapData()

Check that data variables include map variables

Usage
TornadoDataMapping$checkMapData(data, metaData = NULL)
Arguments
data

data.frame to check

metaData

list containing information on data

Returns

A data.frame with map and defaultAes variables. Dummy variable defaultAes is necessary to allow further modification of plots.

Method clone()

The objects of this class are cloneable with this method.

Usage
TornadoDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, XYDataMapping, XYGDataMapping

TornadoPlotConfiguration

Description

R6 class defining the configuration of a ggplot object for tornado plots

Super class

tlf::PlotConfiguration -> TornadoPlotConfiguration

Public fields

bar

logical setting if tornado is uses a bar plot instead of regular points

colorPalette

color palette property from ggplot2

dodge

space between the bars/points

defaultYScale

Default yAxis scale value when creating a TornadoPlotConfiguration object

Methods

Public methods

Method new()

Create a new TornadoPlotConfiguration object

Usage
TornadoPlotConfiguration$new(bar = TRUE, colorPalette = NULL, dodge = 0.5, ...)
Arguments
bar

logical setting if tornado is uses a bar plot instead of regular points

colorPalette

color palette property from ggplot2

dodge

space between the bars/points

...

parameters inherited from PlotConfiguration

Returns

A new TornadoPlotConfiguration object

Method clone()

The objects of this class are cloneable with this method.

Usage
TornadoPlotConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, XAxisConfiguration, YAxisConfiguration

updateExportDimensionsForLegend

Description

Update plot dimensions based on size and position of legend

Usage

updateExportDimensionsForLegend(plotObject)

Arguments

plotObject

A ggplot object

Value

A ggplot object

updateTimeProfileLegend

Description

Update time profile legend caption

Usage

updateTimeProfileLegend(plotObject, caption)

Arguments

plotObject

A ggplot object
caption

A data.frame as obtained from getLegendCaption to use for updating a plot legend.

Value

A ggplot object

useDarkTheme

Description

Set default Matlab theme to be used as the current default of the tlf environment

Usage

useDarkTheme()

Examples

useDarkTheme()
addScatter(x = seq(1, 10), y = rnorm(10))

useExcelTheme

Description

Set default Excel theme to be used as the current default of the tlf environment

Usage

useExcelTheme()

Examples

useExcelTheme()
addScatter(x = seq(1, 10), y = rnorm(10))

useHighChartTheme

Description

Set default HighChart theme to be used as the current default of the tlf environment

Usage

useHighChartTheme()

Examples

useHighChartTheme()
addScatter(x = seq(1, 10), y = rnorm(10))

useMatlabTheme

Description

Set default Matlab theme to be used as the current default of the tlf environment

Usage

useMatlabTheme()

Examples

useMatlabTheme()
addScatter(x = seq(1, 10), y = rnorm(10))

useMinimalTheme

Description

Set default minimal theme to be used as the current default of the tlf environment

Usage

useMinimalTheme()

Examples

useMinimalTheme()
addScatter(x = seq(1, 10), y = rnorm(10))

useTemplateTheme

Description

Set default theme to be used as the current default of the tlf environment

Usage

useTemplateTheme()

Examples

useTemplateTheme()
addScatter(x = seq(1, 10), y = rnorm(10))

useTheme

Description

set the theme to be used as the current default of the tlf environment

Usage

useTheme(theme)

Arguments

theme

Theme to be used as default of the tlf environment

VerticalJustification

Description

List of all available vertical justifications for plot annotation text.

Usage

VerticalJustification

Format

An object of class list of length 3.

See Also

Other enum helpers: AestheticFields, AestheticProperties, AestheticSelectionKeys, Alignments, AtomPlots, ColorMaps, ColorPalettes, DataMappings, DefaultDataMappingValues, Directions, ExportFormats, ExportUnits, FontFaces, HorizontalJustification, LegendPositions, LegendTypes, Linetypes, MoleculePlots, PlotAnnotationTextSize, PlotConfigurations, Scaling, Shapes, TagPositions, TickLabelTransforms, tlfSettingsNames, tlfStatFunctions

XAxisConfiguration

Description

R6 class defining the configuration of X-axis

Super class

tlf::AxisConfiguration -> XAxisConfiguration

Methods

Public methods

Inherited methods

Method updatePlot()

Update axis configuration on a ggplot object

Usage
XAxisConfiguration$updatePlot(
  plotObject,
  yAxisLimits = NULL,
  ylim = lifecycle::deprecated()
)
Arguments
plotObject

ggplot object

yAxisLimits

values of axisLimits for y axis to prevent coord_cartesian to overwrite its properties

ylim

[Deprecated]. Replaced by yAxisLimits argument.

Returns

A ggplot object with updated axis properties

Method clone()

The objects of this class are cloneable with this method.

Usage
XAxisConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, YAxisConfiguration

XYDataMapping

Description

R6 class for mapping x and y variable to data

Public fields

x

Name of x variable to map

y

Name of y variable to map

data

data.frame used for mapping

Methods

Public methods

Method new()

Create a new XYDataMapping object

Usage
XYDataMapping$new(x, y = NULL)
Arguments
x

Name of x variable to map

y

Name of y variable to map

Returns

A new XYDataMapping object

Method checkMapData()

Check that data variables include map variables

Usage
XYDataMapping$checkMapData(data, metaData = NULL)
Arguments
data

data.frame to check

metaData

list containing information on data

Returns

A data.frame with map and defaultAes variables. Dummy variable defaultAes is necessary to allow further modification of plots.

Method clone()

The objects of this class are cloneable with this method.

Usage
XYDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYGDataMapping

XYGDataMapping

Description

R6 class for mapping x, y and GroupMapping variables to data

Super class

tlf::XYDataMapping -> XYGDataMapping

Public fields

groupMapping

R6 class GroupMapping object

Methods

Public methods

Method new()

Create a new XYGDataMapping object

Usage
XYGDataMapping$new(
  x = NULL,
  y = NULL,
  groupMapping = NULL,
  color = NULL,
  fill = NULL,
  linetype = NULL,
  shape = NULL,
  size = NULL,
  group = NULL,
  data = NULL
)
Arguments
x

Name of x variable to map

y

Name of y variable to map

groupMapping

R6 class GroupMapping object

color

R6 class Grouping object or its input

fill

R6 class Grouping object or its input

linetype

R6 class Grouping object or its input

shape

R6 class Grouping object or its input

size

R6 class Grouping object or its input

group

R6 class Grouping object or its input

data

data.frame to map used by .smartMapping

Returns

A new XYGDataMapping object

Method checkMapData()

Check that data variables include map variables

Usage
XYGDataMapping$checkMapData(data, metaData = NULL)
Arguments
data

data.frame to check

metaData

list containing information on data

Returns

A data.frame with map and defaultAes variables. Dummy variable defaultAes is necessary to allow further modification of plots.

Method clone()

The objects of this class are cloneable with this method.

Usage
XYGDataMapping$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other DataMapping classes: BoxWhiskerDataMapping, CumulativeTimeProfileDataMapping, DDIRatioDataMapping, GroupMapping, Grouping, HistogramDataMapping, ObsVsPredDataMapping, ObservedDataMapping, PKRatioDataMapping, PieChartDataMapping, QQDataMapping, RangeDataMapping, ResVsPredDataMapping, ResVsTimeDataMapping, TimeProfileDataMapping, TornadoDataMapping, XYDataMapping

YAxisConfiguration

Description

R6 class defining the configuration of Y-axis

Super class

tlf::AxisConfiguration -> YAxisConfiguration

Public fields

position

character position of the Y-axis

Methods

Public methods

Inherited methods

Method updatePlot()

Update axis configuration on a ggplot object

Usage
YAxisConfiguration$updatePlot(
  plotObject,
  xAxisLimits = NULL,
  xlim = lifecycle::deprecated()
)
Arguments
plotObject

ggplot object

xAxisLimits

limits of x axis to prevent coord_cartesian to overwrite its properties

xlim

[Deprecated]. Replaced by xAxisLimits argument.

Returns

A ggplot object with updated axis properties

Method clone()

The objects of this class are cloneable with this method.

Usage
YAxisConfiguration$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other PlotConfiguration classes: AxisConfiguration, BackgroundConfiguration, BackgroundElement, BoxWhiskerPlotConfiguration, CumulativeTimeProfilePlotConfiguration, DDIRatioPlotConfiguration, ExportConfiguration, HistogramPlotConfiguration, LabelConfiguration, LegendConfiguration, LineElement, ObsVsPredPlotConfiguration, PKRatioPlotConfiguration, PieChartPlotConfiguration, PlotConfiguration, PlotGridConfiguration, QQPlotConfiguration, ResVsPredPlotConfiguration, ResVsTimePlotConfiguration, TimeProfilePlotConfiguration, TornadoPlotConfiguration, XAxisConfiguration