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374 enum listing molecules #380

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Sep 13, 2022
Merged

374 enum listing molecules #380

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7d88fa8
Fixes #375 enums listing all molecules, atoms and their configurations
pchelle Sep 9, 2022
ef51f9e
Fixes #379 Synchronize theme and molecule plots
pchelle Sep 9, 2022
b69e36f
Rename Atoms and Molecules to AtomPlots and MoleculePlots
pchelle Sep 13, 2022
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5 changes: 5 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -27,11 +27,13 @@ export("median+1.5IQR")
export("median+IQR")
export("median-1.5IQR")
export("median-IQR")
export(AestheticFields)
export(AestheticProperties)
export(AestheticSelectionKeys)
export(AggregationInput)
export(AggregationSummary)
export(Alignments)
export(AtomPlots)
export(AxisConfiguration)
export(BackgroundConfiguration)
export(BackgroundElement)
Expand All @@ -41,6 +43,7 @@ export(CaptionProperties)
export(ColorMaps)
export(DDIRatioDataMapping)
export(DDIRatioPlotConfiguration)
export(DataMappings)
export(ExportConfiguration)
export(ExportFormats)
export(ExportUnits)
Expand All @@ -58,13 +61,15 @@ export(LegendPositions)
export(LegendTypes)
export(LineElement)
export(Linetypes)
export(MoleculePlots)
export(ObsVsPredDataMapping)
export(ObsVsPredPlotConfiguration)
export(ObservedDataMapping)
export(PKRatioDataMapping)
export(PKRatioPlotConfiguration)
export(PlotAnnotationTextSize)
export(PlotConfiguration)
export(PlotConfigurations)
export(PlotGridConfiguration)
export(QQDataMapping)
export(QQPlotConfiguration)
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105 changes: 36 additions & 69 deletions R/themes.R
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Expand Up @@ -339,103 +339,70 @@ ThemeAestheticSelections <- R6::R6Class(
#' @field addLine theme properties for `PlotConfiguration` objects as used in function `addLine()`
#' @field addRibbon theme properties for `PlotConfiguration` objects as used in function `addRibbon()`
#' @field addErrorbar theme properties for `PlotConfiguration` objects as used in function `addErrorbar()`
#' @field plotPKRatio theme properties for `PlotConfiguration` objects as used in function `plotPKRatio()`
#' @field plotDDIRatio theme properties for `PlotConfiguration` objects as used in function `plotDDIRatio()`
#' @field plotTimeProfile theme properties for `PlotConfiguration` objects as used in function `plotTimeProfile()`
#' @field plotObsVsPred theme properties for `PlotConfiguration` objects as used in function `plotObsVsPred()`
#' @field plotBoxWhisker theme properties for `PlotConfiguration` objects as used in function `plotBoxWhisker()`
#' @field plotTornado theme properties for `PlotConfiguration` objects as used in function `plotTornado()`
#' @field plotHistogram theme properties for `PlotConfiguration` objects as used in function `plotHistogram()`
#' @export
ThemePlotConfigurations <- R6::R6Class(
"ThemePlotConfigurations",
# This allows the R6 class to accept new fields
lock_objects = FALSE,
Comment on lines +345 to +346
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interesting feature :)

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Totally.
I think it could be beneficial to apply it to other R6 objects such as workflows or task settings in RE (that would make user defined tasks or settings more flexible)

public = list(
addScatter = NULL,
addLine = NULL,
addRibbon = NULL,
addErrorbar = NULL,
plotPKRatio = NULL,
plotDDIRatio = NULL,
plotTimeProfile = NULL,
plotObsVsPred = NULL,
plotBoxWhisker = NULL,
plotTornado = NULL,
plotHistogram = NULL,

#' @description Create a new `ThemePlotConfigurations` object
#' @param addScatter theme properties for `PlotConfiguration` objects as used in function `addScatter()`
#' @param addLine theme properties for `PlotConfiguration` objects as used in function `addLine()`
#' @param addRibbon theme properties for `PlotConfiguration` objects as used in function `addRibbon()`
#' @param addErrorbar theme properties for `PlotConfiguration` objects as used in function `addErrorbar()`
#' @param plotPKRatio theme properties for `PlotConfiguration` objects as used in function `plotPKRatio()`
#' @param plotDDIRatio theme properties for `PlotConfiguration` objects as used in function `plotDDIRatio()`
#' @param plotTimeProfile theme properties for `PlotConfiguration` objects as used in function `plotTimeProfile()`
#' @param plotObsVsPred theme properties for `PlotConfiguration` objects as used in function `plotObsVsPred()`
#' @param plotBoxWhisker theme properties for `PlotConfiguration` objects as used in function `plotBoxWhisker()`
#' @param plotTornado theme properties for `PlotConfiguration` objects as used in function `plotTornado()`
#' @param plotHistogram theme properties for `PlotConfiguration` objects as used in function `plotHistogram()`
#' @param ... theme properties for `PlotConfiguration` objects as used in molecule plots
#' @return A new `ThemePlotConfigurations` object
initialize = function(addScatter = NULL,
addLine = NULL,
addRibbon = NULL,
addErrorbar = NULL,
plotPKRatio = NULL,
plotDDIRatio = NULL,
plotTimeProfile = NULL,
plotObsVsPred = NULL,
plotBoxWhisker = NULL,
plotTornado = NULL,
plotHistogram = NULL) {
...) {
# Validate necessary input
atomPlotInputs <- c("addScatter", "addLine", "addRibbon", "addErrorbar")
moleculePlotInputs <- c("plotPKRatio", "plotDDIRatio", "plotTimeProfile", "plotObsVsPred", "plotBoxWhisker", "plotTornado", "plotHistogram")

atomPlotInputs <- as.character(setdiff(AtomPlots, "initializePlot"))
validateExpressions <- parse(text = paste0("validateIsOfType(", atomPlotInputs, ", 'ThemeAestheticSelections', nullAllowed = TRUE)"))
eval(validateExpressions)
validateExpressions <- parse(text = paste0("validateIsOfType(c(", moleculePlotInputs, "), 'ThemeAestheticSelections', nullAllowed = TRUE)"))
eval(validateExpressions)

# Default aesthetic for atom plots
# Default aesthetics for atom plots
self$addScatter <- addScatter %||% ThemeAestheticSelections$new(color = "next", fill = NA, shape = "next", linetype = "blank", size = "first", alpha = 1)
self$addLine <- addLine %||% ThemeAestheticSelections$new(color = "next", fill = NA, shape = "blank", linetype = "reset", size = "first", alpha = 1)
self$addRibbon <- addRibbon %||% ThemeAestheticSelections$new(color = "next", fill = "next", shape = "blank", linetype = "first", size = "same", alpha = 1)
self$addErrorbar <- addErrorbar %||% ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "blank", linetype = "first", size = "same", alpha = 1)

# Default aesthetic for molecule plots
self$plotPKRatio <- plotPKRatio %||% list(
lines = ThemeAestheticSelections$new(color = c("#000000", "#0078D7", "#D83B01"), linetype = c("longdash", "longdash", "longdash"), size = 0.5, alpha = 1),
points = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "reset", linetype = "blank", size = 3),
errorbars = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "blank", linetype = "solid", size = 1)
)
self$plotDDIRatio <- plotDDIRatio %||% list(
lines = ThemeAestheticSelections$new(color = c("#000000", "#0078D7", "#D83B01"), linetype = c("longdash", "longdash", "longdash"), size = 0.5, alpha = 1),
points = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "reset", linetype = "blank", size = 3),
errorbars = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "blank", linetype = "solid", size = 1)
)
self$plotTimeProfile <- plotTimeProfile %||% list(
lines = ThemeAestheticSelections$new(color = "reset", fill = "reset", shape = "blank", linetype = "reset", size = 1),
ribbons = ThemeAestheticSelections$new(color = "reset", fill = "reset", shape = "blank", linetype = "blank", size = 1, alpha = "first"),
points = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "reset", linetype = "blank", size = 3),
errorbars = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "blank", linetype = "solid", size = 1)
)
self$plotObsVsPred <- plotObsVsPred %||% list(
lines = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "blank", linetype = "reset", size = 1),
points = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "reset", linetype = "blank", size = 3),
errorbars = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "blank", linetype = "solid", size = 1)
)
self$plotBoxWhisker <- plotBoxWhisker %||% list(
ribbons = ThemeAestheticSelections$new(color = "#000000", fill = "next", linetype = "solid", size = 1, alpha = "first"),
points = ThemeAestheticSelections$new(color = "#000000", shape = "first", linetype = "blank", size = 1)
)
self$plotTornado <- plotTornado %||% list(
lines = ThemeAestheticSelections$new(color = "#000000", fill = NA, shape = "blank", linetype = "longdash", size = 1),
ribbons = ThemeAestheticSelections$new(color = "reset", fill = "reset", shape = "blank", linetype = "solid", size = 1, alpha = "first"),
points = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "reset", linetype = "blank", size = 3)
)
self$plotHistogram <- plotHistogram %||% list(
lines = ThemeAestheticSelections$new(color = "reset", fill = NA, shape = "blank", linetype = "reset", size = 1),
ribbons = ThemeAestheticSelections$new(color = "#000000", fill = "reset", shape = "blank", linetype = "solid", size = 0.5, alpha = "first")
)
# Aesthetics for molecule plots
# This allows also user defined molecule plots
userMoleculePlots <- list(...)
moleculePlotInputs <- union(names(userMoleculePlots), as.character(MoleculePlots))

for (molecule in moleculePlotInputs) {
# Empty list if not defined by user
userMoleculePlot <- list()
if (isIncluded(molecule, names(userMoleculePlots))) {
# Need to clone R6 classes to prevent linking between each aesthetic
# ie. changing one property will change them all
userMoleculePlot <- lapply(
AestheticFields,
FUN = function(fieldName) {
fieldProperties <- userMoleculePlots[[molecule]][[fieldName]]
if (isEmpty(fieldProperties)) {
return(NULL)
}
fieldProperties <- .asThemeAestheticSelections(fieldProperties)
return(fieldProperties$clone())
}
)
}
self[[molecule]] <- list(
points = userMoleculePlot$points %||% self$addScatter$clone(),
lines = userMoleculePlot$lines %||% self$addLine$clone(),
ribbons = userMoleculePlot$ribbons %||% self$addRibbon$clone(),
errorbars = userMoleculePlot$errorbars %||% self$addErrorbar$clone()
)
}
},

#' @description Translate object into a json list
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81 changes: 81 additions & 0 deletions R/utilities-enums.R
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@@ -1,3 +1,84 @@
#' @title .getTitlesFromFamilyTag
#' @description Get all title names from documented functions/R6 classes that have specific family tags.
#' The function aims at created automated and synchronized enums
#' @param familyTag Family tag used to document functions or R6 classes
#' @return character array of titles
#' @import ospsuite.utils
#' @keywords internal
.getTitlesFromFamilyTag <- function(familyTag) {
functionNames <- NULL
for (filePath in list.files("./R", full.names = TRUE)) {
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edited
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no idea how it works - but it works :)
I thought list.files("./R", ... would require that my current folder is the package root folder, but it seems to work in any folder.

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When building/documenting a package, the working directory is internally set to the package location during the procedure (I did some testing with devtools::check() and devtools::document()).

The function .getTitlesFromFamilyTag is only called during the build of the package to create the enums.
Thus, when the users check for e.g. Atoms, they do not call for .getTitlesFromFamilyTag but directly for the resulting list created during the package construction.

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ok, cool. Thanks for the explanation :)

fileContent <- readLines(filePath, warn = FALSE)
familyTagLines <- grep(pattern = paste0("#' @family ", familyTag), x = fileContent)
if (isEmpty(familyTagLines)) {
next
}
# Get closest title before tag
titleLines <- grep(pattern = "#' @title", x = fileContent)
functionNames <- c(
functionNames,
sapply(
familyTagLines,
# assumes that title tag is defined before family tag
FUN = function(familyTagLine) {
# Get line of closest title tag before family tag
titleLine <- titleLines[which.min(
familyTagLine - titleLines[titleLines < familyTagLine]
)]
functionName <- trimws(gsub(".*@title", "", fileContent[titleLine]))
return(functionName)
}
)
)
}
return(functionNames)
}

#' @title AestheticFields
#' @import ospsuite.utils
#' @export
#' @description
#' List of all available aesthetic fields that manage aesthetic properties
#' @family enum helpers
AestheticFields <- enum(c(
"lines",
"points",
"ribbons",
"errorbars"
))

#' @title AtomPlots
#' @import ospsuite.utils
#' @export
#' @description
#' List of all available atom plots
#' @family enum helpers
AtomPlots <- enum(c(.getTitlesFromFamilyTag("atom plots")))

#' @title MoleculePlots
#' @import ospsuite.utils
#' @export
#' @description
#' List of all available molecule plots
#' @family enum helpers
MoleculePlots <- enum(c(.getTitlesFromFamilyTag("molecule plots")))

#' @title PlotConfigurations
#' @import ospsuite.utils
#' @export
#' @description
#' List of all available molecule plots
#' @family enum helpers
PlotConfigurations <- enum(c(.getTitlesFromFamilyTag("PlotConfiguration classes")))

#' @title DataMappings
#' @import ospsuite.utils
#' @export
#' @description
#' List of all available molecule plots
#' @family enum helpers
DataMappings <- enum(c(.getTitlesFromFamilyTag("DataMapping classes")))

#' @title Alignments
#' @import ospsuite.utils
#' @export
Expand Down
2 changes: 1 addition & 1 deletion R/utils.R
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@@ -1,5 +1,5 @@
# Because collate put tlf-env and themes before utils,
# The curretnTheme is defined here: after the definition of %||%
# The currentTheme is defined here: after the definition of %||%
tlfEnv$currentTheme <- Theme$new()

# Default theme is minimal when package is loaded
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39 changes: 39 additions & 0 deletions man/AestheticFields.Rd
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5 changes: 5 additions & 0 deletions man/AestheticProperties.Rd
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5 changes: 5 additions & 0 deletions man/Alignments.Rd
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39 changes: 39 additions & 0 deletions man/AtomPlots.Rd
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