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f_core_plot.R
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f_core_plot.R
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## |
## | *Plot functions*
## |
## | This file is part of the R package rpact:
## | Confirmatory Adaptive Clinical Trial Design and Analysis
## |
## | Author: Gernot Wassmer, PhD, and Friedrich Pahlke, PhD
## | Licensed under "GNU Lesser General Public License" version 3
## | License text can be found here: https://www.r-project.org/Licenses/LGPL-3
## |
## | RPACT company website: https://www.rpact.com
## | rpact package website: https://www.rpact.org
## |
## | Contact us for information about our services: info@rpact.com
## |
## | File version: $Revision: 7750 $
## | Last changed: $Date: 2024-03-26 15:44:44 +0100 (Di, 26 Mrz 2024) $
## | Last changed by: $Author: pahlke $
## |
#' @include f_core_utilities.R
NULL
.addNumberToPlotCaption <- function(caption, type, numberInCaptionEnabled = FALSE) {
if (!numberInCaptionEnabled) {
return(caption)
}
return(paste0(caption, " [", type, "]"))
}
.getPlotCaption <- function(obj, type, numberInCaptionEnabled = FALSE, ..., stopIfNotFound = FALSE) {
if (is.null(obj) || length(type) == 0) {
return(NA_character_)
}
.assertIsSingleInteger(type, "type", validateType = FALSE)
if (inherits(obj, "TrialDesignPlan")) {
if (type == 1) {
if (.isTrialDesignPlanSurvival(obj)) {
return(.addNumberToPlotCaption("Boundaries Z Scale", type, numberInCaptionEnabled))
} else {
return(.addNumberToPlotCaption("Boundaries", type, numberInCaptionEnabled))
}
} else if (type == 2) {
return(.addNumberToPlotCaption("Boundaries Effect Scale", type, numberInCaptionEnabled))
} else if (type == 3) {
return(.addNumberToPlotCaption("Boundaries p Values Scale", type, numberInCaptionEnabled))
} else if (type == 4) {
return(.addNumberToPlotCaption("Error Spending", type, numberInCaptionEnabled))
}
}
if (.isMultiArmSimulationResults(obj)) {
if (type == 1) { # Multi-arm, Overall Success
return(.addNumberToPlotCaption("Overall Success", type, numberInCaptionEnabled))
} else if (type == 2) { # Multi-arm, Success per Stage
return(.addNumberToPlotCaption("Success per Stage", type, numberInCaptionEnabled))
} else if (type == 3) { # Multi-arm, Selected Arms per Stage
return(.addNumberToPlotCaption("Selected Arms per Stage", type, numberInCaptionEnabled))
} else if (type == 4) { # Multi-arm, Rejected Arms per Stage
return(.addNumberToPlotCaption(ifelse(obj$.design$kMax > 1,
"Rejected Arms per Stage", "Rejected Arms"
), type, numberInCaptionEnabled))
}
} else if (.isEnrichmentSimulationResults(obj)) {
if (type == 1) { # Enrichment, Overall Success
return(.addNumberToPlotCaption("Overall Success", type, numberInCaptionEnabled))
} else if (type == 2) { # Enrichment, Success per Stage
return(.addNumberToPlotCaption("Success per Stage", type, numberInCaptionEnabled))
} else if (type == 3) { # Enrichment, Selected Populations per Stage
return(.addNumberToPlotCaption("Selected Populations per Stage", type, numberInCaptionEnabled))
} else if (type == 4) { # Enrichment, Rejected Populations per Stage
return(.addNumberToPlotCaption(ifelse(obj$.design$kMax > 1,
"Rejected Populations per Stage", "Rejected Populations"
), type, numberInCaptionEnabled))
}
} else if (inherits(obj, "SimulationResults") && type == 4) {
return(.addNumberToPlotCaption("Reject per Stage", type, numberInCaptionEnabled))
}
if (inherits(obj, "TrialDesignPlan") || inherits(obj, "SimulationResults")) {
if (type == 5) {
if (obj$.isSampleSizeObject()) {
return(.addNumberToPlotCaption("Sample Size", type, numberInCaptionEnabled))
} else {
return(.addNumberToPlotCaption(
"Overall Power and Early Stopping",
type, numberInCaptionEnabled
))
}
} else if (type == 6) {
return(.addNumberToPlotCaption(ifelse(.isTrialDesignPlanSurvival(obj) ||
inherits(obj, "SimulationResultsSurvival"),
"Number of Events", "Sample Size"
), type, numberInCaptionEnabled))
} else if (type == 7) {
return(.addNumberToPlotCaption("Overall Power", type, numberInCaptionEnabled))
} else if (type == 8) {
return(.addNumberToPlotCaption("Overall Early Stopping", type, numberInCaptionEnabled))
} else if (type == 9) {
if (.isTrialDesignPlanSurvival(obj) ||
inherits(obj, "SimulationResultsSurvival")) {
return(.addNumberToPlotCaption("Expected Number of Events", type, numberInCaptionEnabled))
} else {
return(.addNumberToPlotCaption("Expected Sample Size", type, numberInCaptionEnabled))
}
} else if (type == 10) {
return(.addNumberToPlotCaption("Study Duration", type, numberInCaptionEnabled))
} else if (type == 11) {
return(.addNumberToPlotCaption("Expected Number of Subjects", type, numberInCaptionEnabled))
} else if (type == 12) {
return(.addNumberToPlotCaption("Analysis Time", type, numberInCaptionEnabled))
} else if (type == 13) {
return(.addNumberToPlotCaption("Cumulative Distribution Function", type, numberInCaptionEnabled))
} else if (type == 14) {
return(.addNumberToPlotCaption("Survival Function", type, numberInCaptionEnabled))
}
} else if (inherits(obj, "TrialDesign") || inherits(obj, "TrialDesignSet")) {
if (type == 1) {
return(.addNumberToPlotCaption("Boundaries", type, numberInCaptionEnabled))
} else if (type == 3) {
return(.addNumberToPlotCaption("Stage Levels", type, numberInCaptionEnabled))
} else if (type == 4) {
return(.addNumberToPlotCaption("Error Spending", type, numberInCaptionEnabled))
} else if (type == 5) {
return(.addNumberToPlotCaption("Power and Early Stopping", type, numberInCaptionEnabled))
} else if (type == 6) {
return(.addNumberToPlotCaption(
"Average Sample Size and Power / Early Stop",
type, numberInCaptionEnabled
))
} else if (type == 7) {
return(.addNumberToPlotCaption("Power", type, numberInCaptionEnabled))
} else if (type == 8) {
return(.addNumberToPlotCaption("Early Stopping", type, numberInCaptionEnabled))
} else if (type == 9) {
return(.addNumberToPlotCaption("Average Sample Size", type, numberInCaptionEnabled))
}
} else if (inherits(obj, "AnalysisResults")) {
if (type == 1) {
return(.addNumberToPlotCaption(C_PLOT_MAIN_CONDITIONAL_POWER_WITH_LIKELIHOOD, type, numberInCaptionEnabled))
} else if (type == 2) {
return(.addNumberToPlotCaption("Repeated Confidence Intervals", type, numberInCaptionEnabled))
}
} else if (inherits(obj, "StageResults")) {
return(.addNumberToPlotCaption(C_PLOT_MAIN_CONDITIONAL_POWER_WITH_LIKELIHOOD, type, numberInCaptionEnabled))
}
if (stopIfNotFound) {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, "could not find plot caption for ", .getClassName(obj), " and type ", type)
}
return(NA_character_)
}
.getPlotTypeNumber <- function(type, x) {
if (missing(type) || is.null(type) || length(type) == 0 || all(is.na(type))) {
stop(C_EXCEPTION_TYPE_MISSING_ARGUMENT, "'type' must be defined")
}
if (!is.numeric(type) && !is.character(type)) {
stop(
C_EXCEPTION_TYPE_MISSING_ARGUMENT,
"'type' must be an integer or character value or vector (is ", .getClassName(type), ")"
)
}
if (is.numeric(type)) {
.assertIsIntegerVector(type, "type", naAllowed = FALSE, validateType = FALSE)
}
if (is.character(type)) {
if (length(type) == 1 && type == "all") {
availablePlotTypes <- getAvailablePlotTypes(x)
if (is.null(availablePlotTypes)) {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, "function 'getAvailablePlotTypes' not implemented for ", .getClassName(x))
}
return(availablePlotTypes)
}
types <- getAvailablePlotTypes(x, output = "numeric")
captions <- tolower(getAvailablePlotTypes(x, output = "caption"))
typeNumbers <- c()
for (typeStr in type) {
if (grepl("^\\d+$", typeStr)) {
typeNumbers <- c(typeNumbers, as.integer(typeStr))
} else {
index <- pmatch(tolower(typeStr), captions)
if (!is.na(index)) {
typeNumbers <- c(typeNumbers, types[index])
} else {
index <- grep(tolower(typeStr), captions)
if (length(index) > 0) {
for (i in index) {
typeNumbers <- c(typeNumbers, types[i])
}
}
}
}
}
if (length(typeNumbers) > 0) {
return(unique(typeNumbers))
}
message("Available plot types: ", .arrayToString(tolower(
getAvailablePlotTypes(x, output = "caption")
), encapsulate = TRUE))
stop(C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT, "'type' (", .arrayToString(type), ") could not be identified")
}
return(type)
}
.createPlotResultObject <- function(plotList, grid = 1) {
.assertIsSingleInteger(grid, "grid", naAllowed = FALSE, validateType = FALSE)
.assertIsInClosedInterval(grid, "grid", lower = 0, upper = 100)
if (length(plotList) == 0) {
if (grid == 0) {
return(invisible(plotList))
}
return(plotList)
}
if (!inherits(plotList[[1]], "ggplot") || grid == 1) {
return(plotList)
}
if (grid == 0) {
for (p in plotList) {
suppressMessages(print(p))
}
return(invisible(plotList))
}
if (length(plotList) > grid) {
return(plotList)
}
plotCmd <- NA_character_
if (grid > 1) {
if ("ggpubr" %in% rownames(installed.packages())) {
if (length(plotList) < 8 && length(plotList) %% 2 == 1) {
plotCmd <- paste0(
"ggpubr::ggarrange(plotList[[1]], ",
"ggpubr::ggarrange(plotlist = plotList[2:", length(plotList), "]), ncol = 1)"
)
} else if (length(plotList) == 2) {
plotCmd <- paste0("ggpubr::ggarrange(plotlist = plotList, ncol = 1)")
} else {
plotCmd <- paste0("ggpubr::ggarrange(plotlist = plotList)")
}
} else if ("gridExtra" %in% rownames(installed.packages())) {
ncol <- ifelse(length(plotList) == 2, 1, 2)
plotCmd <- paste0("gridExtra::grid.arrange(grobs = plotList, ncol = ", ncol, ")")
} else if ("cowplot" %in% rownames(installed.packages())) {
plotCmd <- "cowplot::plot_grid(plotlist = plotList)"
} else {
message(
"Unable to create grid plot because neither 'ggpubr', 'gridExtra', nor 'cowplot' are installed. ",
"Install one of these packages to enable grid plots"
)
}
}
if (!is.na(plotCmd)) {
tryCatch(
{
return(eval(parse(text = plotCmd)))
},
error = function(e) {
warning("Failed to create grid plot using command '", plotCmd, "': ", e$message)
}
)
}
return(plotList)
}
.printPlotShowSourceSeparator <- function(showSource, typeNumber, typeNumbers) {
if (is.logical(showSource) && !showSource) {
return(invisible())
}
if (length(typeNumbers) == 1) {
return(invisible())
}
if (typeNumber == typeNumbers[length(typeNumbers)]) {
return(invisible())
}
cat("--\n")
}
#' @rdname getAvailablePlotTypes
#' @export
plotTypes <- function(obj, output = c("numeric", "caption", "numcap", "capnum"),
numberInCaptionEnabled = FALSE) {
return(getAvailablePlotTypes(
obj = obj, output = output,
numberInCaptionEnabled = numberInCaptionEnabled
))
}
.isValidVariedParameterVectorForPlotting <- function(resultObject, plotType) {
if (plotType > 12) {
return(TRUE)
}
for (param in c("alternative", "pi1", "hazardRatio", "muMaxVector", "piMaxVector", "omegaMaxVector")) {
if (!is.null(resultObject[[param]]) &&
resultObject$.getParameterType(param) != C_PARAM_NOT_APPLICABLE &&
(any(is.na(resultObject[[param]])) ||
length(resultObject[[param]]) <= 1)) {
return(FALSE)
}
}
if (!is.null(resultObject[["hazardRatio"]]) && !is.null(resultObject[["overallReject"]]) &&
resultObject$.getParameterType("hazardRatio") != C_PARAM_NOT_APPLICABLE &&
resultObject$.getParameterType("overallReject") != C_PARAM_NOT_APPLICABLE &&
length(resultObject$hazardRatio) > 0 &&
length(resultObject$hazardRatio) != length(resultObject$overallReject)) {
return(FALSE)
}
return(TRUE)
}
.removeInvalidPlotTypes <- function(resultObject, plotTypes, plotTypesToCheck) {
if (is.null(plotTypes) || length(plotTypes) == 0) {
return(integer(0))
}
validPlotTypes <- integer(0)
for (plotType in plotTypes) {
if (!(plotType %in% plotTypesToCheck)) {
validPlotTypes <- c(validPlotTypes, plotType)
} else if (.isValidVariedParameterVectorForPlotting(resultObject, plotType)) {
validPlotTypes <- c(validPlotTypes, plotType)
}
}
return(validPlotTypes)
}
#'
#' @title
#' Get Available Plot Types
#'
#' @description
#' Function to identify the available plot types of an object.
#'
#' @param obj The object for which the plot types shall be identified, e.g. produced by
#' \code{\link[=getDesignGroupSequential]{getDesignGroupSequential()}} or \code{\link[=getSampleSizeMeans]{getSampleSizeMeans()}}.
#' @param output The output type. Can be one of \code{c("numeric", "caption", "numcap", "capnum")}.
#' @param numberInCaptionEnabled If \code{TRUE}, the number will be added to the
#' caption, default is \code{FALSE}.
#'
#' @details
#' \code{plotTypes} and \code{getAvailablePlotTypes()} are equivalent, i.e.,
#' \code{plotTypes} is a short form of \code{getAvailablePlotTypes()}.
#'
#' \code{output}:
#' \enumerate{
#' \item \code{numeric}: numeric output
#' \item \code{caption}: caption as character output
#' \item \code{numcap}: list with number and caption
#' \item \code{capnum}: list with caption and number
#' }
#'
#' @return Returns a list if \code{option} is either \code{capnum} or \code{numcap}
#' or returns a vector that is of character type for \code{option=caption} or
#' of numeric type for \code{option=numeric}.
#'
#' @examples
#' design <- getDesignInverseNormal(kMax = 2)
#' getAvailablePlotTypes(design, "numeric")
#' plotTypes(design, "caption")
#' getAvailablePlotTypes(design, "numcap")
#' plotTypes(design, "capnum")
#'
#' @export
#'
getAvailablePlotTypes <- function(obj, output = c("numeric", "caption", "numcap", "capnum"),
numberInCaptionEnabled = FALSE) {
output <- match.arg(output)
if (is.null(obj)) {
if (output == "numeric") {
return(NA_real_)
}
if (output == "caption") {
return(NA_character_)
}
return(list())
}
types <- integer(0)
if (inherits(obj, "TrialDesignPlan")) {
if (obj$.design$kMax > 1) {
types <- c(types, 1)
if (!.isTrialDesignPlanCountData(obj)) {
types <- c(types, 2)
}
types <- c(types, 3:4)
}
if (obj$.isSampleSizeObject()) {
if (!.isTrialDesignPlanCountData(obj) || length(obj[["theta"]]) > 1) {
types <- c(types, 5)
}
if (.isTrialDesignPlanSurvival(obj)) {
types <- c(types, 13, 14)
}
} else {
if (obj$.design$kMax > 1) {
types <- c(types, 5, 6)
}
types <- c(types, 7)
if (obj$.design$kMax > 1) {
types <- c(types, 8)
if (!.isTrialDesignPlanCountData(obj) ||
obj$.getParameterType("expectedNumberOfSubjectsH1") == C_PARAM_GENERATED) {
types <- c(types, 9)
}
}
if (.isTrialDesignPlanSurvival(obj)) {
types <- c(types, 10:14)
}
}
types <- .removeInvalidPlotTypes(obj, types, c(5:14))
} else if (inherits(obj, "SimulationResults")) {
if (grepl("Enrichment", .getClassName(obj)) && !.getSimulationEnrichmentEffectData(
obj,
validatePlotCapability = FALSE
)$valid) {
if (output == "numeric") {
return(NA_real_)
}
if (output == "caption") {
return(NA_character_)
}
return(list())
}
if (grepl("MultiArm|Enrichment", .getClassName(obj))) {
types <- c(types, 1)
if (obj$.design$kMax > 1) {
types <- c(types, 2:3)
}
}
types <- c(types, 4)
if (!grepl("MultiArm", .getClassName(obj)) || obj$.design$kMax > 1) {
types <- c(types, 5:6)
}
types <- c(types, 7)
if (obj$.design$kMax > 1) {
types <- c(types, 8)
}
if (!grepl("MultiArm", .getClassName(obj)) || obj$.design$kMax > 1) {
types <- c(types, 9)
}
if (inherits(obj, "SimulationResultsSurvival")) {
types <- c(types, 10:14)
}
plotTypesToCheck <- c(4:14)
if (grepl("MultiArm", .getClassName(obj))) {
plotTypesToCheck <- c(1:14)
}
types <- .removeInvalidPlotTypes(obj, types, plotTypesToCheck)
} else if (inherits(obj, "TrialDesign") || inherits(obj, "TrialDesignSet")) {
design <- obj
if (inherits(obj, "TrialDesignSet")) {
design <- obj$getDesignMaster()
}
if (design$kMax > 1) {
types <- c(types, 1, 3)
}
if (inherits(design, "TrialDesignFisher")) {
types <- c(types, 4)
} else {
types <- c(types, 4:9)
}
} else if (inherits(obj, "AnalysisResults")) {
types <- integer(0)
if (.isConditionalPowerEnabled(obj$nPlanned)) {
types <- c(1)
}
types <- c(types, 2)
} else if (inherits(obj, "StageResults")) {
types <- c(1)
}
if (output == "numeric") {
return(types)
}
if (output == "caption") {
captions <- character()
for (type in types) {
captions <- c(captions, .getPlotCaption(obj,
type = type,
numberInCaptionEnabled = numberInCaptionEnabled
))
}
return(captions)
}
if (output == "numcap") {
numcap <- list()
for (type in types) {
numcap[[as.character(type)]] <- .getPlotCaption(obj,
type = type,
numberInCaptionEnabled = numberInCaptionEnabled
)
}
return(numcap)
}
capnum <- list()
for (type in types) {
capnum[[.getPlotCaption(obj,
type = type,
numberInCaptionEnabled = numberInCaptionEnabled
)]] <- type
}
return(capnum)
}
.getVariedParameterHint <- function(variedParameter, variedParameterName) {
if (length(variedParameter) != 2) {
return("")
}
return(paste0(
"Note: interim values between ", round(variedParameter[1], 4), " and ",
round(variedParameter[2], 4), " were calculated to get smoother lines; use, e.g., '",
variedParameterName, " = ",
.getVariedParameterVectorSeqCommand(variedParameter), "' to get all interim values"
))
}
.getRexepSaveCharacter <- function(x) {
x <- gsub("\\$", "\\\\$", x)
x <- gsub("\\.", "\\\\.", x)
return(x)
}
.createValidParameterName <- function(objectName, parameterName) {
if (grepl(paste0(.getRexepSaveCharacter(objectName), "\\$"), parameterName) &&
!grepl("^\\.design", parameterName)) {
return(parameterName)
}
if (is.null(objectName) || length(objectName) == 0 || is.na(objectName)) {
return(parameterName)
}
if (grepl("^-?\\.?get[A-Z]{1}", parameterName)) {
return(parameterName)
}
if (grepl("^rpact::", parameterName)) {
return(parameterName)
}
return(paste0(objectName, "$", parameterName))
}
.showPlotSourceInformation <- function(objectName, ...,
xParameterName, yParameterNames,
hint = NA_character_, nMax = NA_integer_, type = NA_integer_,
showSource = FALSE, xValues = NA_real_,
lineType = TRUE) {
if (is.character(showSource)) {
if (length(showSource) != 1 || trimws(showSource) == "") {
return(invisible(NULL))
}
if (!(showSource %in% C_PLOT_SHOW_SOURCE_ARGUMENTS)) {
warning("'showSource' (", showSource, ") is not allowed and will be ignored", call. = FALSE)
return(invisible())
}
} else if (!isTRUE(showSource)) {
return(invisible(NULL))
}
.assertIsSingleCharacter(xParameterName, "xParameterName")
if (length(yParameterNames) == 0 || !all(is.character(yParameterNames)) || all(is.na(yParameterNames))) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT, "'yParameterNames' (", .arrayToString(yParameterNames),
") must be a valid character vector"
)
}
.assertIsSingleCharacter(hint, "hint", naAllowed = TRUE)
.assertIsSingleNumber(nMax, "nMax", naAllowed = TRUE)
.assertIsNumericVector(xValues, "xValues", naAllowed = TRUE)
cat("Source data of the plot", ifelse(!is.na(type), paste0(
" (type ",
type, ")"
), ""), ":\n", sep = "")
xAxisCmd <- .reconstructSequenceCommand(xValues)
if (is.na(xAxisCmd)) {
if (!grepl("(\\$)|(^c\\()", xParameterName) || grepl("^\\.design", xParameterName)) {
if (length(objectName) == 0 || is.na(objectName)) {
objectName <- "x"
}
xAxisCmd <- paste0(objectName, "$", xParameterName)
} else {
xAxisCmd <- xParameterName
}
}
if (!is.na(nMax) && length(yParameterNames) < 3 &&
xParameterName == "informationRates") {
xAxisCmd <- paste0(xAxisCmd, " * ", round(nMax, 1))
}
cat(" x-axis: ", xAxisCmd, "\n", sep = "")
if (all(c("futilityBounds", "criticalValues") %in% yParameterNames)) {
yParameterNames[1] <- paste0(
"c(", objectName, "$futilityBounds, ",
objectName, "$criticalValues[length(", objectName, "$criticalValues)])"
)
} else if (identical(yParameterNames, c("futilityBoundsEffectScale", "criticalValuesEffectScale"))) {
yParameterNames[1] <- paste0(
"c(", objectName, "$futilityBoundsEffectScale, ",
objectName, "$criticalValuesEffectScale[length(", objectName, "$criticalValuesEffectScale)])"
)
}
yAxisCmds <- c()
if (length(yParameterNames) == 1) {
yAxisCmds <- .createValidParameterName(objectName, yParameterNames)
} else {
for (yParameterName in yParameterNames) {
yAxisCmds <- c(yAxisCmds, .createValidParameterName(objectName, yParameterName))
}
}
if (length(yAxisCmds) == 1) {
cat(" y-axis: ", yAxisCmds, "\n", sep = "")
} else {
cat(" y-axes:\n")
for (i in 1:length(yAxisCmds)) {
cat(" y", i, ": ", yAxisCmds[i], "\n", sep = "")
}
}
if (!is.na(hint) && is.character(hint) && nchar(hint) > 0) {
cat(hint, "\n", sep = "")
}
# add simple plot command examples
cat("Simple plot command example", ifelse(length(yAxisCmds) == 1, "", "s"), ":\n", sep = "")
plotCmds <- c()
for (yAxisCmd in yAxisCmds) {
plotCmd <- paste0("plot(", xAxisCmd, ", ", yAxisCmd)
if (lineType) {
plotCmd <- paste0(plotCmd, ", type = \"l\"")
}
plotCmd <- paste0(plotCmd, ")")
plotCmds <- c(plotCmds, plotCmd)
cat(" ", plotCmd, "\n", sep = "")
}
if (showSource == "commands") {
return(invisible(plotCmds))
} else if (showSource == "axes") {
return(invisible(list(x = xAxisCmd, y = yAxisCmds)))
} else if (showSource == "test") {
success <- TRUE
for (plotCmd in plotCmds) {
if (!.testPlotCommand(plotCmd)) {
success <- FALSE
}
}
if (success) {
cat("All plot commands are valid\n")
} else {
cat("One ore more plot commands are invalid\n")
}
return(invisible(plotCmds))
} else if (showSource == "validate") {
for (plotCmd in plotCmds) {
.testPlotCommand(plotCmd, silent = FALSE)
}
return(invisible(plotCmds))
}
return(invisible(NULL))
}
.testPlotCommand <- function(plotCmd, silent = TRUE) {
tryCatch(
{
eval(parse(text = plotCmd))
return(invisible(TRUE))
},
error = function(e) {
msg <- paste0(
"failed to evaluate plot command \"", plotCmd, "\" ",
"('", as.character(e$call), "'): ", e$message
)
if (!silent) {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, msg[1])
}
cat(.firstCharacterToUpperCase(msg), "\n")
}
)
return(invisible(FALSE))
}
.getParameterSetAsDataFrame <- function(...,
parameterSet,
designMaster,
addPowerAndAverageSampleNumber = FALSE,
theta = seq(-1, 1, 0.02),
nMax = NA_integer_,
mandatoryParameterNames = character(),
yParameterNames = character()) {
if (.isTrialDesignSet(parameterSet) && parameterSet$getSize() > 1 &&
(is.null(parameterSet$variedParameters) || length(parameterSet$variedParameters) == 0)) {
stop(
C_EXCEPTION_TYPE_RUNTIME_ISSUE, "'variedParameters' must be not empty; ",
"use 'DesignSet$addVariedParameters(character)' to add one or more varied parameters"
)
}
if (inherits(parameterSet, "TrialDesignSet")) {
suppressWarnings(data <- as.data.frame(
parameterSet,
niceColumnNamesEnabled = FALSE,
includeAllParameters = TRUE,
addPowerAndAverageSampleNumber = addPowerAndAverageSampleNumber,
theta = theta,
nMax = nMax
))
} else {
parameterNames <- parameterSet$.getVisibleFieldNamesOrdered()
suppressWarnings(data <- .getAsDataFrame(
parameterSet = parameterSet,
parameterNames = parameterNames,
niceColumnNamesEnabled = FALSE,
includeAllParameters = FALSE,
mandatoryParameterNames = mandatoryParameterNames
))
}
if (!.isTrialDesignSet(parameterSet)) {
variedParameters <- logical(0)
if ("stages" %in% colnames(data)) {
if ((!.isTrialDesignPlan(parameterSet) && !("overallReject" %in% yParameterNames)) ||
any(grepl("rejectPerStage|numberOfSubjects", yParameterNames))) {
variedParameters <- "stages"
names(variedParameters) <- "Stage"
}
}
return(list(data = data, variedParameters = variedParameters))
}
if (parameterSet$getSize() <= 1) {
return(list(data = data, variedParameters = parameterSet$variedParameters))
}
variedParameters <- parameterSet$variedParameters
if (nrow(data) > 1) {
for (variedParameter in variedParameters) {
column <- data[[variedParameter]]
if (length(column) <= 1) {
stop(
C_EXCEPTION_TYPE_RUNTIME_ISSUE,
"varied parameter '", variedParameter, "' has length ", length(column)
)
}
valueBefore <- column[1]
for (i in 2:length(column)) {
if (is.na(column[i])) {
column[i] <- valueBefore
} else {
valueBefore <- column[i]
}
}
data[[variedParameter]] <- column
}
}
variedParameterNames <- c()
for (variedParameter in variedParameters) {
variedParameterNames <- c(
variedParameterNames,
.getParameterCaption(variedParameter, designMaster, tableOutputEnabled = TRUE)
)
}
names(variedParameters) <- variedParameterNames
return(list(data = data, variedParameters = variedParameters))
}
.getCategories <- function(data, yParameterName, parameterSet) {
axisLabel <- .getAxisLabel(yParameterName, parameterSet)
if (is.null(data$categories) || sum(is.na(data$categories)) > 0) {
return(rep(axisLabel, nrow(data)))
}
return(paste(data$categories, axisLabel, sep = ", "))
}
.getAxisLabel <- function(parameterName, parameterSet) {
axisLabel <- .getParameterCaption(parameterName, parameterSet, tableOutputEnabled = TRUE)
if (is.null(axisLabel)) {
return(paste0("%", parameterName, "%"))
}
return(axisLabel)
}
.allGroupValuesEqual <- function(data, parameterName, groupName) {
groupedValues <- base::by(data[[parameterName]], data[[groupName]], paste, collapse = ",")
groupedValues <- groupedValues[!grepl("^NA(,NA)*$", groupedValues)]
if (length(groupedValues) <= 1) {
return(TRUE)
}
for (i in 1:(length(groupedValues) - 1)) {
for (j in (i + 1):length(groupedValues)) {
if (!is.na(groupedValues[i]) && !is.na(groupedValues[j]) &&
groupedValues[i] != groupedValues[j]) {
return(FALSE)
}
}
}
return(TRUE)
}
.plotParameterSet <- function(..., parameterSet, designMaster, xParameterName, yParameterNames,
mainTitle = NA_character_, xlab = NA_character_, ylab = NA_character_,
palette = "Set1", theta = seq(-1, 1, 0.02), nMax = NA_integer_,
plotPointsEnabled = NA, legendPosition = NA_integer_,
variedParameters = logical(0),
qnormAlphaLineEnabled = TRUE,
yAxisScalingEnabled = TRUE,
ratioEnabled = NA, plotSettings = NULL) {
simulationEnrichmentEnmabled <- grepl("SimulationResultsEnrichment", .getClassName(parameterSet))
if (.isParameterSet(parameterSet) || .isTrialDesignSet(parameterSet)) {
parameterNames <- c(xParameterName, yParameterNames)
parameterNames <- parameterNames[!(parameterNames %in% c(
"theta", "averageSampleNumber",
"overallEarlyStop", "calculatedPower"
))]
fieldNames <- c(
names(parameterSet), # alternatively use parameterSet$.getFieldNames()
names(designMaster)
)
if (simulationEnrichmentEnmabled) {
fieldNames <- c(fieldNames, gsub("s$", "", names(parameterSet$effectList)), "situation")
}
for (parameterName in parameterNames) {
if (!is.na(parameterName) && !(parameterName %in% fieldNames)) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'", .getClassName(parameterSet), "' and '", .getClassName(designMaster), "' ",
"do not contain a field with name '", parameterName, "'"
)
}
}
if (is.null(plotSettings) || !inherits(plotSettings, "PlotSettings")) {
plotSettings <- parameterSet$getPlotSettings()
}
} else {
if (is.null(plotSettings) || !inherits(plotSettings, "PlotSettings")) {
plotSettings <- PlotSettings$new()
}
}
if (.isTrialDesignSet(parameterSet)) {
parameterSet$assertHaveEqualSidedValues()
}
addPowerAndAverageSampleNumber <- xParameterName == "theta" &&
yParameterNames[1] %in% c(
"averageSampleNumber", "calculatedPower", "overallEarlyStop",
"overallReject", "overallFutility"
)
if (!addPowerAndAverageSampleNumber) {
addPowerAndAverageSampleNumber <- xParameterName %in% c("effect", "effectMatrix") &&
yParameterNames[1] %in% c(
"overallReject", "futilityStop",
"earlyStop", "expectedNumberOfSubjects", "expectedNumberOfEvents"
)
}
if (addPowerAndAverageSampleNumber && .isMultiArmSimulationResults(parameterSet)) {
addPowerAndAverageSampleNumber <- FALSE
}
if (.isParameterSet(parameterSet) || .isTrialDesignSet(parameterSet)) {
df <- .getParameterSetAsDataFrame(
parameterSet = parameterSet,
designMaster = designMaster,
addPowerAndAverageSampleNumber = addPowerAndAverageSampleNumber,
theta = theta,
nMax = nMax,
mandatoryParameterNames = c(xParameterName, yParameterNames),
yParameterNames = yParameterNames
)
data <- df$data
variedParameters <- df$variedParameters
variedParameters <- na.omit(variedParameters)
variedParameters <- variedParameters[variedParameters != "NA"]
if (length(variedParameters) == 1 && length(yParameterNames) == 1) {
if (.allGroupValuesEqual(data, parameterName = yParameterNames, groupName = variedParameters)) {
variedParameters <- logical(0)
}
}
} else if (is.data.frame(parameterSet)) {
data <- parameterSet
} else {
stop(
C_EXCEPTION_TYPE_RUNTIME_ISSUE,
"'parameterSet' (", .getClassName(parameterSet), ") must be a data.frame, a 'TrialDesignSet' ",
"or an object that inherits from 'ParameterSet'"
)
}
if (length(variedParameters) > 0) {
legendTitle <- .firstCharacterToUpperCase(paste(names(variedParameters), collapse = "\n"))
categoryParameterName <- variedParameters[1]
} else {
legendTitle <- NA_character_
categoryParameterName <- NA_character_
}
yParameterName1 <- yParameterNames[1]
yParameterName2 <- NULL
yParameterName3 <- NULL
if (length(yParameterNames) >= 2) {
yParameterName2 <- yParameterNames[2]
}
if (length(yParameterNames) >= 3) {
yParameterName3 <- yParameterNames[3]
}
mirrorModeEnabled <- any(grepl("Mirrored$", yParameterNames))
xAxisLabel <- .getAxisLabel(xParameterName, parameterSet)
yAxisLabel1 <- .getAxisLabel(yParameterName1, parameterSet)
yAxisLabel2 <- NULL
if (!is.null(yParameterName2) && !is.null(yParameterName3)) {
if (!is.na(yParameterName2)) {
pn2 <- .getAxisLabel(yParameterName2, parameterSet)
if (yParameterName2 == "overallEarlyStop") {
pn2 <- "Stopping Probability"
}
yAxisLabel2 <- paste(pn2, .getAxisLabel(yParameterName3, parameterSet), sep = " and ")
} else {
yAxisLabel2 <- .getAxisLabel(yParameterName3, parameterSet)
}
} else if (xParameterName == "effectMatrix" && !is.null(yParameterName2) && !is.na(yParameterName2) &&
yParameterName1 %in% c("expectedNumberOfEvents", "expectedNumberOfSubjects") &&
yParameterName2 == "rejectAtLeastOne") {
# special case: simulation results, plot type 6 (expected number of subjects and power)
yAxisLabel2 <- .getAxisLabel(yParameterName2, parameterSet)
yParameterName3 <- yParameterName2
yParameterName2 <- NA_character_
} else if (!is.null(yParameterName2) && !mirrorModeEnabled) {
yAxisLabel1 <- paste(yAxisLabel1, .getAxisLabel(yParameterName2, parameterSet), sep = " and ")
}
if (yParameterName1 %in% c("alphaSpent", "betaSpent")) {
yAxisLabel1 <- "Cumulative Error"
if (is.null(yParameterName2)) {
yAxisLabel1 <- paste0(yAxisLabel1, " (", .getAxisLabel(yParameterName1, parameterSet), ")")
}
}
yAxisLabel1 <- sub(paste0(.getParameterCaption("futilityBoundsDelayedInformation"), " and"),
"Lower and", yAxisLabel1,
fixed = TRUE
)
yAxisLabel1 <- sub(paste0(.getParameterCaption("futilityBoundsDelayedInformationNonBinding"), " and"),
"Lower and", yAxisLabel1,
fixed = TRUE
)
if (!("xValues" %in% colnames(data)) || !("yValues" %in% colnames(data))) {
if (!(xParameterName %in% colnames(data))) {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, sQuote(xParameterName), " is not available in dataset")
}
if (!(yParameterName1 %in% colnames(data))) {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, sQuote(yParameterName1), " is not available in dataset")
}
data$xValues <- data[[xParameterName]]
data$yValues <- data[[yParameterName1]]
if (yParameterName1 == "futilityBounds") {
data$yValues[!is.na(data$yValues) &
(is.infinite(data$yValues) | data$yValues == C_FUTILITY_BOUNDS_DEFAULT)] <- NA_real_