Nothing
###############################################################################
# CHANGE LOG (last 20 changes)
# 08.09.2022: Compacted gui. Fixed narrow dropdowns. Removed destroy workaround.
# 07.03.2020: Added language support.
# 23.03.2019: Fixed Error in paste(parent$ID, parent$env$num.subwin... (tcltk)
# 17.02.2019: Fixed Error in if (svalue(savegui_chk)) { : argument is of length zero (tcltk)
# 07.08.2017: Added audit trail.
# 13.07.2017: Fixed issue with button handlers.
# 13.07.2017: Fixed narrow dropdown with hidden argument ellipsize = "none".
# 07.07.2017: Replaced 'droplist' with 'gcombobox'.
# 07.07.2017: Removed argument 'border' for 'gbutton'.
# 18.09.2016: Added attributes to result.
# 29.04.2016: 'Save as' textbox expandable.
# 28.08.2015: Added importFrom.
# 04.06.2015: Changed button label 'Calculate result type' to 'Calculate'.
# 11.10.2014: Added 'focus', added 'parent' parameter.
# 28.06.2014: Added help button and moved save gui checkbox.
# 08.05.2014: Implemented 'checkDataset'.
# 15.01.2014: Added option for parameter to add missing markers.
# 10.11.2013: Added kit dropbox.
# 03.11.2013: First version.
#' @title Calculate Result Type
#'
#' @description
#' GUI wrapper for the \code{\link{calculateResultType}} function.
#'
#' @details Simplifies the use of \code{\link{calculateResultType}} by providing a
#' graphical user interface.
#'
#' @param env environment in which to search for data frames and save result.
#' @param savegui logical indicating if GUI settings should be saved in the environment.
#' @param debug logical indicating printing debug information.
#' @param parent widget to get focus when finished.
#'
#' @export
#'
#' @importFrom utils help
#'
#' @return TRUE
#'
#' @seealso \code{\link{calculateResultType}}
calculateResultType_gui <- function(env = parent.frame(), savegui = NULL,
debug = FALSE, parent = NULL) {
# Global variables.
.gData <- NULL
.gDataName <- NULL
# Language ------------------------------------------------------------------
# Get this functions name from call.
fnc <- as.character(match.call()[[1]])
if (debug) {
print(paste("IN:", fnc))
}
# Default strings.
strWinTitle <- "Calculate result type"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Dataset and kit"
strLblDataset <- "Sample dataset:"
strDrpDataset <- "<Select dataset>"
strLblSamples <- "samples"
strLblKit <- "Kit:"
strFrmOptions <- "Options"
strLblNB <- "NB! All markers must be present in each sample for correct results."
strLblPre <- "Pre-processing:"
strChkMissing <- "Add missing markers (can be slow on large datasets)"
strLblMethod <- "Calculate result type:"
strLblHeight <- "Define subtypes of complete profiles by all peaks > peak height threshold (RFU):"
strTipHeight <- "Complete >[RFU]"
strLblMarker <- "Define subtypes of mixtures by number of markers with > 2 detected peaks:"
strTipMarker <- "Mixture >[markers]"
strLblPeak <- "Define subtypes of partial profiles by number of detected peaks:"
strTipPeak <- "Partial >[peaks]"
strLblFullKit <- "Define subtypes of partial profiles by kit:"
strDrpKit <- "<Select kit>"
strTipFullKit <- "Partial Complete [kit]"
strFrmSave <- "Save as"
strLblSave <- "Name for result:"
strBtnCalculate <- "Calculate"
strBtnProcessing <- "Processing..."
strMsgDataset <- "A sample dataset must be selected."
strMsgTitleDataset <- "Dataset not selected"
# Get strings from language file.
dtStrings <- getStrings(gui = fnc)
# If language file is found.
if (!is.null(dtStrings)) {
# Get language strings, use default if not found.
strtmp <- dtStrings["strWinTitle"]$value
strWinTitle <- ifelse(is.na(strtmp), strWinTitle, strtmp)
strtmp <- dtStrings["strChkGui"]$value
strChkGui <- ifelse(is.na(strtmp), strChkGui, strtmp)
strtmp <- dtStrings["strBtnHelp"]$value
strBtnHelp <- ifelse(is.na(strtmp), strBtnHelp, strtmp)
strtmp <- dtStrings["strFrmDataset"]$value
strFrmDataset <- ifelse(is.na(strtmp), strFrmDataset, strtmp)
strtmp <- dtStrings["strLblDataset"]$value
strLblDataset <- ifelse(is.na(strtmp), strLblDataset, strtmp)
strtmp <- dtStrings["strDrpDataset"]$value
strDrpDataset <- ifelse(is.na(strtmp), strDrpDataset, strtmp)
strtmp <- dtStrings["strLblSamples"]$value
strLblSamples <- ifelse(is.na(strtmp), strLblSamples, strtmp)
strtmp <- dtStrings["strLblKit"]$value
strLblKit <- ifelse(is.na(strtmp), strLblKit, strtmp)
strtmp <- dtStrings["strFrmOptions"]$value
strFrmOptions <- ifelse(is.na(strtmp), strFrmOptions, strtmp)
strtmp <- dtStrings["strLblNB"]$value
strLblNB <- ifelse(is.na(strtmp), strLblNB, strtmp)
strtmp <- dtStrings["strLblPre"]$value
strLblPre <- ifelse(is.na(strtmp), strLblPre, strtmp)
strtmp <- dtStrings["strChkMissing"]$value
strChkMissing <- ifelse(is.na(strtmp), strChkMissing, strtmp)
strtmp <- dtStrings["strLblMethod"]$value
strLblMethod <- ifelse(is.na(strtmp), strLblMethod, strtmp)
strtmp <- dtStrings["strLblHeight"]$value
strLblHeight <- ifelse(is.na(strtmp), strLblHeight, strtmp)
strtmp <- dtStrings["strTipHeight"]$value
strTipHeight <- ifelse(is.na(strtmp), strTipHeight, strtmp)
strtmp <- dtStrings["strLblMarker"]$value
strLblMarker <- ifelse(is.na(strtmp), strLblMarker, strtmp)
strtmp <- dtStrings["strTipMarker"]$value
strTipMarker <- ifelse(is.na(strtmp), strTipMarker, strtmp)
strtmp <- dtStrings["strLblPeak"]$value
strLblPeak <- ifelse(is.na(strtmp), strLblPeak, strtmp)
strtmp <- dtStrings["strTipPeak"]$value
strTipPeak <- ifelse(is.na(strtmp), strTipPeak, strtmp)
strtmp <- dtStrings["strLblFullKit"]$value
strLblFullKit <- ifelse(is.na(strtmp), strLblFullKit, strtmp)
strtmp <- dtStrings["strTipFullKit"]$value
strTipFullKit <- ifelse(is.na(strtmp), strTipFullKit, strtmp)
strtmp <- dtStrings["strDrpKit"]$value
strDrpKit <- ifelse(is.na(strtmp), strDrpKit, strtmp)
strtmp <- dtStrings["strFrmSave"]$value
strFrmSave <- ifelse(is.na(strtmp), strFrmSave, strtmp)
strtmp <- dtStrings["strLblSave"]$value
strLblSave <- ifelse(is.na(strtmp), strLblSave, strtmp)
strtmp <- dtStrings["strBtnCalculate"]$value
strBtnCalculate <- ifelse(is.na(strtmp), strBtnCalculate, strtmp)
strtmp <- dtStrings["strBtnProcessing"]$value
strBtnProcessing <- ifelse(is.na(strtmp), strBtnProcessing, strtmp)
strtmp <- dtStrings["strMsgDataset"]$value
strMsgDataset <- ifelse(is.na(strtmp), strMsgDataset, strtmp)
strtmp <- dtStrings["strMsgTitleDataset"]$value
strMsgTitleDataset <- ifelse(is.na(strtmp), strMsgTitleDataset, strtmp)
}
# WINDOW ####################################################################
# Main window.
w <- gwindow(title = strWinTitle, visible = FALSE)
# Runs when window is closed.
addHandlerUnrealize(w, handler = function(h, ...) {
# Save GUI state.
.saveSettings()
# Focus on parent window.
if (!is.null(parent)) {
focus(parent)
}
# Destroy window.
return(FALSE)
})
# Vertical main group.
gv <- ggroup(
horizontal = FALSE,
spacing = 1,
use.scrollwindow = FALSE,
container = w,
expand = TRUE
)
# Help button group.
gh <- ggroup(container = gv, expand = FALSE, fill = "both")
savegui_chk <- gcheckbox(text = strChkGui, checked = FALSE, container = gh)
addSpring(gh)
help_btn <- gbutton(text = strBtnHelp, container = gh)
addHandlerChanged(help_btn, handler = function(h, ...) {
# Open help page for function.
print(help(fnc, help_type = "html"))
})
# FRAME 0 ###################################################################
f0 <- gframe(
text = strFrmDataset,
horizontal = FALSE,
spacing = 1,
container = gv
)
# Datasets ------------------------------------------------------------------
g0 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblDataset, container = g0)
samples_lbl <- glabel(
text = paste(" 0", strLblSamples),
container = g0
)
dataset_drp <- gcombobox(
items = c(
strDrpDataset,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1,
editable = FALSE,
container = g0,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
# Kit -----------------------------------------------------------------------
g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblKit, container = g1)
kit_drp <- gcombobox(
items = getKit(),
selected = 1,
editable = FALSE,
container = g1,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(dataset_drp, handler = function(h, ...) {
val_obj <- svalue(dataset_drp)
# Check if suitable.
requiredCol <- c("Sample.Name", "Marker", "Allele", "Height")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
.gData <<- get(val_obj, envir = env)
.gDataName <<- val_obj
samples <- length(unique(.gData$Sample.Name))
svalue(samples_lbl) <- paste("", samples, strLblSamples)
svalue(save_edt) <- paste(val_obj, "_type", sep = "")
# Detect kit.
kitIndex <- detectKit(.gData, index = TRUE)
# Select in dropdown.
svalue(kit_drp, index = TRUE) <- kitIndex
} else {
# Reset components.
.gData <<- NULL
.gDataName <<- NULL
svalue(dataset_drp, index = TRUE) <- 1
svalue(samples_lbl) <- paste(" 0", strLblSamples)
svalue(save_edt) <- ""
}
})
# FRAME 1 ###################################################################
f1 <- gframe(
text = strFrmOptions,
horizontal = FALSE,
spacing = 1,
container = gv
)
glabel(text = strLblNB, container = f1, anchor = c(-1, 0))
glabel(text = strLblPre, container = f1, anchor = c(-1, 0))
f1_add_chk <- gcheckbox(text = strChkMissing, checked = TRUE, container = f1)
glabel(text = strLblMethod, container = f1, anchor = c(-1, 0))
glabel(text = strLblHeight, container = f1, anchor = c(-1, 0))
f1_rfu_edt <- gedit(text = "", width = 6, container = f1)
tooltip(f1_rfu_edt) <- strTipHeight
glabel(text = strLblMarker, container = f1, anchor = c(-1, 0))
f1_mix_edt <- gedit(text = "", width = 6, container = f1)
tooltip(f1_mix_edt) <- strTipMarker
glabel(text = strLblPeak, container = f1, anchor = c(-1, 0))
f1_par_edt <- gedit(text = "", width = 6, container = f1)
tooltip(f1_par_edt) <- strTipPeak
glabel(text = strLblFullKit, container = f1, anchor = c(-1, 0))
f1_kit_drp <- gcombobox(
items = c(strDrpKit, getKit()),
selected = 1,
editable = FALSE,
container = f1,
ellipsize = "none"
)
# SAVE ######################################################################
save_frame <- gframe(text = strFrmSave, container = gv)
glabel(text = strLblSave, container = save_frame)
save_edt <- gedit(expand = TRUE, fill = TRUE, container = save_frame)
# BUTTON ####################################################################
calculate_btn <- gbutton(text = strBtnCalculate, container = gv)
addHandlerClicked(calculate_btn, handler = function(h, ...) {
val_data <- .gData
val_name_data <- .gDataName
val_threshold <- as.numeric(svalue(f1_rfu_edt))
val_mix <- svalue(f1_mix_edt)
val_par <- svalue(f1_par_edt)
val_subkit <- svalue(f1_kit_drp)
val_name <- svalue(save_edt)
val_marker <- NULL
val_kit <- svalue(kit_drp)
val_add <- svalue(f1_add_chk)
if (debug) {
print("GUI options:")
print("val_threshold")
print(val_threshold)
print("val_mix")
print(val_mix)
print("val_par")
print(val_par)
print("val_subkit")
print(val_subkit)
print("val_marker")
print(val_marker)
print("val_name")
print(val_name)
print("val_kit")
print(val_kit)
print("val_add")
print(val_add)
}
# Prepare arguments -------------------------------------------------------
# No threshold is represented by NULL.
if (is.na(val_threshold)) {
val_threshold <- NULL
}
# Check if empty.
if (nchar(val_mix) == 0) {
# No limit is represented by NULL.
val_mix <- NULL
} else {
# Convert string to numeric vector.
val_mix <- unlist(strsplit(x = val_mix, split = ",", fixed = TRUE))
val_mix <- as.numeric(val_mix)
}
# Check if empty.
if (nchar(val_par) == 0) {
# No limit is represented by NULL.
val_par <- NULL
} else {
# Convert string to numeric vector.
val_par <- unlist(strsplit(x = val_par, split = ",", fixed = TRUE))
val_par <- as.numeric(val_par)
}
# Check if kit is provided and available.
if (val_subkit %in% getKit()) {
# Get marker names and create string.
val_marker <- paste(getKit(kit = val_subkit, what = "Marker"), collapse = "|")
} else {
# Set to NA.
val_subkit <- NA
}
if (debug) {
print("Function arguments:")
print("val_threshold")
print(val_threshold)
print("val_mix")
print(val_mix)
print("val_par")
print(val_par)
print("val_subkit")
print(val_subkit)
print("val_marker")
print(val_marker)
print("val_name")
print(val_name)
print("val_kit")
print(val_kit)
}
if (!is.null(val_data)) {
# Change button.
blockHandlers(calculate_btn)
svalue(calculate_btn) <- strBtnProcessing
unblockHandlers(calculate_btn)
enabled(calculate_btn) <- FALSE
datanew <- calculateResultType(
data = val_data,
kit = val_kit,
add.missing.marker = val_add,
threshold = val_threshold,
mixture.limits = val_mix,
partial.limits = val_par,
subset.name = val_subkit,
marker.subset = val_marker,
debug = debug
)
# Add attributes to result.
attr(datanew, which = "kit") <- val_kit
# Create key-value pairs to log.
keys <- list(
"data", "add.missing.marker", "threshold", "mixture.limits",
"partial.limits", "subset.name", "marker.subset"
)
values <- list(
val_name_data, val_add, val_threshold, val_mix,
val_par, val_subkit, val_marker
)
# Update audit trail.
datanew <- auditTrail(
obj = datanew, key = keys, value = values,
label = fnc,
arguments = FALSE, package = "strvalidator"
)
# Save data.
saveObject(name = val_name, object = datanew, parent = w, env = env)
if (debug) {
print(paste("EXIT:", fnc))
}
# Close GUI.
.saveSettings()
dispose(w)
} else {
gmessage(
msg = strMsgDataset,
title = strMsgTitleDataset,
icon = "error",
parent = w
)
}
})
# INTERNAL FUNCTIONS ########################################################
.loadSavedSettings <- function() {
# First check status of save flag.
if (!is.null(savegui)) {
svalue(savegui_chk) <- savegui
enabled(savegui_chk) <- FALSE
if (debug) {
print("Save GUI status set!")
}
} else {
# Load save flag.
if (exists(".strvalidator_calculateResultType_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculateResultType_gui_savegui", envir = env)
}
if (debug) {
print("Save GUI status loaded!")
}
}
if (debug) {
print(svalue(savegui_chk))
}
# Then load settings if true.
if (svalue(savegui_chk)) {
if (exists(".strvalidator_calculateResultType_gui_rfu", envir = env, inherits = FALSE)) {
svalue(f1_rfu_edt) <- get(".strvalidator_calculateResultType_gui_rfu", envir = env)
}
if (exists(".strvalidator_calculateResultType_gui_mix", envir = env, inherits = FALSE)) {
svalue(f1_mix_edt) <- get(".strvalidator_calculateResultType_gui_mix", envir = env)
}
if (exists(".strvalidator_calculateResultType_gui_par", envir = env, inherits = FALSE)) {
svalue(f1_par_edt) <- get(".strvalidator_calculateResultType_gui_par", envir = env)
}
if (exists(".strvalidator_calculateResultType_gui_kit", envir = env, inherits = FALSE)) {
svalue(f1_kit_drp) <- get(".strvalidator_calculateResultType_gui_kit", envir = env)
}
if (exists(".strvalidator_calculateResultType_gui_add", envir = env, inherits = FALSE)) {
svalue(f1_add_chk) <- get(".strvalidator_calculateResultType_gui_add", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculateResultType_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculateResultType_gui_rfu", value = svalue(f1_rfu_edt), envir = env)
assign(x = ".strvalidator_calculateResultType_gui_mix", value = svalue(f1_mix_edt), envir = env)
assign(x = ".strvalidator_calculateResultType_gui_par", value = svalue(f1_par_edt), envir = env)
assign(x = ".strvalidator_calculateResultType_gui_kit", value = svalue(f1_kit_drp), envir = env)
assign(x = ".strvalidator_calculateResultType_gui_add", value = svalue(f1_add_chk), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculateResultType_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateResultType_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculateResultType_gui_rfu", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateResultType_gui_rfu", envir = env)
}
if (exists(".strvalidator_calculateResultType_gui_mix", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateResultType_gui_mix", envir = env)
}
if (exists(".strvalidator_calculateResultType_gui_par", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateResultType_gui_par", envir = env)
}
if (exists(".strvalidator_calculateResultType_gui_kit", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateResultType_gui_kit", envir = env)
}
if (exists(".strvalidator_calculateResultType_gui_add", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateResultType_gui_add", envir = env)
}
if (debug) {
print("Settings cleared!")
}
}
if (debug) {
print("Settings saved!")
}
}
# END GUI ###################################################################
# Load GUI settings.
.loadSavedSettings()
# Show GUI.
visible(w) <- TRUE
focus(w)
}
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