################################################################################
# CHANGE LOG (last 20 changes)
# 20.06.2023: Fixed Error in !is.null(val_data) && !is.na(val_data) in coercion to 'logical(1)
# 10.09.2022: Compacted the gui. Fixed narrow dropdowns. Removed destroy workaround.
# 02.05.2020: Added language support.
# 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 narrow dropdown with hidden argument ellipsize = "none".
# 07.07.2017: Replaced 'droplist' with 'gcombobox'.
# 07.07.2017: Removed argument 'border' for 'gbutton'.
# 02.05.2016: First version.
#' @title Remove Artefact
#'
#' @description
#' GUI wrapper for the \code{\link{removeArtefact}} function.
#'
#' @details
#' Simplifies the use of the \code{\link{removeArtefact}} function by providing a
#' graphical user interface to it.
#'
#' @param env environment in which to search for data frames.
#' @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
removeArtefact_gui <- function(env = parent.frame(), savegui = NULL, debug = FALSE, parent = NULL) {
# Global variables.
.gData <- NULL
.gDataName <- NULL
.gArtefact <- NULL
.gArtefactName <- NULL
# Language ------------------------------------------------------------------
# Get this functions name from call.
fnc <- as.character(match.call()[[1]])
if (debug) {
print(paste("IN:", fnc))
}
# Default strings.
strWinTitle <- "Remove artefacts"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Dataset"
strLblDataset <- "Dataset:"
strDrpDataset <- "<Select dataset>"
strLblRows <- "rows"
strLblArtefacts <- "Artefact list:"
strFrmOptions <- "Options"
strChkRemoveNA <- "Remove Allele=NA"
strLblThreshold <- "Artefact threshold:"
strFrmSave <- "Save as"
strLblSave <- "Name for result:"
strMsgNotDf <- "Data set must be a data.frame!"
strMsgTitleError <- "Error"
strBtnRemove <- "Remove"
# 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["strLblRows"]$value
strLblRows <- ifelse(is.na(strtmp), strLblRows, strtmp)
strtmp <- dtStrings["strLblArtefacts"]$value
strLblArtefacts <- ifelse(is.na(strtmp), strLblArtefacts, strtmp)
strtmp <- dtStrings["strFrmOptions"]$value
strFrmOptions <- ifelse(is.na(strtmp), strFrmOptions, strtmp)
strtmp <- dtStrings["strChkRemoveNA"]$value
strChkRemoveNA <- ifelse(is.na(strtmp), strChkRemoveNA, strtmp)
strtmp <- dtStrings["strLblThreshold"]$value
strLblThreshold <- ifelse(is.na(strtmp), strLblThreshold, strtmp)
strtmp <- dtStrings["strFrmSave"]$value
strFrmSave <- ifelse(is.na(strtmp), strFrmSave, strtmp)
strtmp <- dtStrings["strLblSave"]$value
strLblSave <- ifelse(is.na(strtmp), strLblSave, strtmp)
strtmp <- dtStrings["strMsgNotDf"]$value
strMsgNotDf <- ifelse(is.na(strtmp), strMsgNotDf, strtmp)
strtmp <- dtStrings["strMsgTitleError"]$value
strMsgTitleError <- ifelse(is.na(strtmp), strMsgTitleError, strtmp)
strtmp <- dtStrings["strBtnRemove"]$value
strBtnRemove <- ifelse(is.na(strtmp), strBtnRemove, 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 = FALSE
)
# 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"))
})
# DATASET ###################################################################
f0 <- gframe(
text = strFrmDataset,
horizontal = FALSE,
spacing = 1,
container = gv
)
# Dataset -------------------------------------------------------------------
f0g0 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblDataset, container = f0g0)
data_col_lbl <- glabel(
text = paste(" 0", strLblRows),
container = f0g0
)
data_drp <- gcombobox(
items = c(
strDrpDataset,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1,
editable = FALSE,
container = f0g0,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(data_drp, handler = function(h, ...) {
val_obj <- svalue(data_drp)
# Check if suitable.
requiredCol <- c("Marker", "Allele")
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
svalue(data_col_lbl) <- paste("", nrow(.gData), strLblRows)
svalue(save_edt) <- paste(.gDataName, "no_artefacts", sep = "_")
} else {
.gData <<- NULL
.gDataName <<- NULL
svalue(data_col_lbl) <- paste(" 0", strLblRows)
svalue(save_edt) <- ""
}
})
# Artefacts -----------------------------------------------------------------
f0g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblArtefacts, container = f0g1)
spike_col_lbl <- glabel(
text = paste(" 0", strLblRows),
container = f0g1
)
spike_drp <- gcombobox(
items = c(
strDrpDataset,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1,
editable = FALSE,
container = f0g1,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(spike_drp, handler = function(h, ...) {
val_obj <- svalue(spike_drp)
# Check if suitable.
requiredCol <- c("Marker", "Allele")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
.gArtefact <<- get(val_obj, envir = env)
.gArtefactName <<- val_obj
svalue(spike_col_lbl) <- paste("", nrow(.gArtefact), strLblRows)
} else {
.gData <<- NULL
.gDataName <<- NULL
svalue(data_col_lbl) <- paste(" 0", strLblRows)
}
})
# OPTIONS ###################################################################
f1 <- gframe(text = strFrmOptions, horizontal = FALSE, spacing = 1, container = gv)
f1_na_chk <- gcheckbox(
text = strChkRemoveNA,
checked = FALSE, container = f1
)
f1g1 <- glayout(container = f1, spacing = 1)
f1g1[1, 1] <- glabel(text = strLblThreshold, container = f1g1)
f1g1[1, 2] <- f1_threshold_spn <- gspinbutton(
from = 0, to = 1, by = 0.1,
digits = 2, container = f1g1
)
# 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 ####################################################################
remove_btn <- gbutton(text = strBtnRemove, container = gv)
addHandlerChanged(remove_btn, handler = function(h, ...) {
val_data <- .gData
val_artefact <- .gArtefact
val_name_data <- .gDataName
val_name_spike <- .gArtefactName
val_name <- svalue(save_edt)
val_na <- svalue(f1_na_chk)
val_threshold <- svalue(f1_threshold_spn)
if (is.data.frame(val_data) & is.data.frame(val_artefact)) {
datanew <- removeArtefact(
data = val_data, artefact = val_artefact,
na.rm = val_na, threshold = val_threshold,
debug = debug
)
# Create key-value pairs to log.
keys <- list("data", "artefact", "na.rm", "threshold")
values <- list(val_name_data, val_name_spike, val_na, val_threshold)
# 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(datanew)
print(paste("EXIT:", fnc))
}
# Close GUI.
.saveSettings()
dispose(w)
} else {
gmessage(
msg = strMsgNotDf,
title = strMsgTitleError,
icon = "error"
)
}
})
# 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_removeArtefact_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_removeArtefact_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_removeArtefact_gui_na", envir = env, inherits = FALSE)) {
svalue(f1_na_chk) <- get(".strvalidator_removeArtefact_gui_na", envir = env)
}
if (exists(".strvalidator_removeArtefact_gui_threshold", envir = env, inherits = FALSE)) {
svalue(f1_threshold_spn) <- get(".strvalidator_removeArtefact_gui_threshold", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_removeArtefact_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_removeArtefact_gui_na", value = svalue(f1_na_chk), envir = env)
assign(x = ".strvalidator_removeArtefact_gui_threshold", value = svalue(f1_threshold_spn), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_removeArtefact_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_removeArtefact_gui_savegui", envir = env)
}
if (exists(".strvalidator_removeArtefact_gui_na", envir = env, inherits = FALSE)) {
remove(".strvalidator_removeArtefact_gui_na", envir = env)
}
if (exists(".strvalidator_removeArtefact_gui_threshold", envir = env, inherits = FALSE)) {
remove(".strvalidator_removeArtefact_gui_threshold", 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)
} # End of GUI
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