Nothing
################################################################################
# CHANGE LOG (last 20 changes)
# 01.09.2022: Compacted gui. Fixed narrow dropdowns. Removed destroy workaround.
# 03.03.2020: Fixed reference to function name.
# 01.03.2020: Added language support.
# 17.02.2019: Fixed Error in if (svalue(savegui_chk)) { : argument is of length zero (tcltk)
# 10.02.2019: Adjusted GUI for tcltk.
# 10.02.2019: Fixed tcltk Error in structure(.External(.C_dotTclObjv, objv)
# 06.08.2017: 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'.
# 20.07.2016: Added attributes to result.
# 20.07.2016: Added new option 'list.all' to include missing samples in result.
# 28.08.2015: Added importFrom
# 11.10.2014: Added 'focus', added 'parent' parameter.
# 28.06.2014: Added help button and moved save gui checkbox.
# 22.06.2014: First version.
#' @title Calculate Concordance
#'
#' @description
#' GUI wrapper for the \code{\link{calculateConcordance}} function.
#'
#' @details
#' Simplifies the use of the \code{\link{calculateConcordance}} function 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.
#'
#' @return TRUE
#'
#' @export
#'
#' @importFrom utils help head str
#'
#' @seealso \code{\link{calculateConcordance}}
calculateConcordance_gui <- function(env = parent.frame(), savegui = NULL,
debug = FALSE, parent = NULL) {
# Global variables.
.gData <- NULL
# Language ------------------------------------------------------------------
# Get this functions name from call.
fnc <- as.character(match.call()[[1]])
if (debug) {
print(paste("IN:", fnc))
}
# Default strings.
strWinTitle <- "Calculate concordance"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Dataset and kit"
strLblDataset <- "Sample dataset:"
strDrpDefault <- "<Select dataset>"
strLblSamples <- "samples"
strLblKit <- "Kit:"
strBtnAdd <- "Add"
strFrmOptions <- "Options"
strLblDelimiter <- "Delimiter for alleles in genotype:"
strLblNoSample <- "String for missing samples:"
strLblNoMarker <- "String for missing markers:"
strChkInclude <- "Include missing samples in result."
strTipInclude <- "Samples not in all datasets will always be included in the result."
strFrmSelected <- "Selected datasets"
strLblSelected <- "Name for datasets to analyse (separated by comma):"
strLblUsedKits <- "Name for analysis kit (separated by comma):"
strFrmSave <- "Save as"
strLblSave <- "Name for discordance table:"
strLblSave2 <- "Name for concordance table:"
strBtnCalculate <- "Calculate"
strBtnProcessing <- "Processing..."
strMsgAddMessage <- "Data frame is NULL!\n\nMake sure to select a dataset"
strMsgTitleError <- "Error"
strMsgDataset <- "A dataset must be selected."
strMsgTitleDataset <- "Datasets 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"]$value
strLblDataset <- ifelse(is.na(strtmp), strLblDataset, strtmp)
strtmp <- dtStrings["strDrpDefault"]$value
strDrpDefault <- ifelse(is.na(strtmp), strDrpDefault, 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["strBtnAdd"]$value
strBtnAdd <- ifelse(is.na(strtmp), strBtnAdd, strtmp)
strtmp <- dtStrings["strFrmOptions"]$value
strFrmOptions <- ifelse(is.na(strtmp), strFrmOptions, strtmp)
strtmp <- dtStrings["strLblDelimiter"]$value
strLblDelimiter <- ifelse(is.na(strtmp), strLblDelimiter, strtmp)
strtmp <- dtStrings["strLblNoSample"]$value
strLblNoSample <- ifelse(is.na(strtmp), strLblNoSample, strtmp)
strtmp <- dtStrings["strLblNoMarker"]$value
strLblNoMarker <- ifelse(is.na(strtmp), strLblNoMarker, strtmp)
strtmp <- dtStrings["strChkInclude"]$value
strChkInclude <- ifelse(is.na(strtmp), strChkInclude, strtmp)
strtmp <- dtStrings["strTipInclude"]$value
strTipInclude <- ifelse(is.na(strtmp), strTipInclude, strtmp)
strtmp <- dtStrings["strFrmSelected"]$value
strFrmSelected <- ifelse(is.na(strtmp), strFrmSelected, strtmp)
strtmp <- dtStrings["strLblSelected"]$value
strLblSelected <- ifelse(is.na(strtmp), strLblSelected, strtmp)
strtmp <- dtStrings["strLblUsedKits"]$value
strLblUsedKits <- ifelse(is.na(strtmp), strLblUsedKits, 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["strLblSave2"]$value
strLblSave2 <- ifelse(is.na(strtmp), strLblSave2, strtmp)
strtmp <- dtStrings["strBtnCalculate"]$value
strBtnCalculate <- ifelse(is.na(strtmp), strBtnCalculate, strtmp)
strtmp <- dtStrings["strBtnProcessing"]$value
strBtnProcessing <- ifelse(is.na(strtmp), strBtnProcessing, strtmp)
strtmp <- dtStrings["strMsgAddMessage"]$value
strMsgAddMessage <- ifelse(is.na(strtmp), strMsgAddMessage, strtmp)
strtmp <- dtStrings["strMsgTitleError"]$value
strMsgTitleError <- ifelse(is.na(strtmp), strMsgTitleError, strtmp)
strtmp <- dtStrings["strMsgDataset"]$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)
})
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
)
# Samples -------------------------------------------------------------------
f0g0 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblDataset, container = f0g0)
f0_samples_lbl <- glabel(
text = paste(" 0", strLblSamples),
container = f0g0
)
f0_list <- c(strDrpDefault, listObjects(env = env, obj.class = "data.frame"))
dataset_drp <- gcombobox(
items = f0_list, selected = 1,
editable = FALSE, container = f0g0,
ellipsize = "none", expand = TRUE, fill = "x"
)
# Sizing --------------------------------------------------------------------
f0g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblKit, container = f0g1)
kit_drp <- gcombobox(
items = getKit(), selected = 1,
editable = FALSE, container = f0g1,
ellipsize = "none", expand = TRUE,
fill = "x"
)
f0_add_btn <- gbutton(text = strBtnAdd, container = f0)
# HANDLERS ------------------------------------------------------------------
addHandlerChanged(dataset_drp, handler = function(h, ...) {
val_obj <- svalue(dataset_drp)
# Check if suitable.
requiredCol <- c("Sample.Name", "Marker", "Allele")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
# Get data.
.gData <<- get(val_obj, envir = env)
svalue(f0_samples_lbl) <- paste(
length(unique(.gData$Sample.Name)),
strLblSamples
)
# Detect kit.
kitIndex <- detectKit(.gData, index = TRUE)
# Select in dropdown.
svalue(kit_drp, index = TRUE) <- kitIndex
} else {
# Reset components.
.gData <<- NULL
svalue(f4_save1_edt) <- ""
svalue(f4_save2_edt) <- ""
svalue(dataset_drp, index = TRUE) <- 1
svalue(f0_samples_lbl) <- paste("0", strLblSamples)
}
})
addHandlerChanged(f0_add_btn, handler = function(h, ...) {
# Get values.
val_obj <- svalue(dataset_drp)
val_dataset <- svalue(f3_dataset_edt)
val_kit <- svalue(f3_kit_edt)
val_new_kit <- svalue(kit_drp)
if (!is.null(.gData)) {
# Add new value to selected.
new <- ifelse(nchar(val_dataset) > 0,
paste(val_dataset, val_obj, sep = ","),
val_obj
)
# Update text box.
svalue(f3_dataset_edt) <- new
# Add new value to selected.
new <- ifelse(nchar(val_kit) > 0,
paste(val_kit, val_new_kit, sep = ","),
val_new_kit
)
# Update text box.
svalue(f3_kit_edt) <- new
} else {
gmessage(
msg = strMsgAddMessage,
title = strMsgTitleError,
icon = "error"
)
}
})
# FRAME 1 ###################################################################
f1 <- gframe(text = strFrmOptions, horizontal = FALSE, spacing = 1, container = gv)
f1g0 <- glayout(container = f1, expand = TRUE, fill = "both", spacing = 1)
f1g0[1, 1] <- glabel(
text = strLblDelimiter,
anchor = c(-1, 0), container = f1g0
)
f1g0[1, 2] <- f1_delimeter_edt <- gedit(
text = ",",
width = 15, container = f1g0
)
f1g0[2, 1] <- glabel(
text = strLblNoSample,
anchor = c(-1, 0), container = f1g0
)
f1g0[2, 2] <- f1_no_sample_edt <- gedit(
text = "NO SAMPLE",
width = 15, container = f1g0
)
f1g0[3, 1] <- glabel(
text = strLblNoMarker,
anchor = c(-1, 0), container = f1g0
)
f1g0[3, 2] <- f1_no_marker_edt <- gedit(
text = "NO MARKER",
width = 15, container = f1g0
)
f1_all_chk <- gcheckbox(
text = strChkInclude,
checked = FALSE, container = f1
)
tooltip(f1_all_chk) <- strTipInclude
# FRAME 3 ###################################################################
f3 <- gframe(
text = strFrmSelected,
horizontal = FALSE,
spacing = 1,
container = gv
)
glabel(
text = strLblSelected,
anchor = c(-1, 0), container = f3
)
f3_dataset_edt <- gedit(container = f3)
glabel(
text = strLblUsedKits,
anchor = c(-1, 0), container = f3
)
f3_kit_edt <- gedit(container = f3)
# FRAME 4 ###################################################################
f4 <- gframe(
text = strFrmSave,
horizontal = FALSE,
spacing = 1,
container = gv
)
glabel(text = strLblSave, anchor = c(-1, 0), container = f4)
f4_save1_edt <- gedit(text = "table_discordance", container = f4)
glabel(text = strLblSave2, anchor = c(-1, 0), container = f4)
f4_save2_edt <- gedit(text = "table_concordance", container = f4)
# BUTTON ####################################################################
calculate_btn <- gbutton(text = strBtnCalculate, container = gv)
addHandlerClicked(calculate_btn, handler = function(h, ...) {
# Get values.
val_datasets <- svalue(f3_dataset_edt)
val_kits <- svalue(f3_kit_edt)
val_name1 <- svalue(f4_save1_edt)
val_name2 <- svalue(f4_save2_edt)
val_del <- svalue(f1_delimeter_edt)
val_nosample <- svalue(f1_no_sample_edt)
val_nomarker <- svalue(f1_no_marker_edt)
val_all <- svalue(f1_all_chk)
val_list <- list()
if (debug) {
print("Read Values:")
print("val_datasets")
print(val_datasets)
print("val_kits")
print(val_kits)
print("val_name1")
print(val_name1)
print("val_name2")
print(val_name2)
print("val_delimeter")
print(val_del)
print("val_nosample")
print(val_nosample)
print("val_nomarker")
print(val_nomarker)
print("val_all")
print(val_all)
}
# Check if data.
if (!val_datasets == "") {
# Create list of datasets.
val_datasets <- unlist(strsplit(val_datasets, ","))
for (d in seq(along = val_datasets)) {
# Get data and store in list.
val_list[[d]] <- get(val_datasets[d], envir = env)
}
# Create vector of kit names.
val_kits <- unlist(strsplit(val_kits, ","))
if (debug) {
print("Sent Values:")
print("val_list")
print(str(val_list))
print("val_kits")
print(val_kits)
print("val_del")
print(val_del)
print("val_nosample")
print(val_nosample)
print("val_nomarker")
print(val_nomarker)
print("val_all")
print(val_all)
}
# Change button.
blockHandlers(calculate_btn)
svalue(calculate_btn) <- strBtnProcessing
unblockHandlers(calculate_btn)
enabled(calculate_btn) <- FALSE
datanew <- calculateConcordance(
data = val_list,
kit.name = val_kits,
no.sample = val_nosample,
no.marker = val_nomarker,
delimeter = val_del,
list.all = val_all,
debug = debug
)
# Create key-value pairs to log.
keys <- list(
"data", "kit.name", "no.sample", "no.marker",
"delimeter", "list.all"
)
values <- list(
val_datasets, val_kits, val_nosample, val_nomarker,
val_del, val_all
)
# Update audit trail.
datanew[[1]] <- auditTrail(
obj = datanew[[1]], key = keys, value = values,
label = fnc,
arguments = FALSE, package = "strvalidator"
)
datanew[[2]] <- auditTrail(
obj = datanew[[2]], key = keys, value = values,
label = fnc,
arguments = FALSE, package = "strvalidator"
)
# Save data.
saveObject(name = val_name1, object = datanew[[1]], parent = w, env = env)
saveObject(name = val_name2, object = datanew[[2]], parent = w, env = env)
if (debug) {
print(str(datanew))
print(head(datanew))
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_calculateConcordance_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculateConcordance_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_calculateConcordance_gui_delimeter", envir = env, inherits = FALSE)) {
svalue(f1_delimeter_edt) <- get(".strvalidator_calculateConcordance_gui_delimeter", envir = env)
}
if (exists(".strvalidator_calculateConcordance_gui_sample", envir = env, inherits = FALSE)) {
svalue(f1_no_sample_edt) <- get(".strvalidator_calculateConcordance_gui_sample", envir = env)
}
if (exists(".strvalidator_calculateConcordance_gui_marker", envir = env, inherits = FALSE)) {
svalue(f1_no_marker_edt) <- get(".strvalidator_calculateConcordance_gui_marker", envir = env)
}
if (exists(".strvalidator_calculateConcordance_gui_all", envir = env, inherits = FALSE)) {
svalue(f1_all_chk) <- get(".strvalidator_calculateConcordance_gui_all", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculateConcordance_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculateConcordance_gui_delimeter", value = svalue(f1_delimeter_edt), envir = env)
assign(x = ".strvalidator_calculateConcordance_gui_sample", value = svalue(f1_no_sample_edt), envir = env)
assign(x = ".strvalidator_calculateConcordance_gui_marker", value = svalue(f1_no_marker_edt), envir = env)
assign(x = ".strvalidator_calculateConcordance_gui_all", value = svalue(f1_all_chk), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculateConcordance_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateConcordance_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculateConcordance_gui_delimeter", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateConcordance_gui_delimeter", envir = env)
}
if (exists(".strvalidator_calculateConcordance_gui_sample", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateConcordance_gui_sample", envir = env)
}
if (exists(".strvalidator_calculateConcordance_gui_marker", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateConcordance_gui_marker", envir = env)
}
if (exists(".strvalidator_calculateConcordance_gui_all", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateConcordance_gui_all", 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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