################################################################################
# CHANGE LOG (last 20 changes)
# 10.09.2022: Compacted the gui. Fixed narrow dropdowns. Removed destroy workaround.
# 03.05.2020: Added language support.
# 02.03.2019: Fixed expansion of widgets under 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'.
# 07.07.2017: Replaced gWidgets:: with gWidgets2::
# 24.06.2016: 'Save as' textbox expandable.
# 06.01.2016: Added attributes to result.
# 29.08.2015: Added importFrom.
# 07.10.2014: Added 'focus', added 'parent' parameter.
# 28.06.2014: Added help button and moved save gui checkbox.
# 08.05.2014: Implemented 'checkDataset'.
# 02.12.2013: Fixed 'Option' frame not visible.
# 20.11.2013: Specified package for function 'gtable' -> 'gWidgets::gtable'
# 06.08.2013: Added rows and columns to info.
# 18.07.2013: Check before overwrite object.
#' @title Slim Data Frames
#'
#' @description
#' GUI wrapper for the \code{\link{slim}} function.
#'
#' @details
#' Simplifies the use of the \code{\link{slim}} function by providing a graphical
#' user interface to it.
#'
#' @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
#'
#' @seealso \code{\link{slim}}
slim_gui <- function(env = parent.frame(), savegui = NULL,
debug = FALSE, parent = NULL) {
# Global variables.
.gData <- data.frame(No.Data = NA)
.gDataName <- NULL
# Language ------------------------------------------------------------------
# Get this functions name from call.
fnc <- as.character(match.call()[[1]])
if (debug) {
print(paste("IN:", fnc))
}
# Default strings.
strWinTitle <- "Slim dataset"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Dataset"
strLblDataset <- "Dataset:"
strDrpDataset <- "<Select dataset>"
strLblSamples <- "samples"
strLblColumns <- "columns"
strLblRows <- "rows"
strFrmOptions <- "Options"
strChkKeep <- "Keep rows in fixed columns even if no data in stacked columns"
strLblKeep <- "(i.e. keep one row per marker for each sample even if no peak)"
strTipColumns <- "Tip: Manually edit the columns to fix and stack (e.g. stack='Allele' will stack 'Allele.1', 'Allele.2'...)"
strFrmFix <- "Fix"
strLblFix <- "Columns to keep fixed (separate by pipe |):"
strEdtMsg <- "Doubleklick or drag column names to list"
strFrmStack <- "Stack"
strLblStack <- "Columns to stack (separate by pipe |):"
strFrmSave <- "Save as"
strLblSave <- "Name for result:"
strMsgName <- "A file name must be provided!"
strBtnSlim <- "Slim dataset"
strBtnProcessing <- "Processing..."
strMsgTitleError <- "Error"
# 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"]$value
strLblSamples <- ifelse(is.na(strtmp), strLblSamples, strtmp)
strtmp <- dtStrings["strLblColumns"]$value
strLblColumns <- ifelse(is.na(strtmp), strLblColumns, strtmp)
strtmp <- dtStrings["strLblRows"]$value
strLblRows <- ifelse(is.na(strtmp), strLblRows, strtmp)
strtmp <- dtStrings["strFrmOptions"]$value
strFrmOptions <- ifelse(is.na(strtmp), strFrmOptions, strtmp)
strtmp <- dtStrings["strChkKeep"]$value
strChkKeep <- ifelse(is.na(strtmp), strChkKeep, strtmp)
strtmp <- dtStrings["strLblKeep"]$value
strLblKeep <- ifelse(is.na(strtmp), strLblKeep, strtmp)
strtmp <- dtStrings["strTipColumns"]$value
strTipColumns <- ifelse(is.na(strtmp), strTipColumns, strtmp)
strtmp <- dtStrings["strFrmFix"]$value
strFrmFix <- ifelse(is.na(strtmp), strFrmFix, strtmp)
strtmp <- dtStrings["strLblFix"]$value
strLblFix <- ifelse(is.na(strtmp), strLblFix, strtmp)
strtmp <- dtStrings["strEdtMsg"]$value
strEdtMsg <- ifelse(is.na(strtmp), strEdtMsg, strtmp)
strtmp <- dtStrings["strFrmStack"]$value
strFrmStack <- ifelse(is.na(strtmp), strFrmStack, strtmp)
strtmp <- dtStrings["strLblStack"]$value
strLblStack <- ifelse(is.na(strtmp), strLblStack, 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["strMsgName"]$value
strMsgName <- ifelse(is.na(strtmp), strMsgName, strtmp)
strtmp <- dtStrings["strBtnSlim"]$value
strBtnSlim <- ifelse(is.na(strtmp), strBtnSlim, strtmp)
strtmp <- dtStrings["strBtnProcessing"]$value
strBtnProcessing <- ifelse(is.na(strtmp), strBtnProcessing, strtmp)
strtmp <- dtStrings["strMsgTitleError"]$value
strMsgTitleError <- ifelse(is.na(strtmp), strMsgTitleError, 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"))
})
# Vertical sub group.
g0 <- ggroup(
horizontal = FALSE,
spacing = 1,
use.scrollwindow = FALSE,
container = gv,
expand = FALSE,
fill = TRUE
)
# Horizontal sub group.
g1 <- ggroup(
horizontal = TRUE,
spacing = 1,
use.scrollwindow = FALSE,
container = gv,
expand = TRUE,
fill = TRUE
)
# Vertical sub group.
g2 <- ggroup(
horizontal = FALSE,
spacing = 1,
use.scrollwindow = FALSE,
container = gv,
expand = FALSE,
fill = TRUE
)
# DATASET ###################################################################
f0 <- gframe(
text = strFrmDataset,
horizontal = TRUE,
spacing = 1,
container = g0
)
glabel(text = strLblDataset, container = f0)
samples_lbl <- glabel(
text = paste(" 0", strLblSamples),
container = f0
)
columns_lbl <- glabel(
text = paste(" 0", strLblColumns),
container = f0
)
rows_lbl <- glabel(
text = paste(" 0", strLblRows),
container = f0
)
dataset_drp <- gcombobox(
items = c(
strDrpDataset,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1,
editable = FALSE,
container = f0,
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")
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
.refresh_fix_tbl()
.refresh_stack_tbl()
samples <- length(unique(.gData$Sample.Name))
# Info.
if ("Sample.Name" %in% names(.gData)) {
samples <- length(unique(.gData$Sample.Name))
svalue(samples_lbl) <- paste(" ", samples, " ",
strLblSamples, ", ",
sep = ""
)
} else {
svalue(samples_lbl) <- paste(" ", "<NA> ",
strLblSamples, ", ",
sep = ""
)
}
svalue(columns_lbl) <- paste(" ", ncol(.gData), " ",
strLblColumns, ", ",
sep = ""
)
svalue(rows_lbl) <- paste(" ", nrow(.gData), " ",
strLblRows, ", ",
sep = ""
)
# Result name.
svalue(save_edt) <- paste(val_obj, "_slim", sep = "")
# Guess column names to keep fixed.
svalue(fix_edt) <- colNames(
data = .gData, slim = TRUE,
numbered = TRUE, concatenate = "|"
)
# Guess column names to stack.
svalue(stack_edt) <- colNames(
data = .gData, slim = FALSE,
numbered = TRUE, concatenate = "|"
)
# Reset button.
svalue(slim_btn) <- strBtnSlim
enabled(slim_btn) <- TRUE
} else {
# Reset components.
.gData <<- data.frame(No.Data = NA)
.gDataName <<- NULL
svalue(fix_edt) <- ""
svalue(stack_edt) <- ""
.refresh_fix_tbl()
.refresh_stack_tbl()
svalue(samples_lbl) <- paste(" ", "<NA> ",
strLblSamples, ", ",
sep = ""
)
svalue(columns_lbl) <- paste(" ", "<NA> ",
strLblColumns, ", ",
sep = ""
)
svalue(rows_lbl) <- paste(" ", "<NA> ",
strLblRows, ", ",
sep = ""
)
svalue(save_edt) <- ""
}
})
# FIX #######################################################################
if (debug) {
print("COLUMNS")
print(names(.gData))
}
fix_f <- gframe(
text = strFrmFix,
horizontal = FALSE, container = g1,
expand = TRUE, fill = TRUE
)
fix_lbl <- glabel(
text = strLblFix,
container = fix_f,
anchor = c(-1, 0)
)
fix_edt <- gedit(
initial.msg = strEdtMsg,
width = 40,
container = fix_f
)
tooltip(fix_edt) <- strTipColumns
fix_tbl <- gWidgets2::gtable(
items = names(.gData),
container = fix_f,
expand = TRUE
)
# Set initial size (only height is important here).
size(fix_tbl) <- c(100, 200)
addDropTarget(fix_edt, handler = function(h, ...) {
if (debug) {
print("SAMPLES:DROPTARGET")
}
# Get values.
drp_val <- h$dropdata
fix_val <- svalue(h$obj)
# Add new value to selected.
new <- ifelse(nchar(fix_val) > 0,
paste(fix_val, drp_val, sep = "|"),
drp_val
)
# Update text box.
svalue(h$obj) <- new
# Update sample name table.
tmp_tbl <- fix_tbl[, ] # Get all values.
print(tmp_tbl)
tmp_tbl <- tmp_tbl[tmp_tbl != drp_val] # Remove value added to selected.
fix_tbl[, ] <- tmp_tbl # Update table.
})
# STACK #####################################################################
if (debug) {
print("STACK")
}
stack_f <- gframe(
text = strFrmStack,
horizontal = FALSE, container = g1,
expand = TRUE, fill = TRUE
)
stack_lbl <- glabel(
text = strLblStack,
container = stack_f,
anchor = c(-1, 0)
)
stack_edt <- gedit(
initial.msg = strEdtMsg,
width = 40,
container = stack_f
)
tooltip(stack_edt) <- strTipColumns
stack_tbl <- gWidgets2::gtable(
items = names(.gData),
container = stack_f,
expand = TRUE
)
addDropTarget(stack_edt, handler = function(h, ...) {
# Get values.
drp_val <- h$dropdata
stack_val <- svalue(h$obj)
# Add new value to selected.
new <- ifelse(nchar(stack_val) > 0,
paste(stack_val, drp_val, sep = "|"),
drp_val
)
# Update text box.
svalue(h$obj) <- new
# Update column name table.
tmp_tbl <- stack_tbl[, ] # Get all values.
print(tmp_tbl)
tmp_tbl <- tmp_tbl[tmp_tbl != drp_val] # Remove value added to selected.
stack_tbl[, ] <- tmp_tbl # Update table.
})
# OPTIONS ###################################################################
option_frm <- gframe(text = strFrmOptions, horizontal = FALSE, container = g0)
keep_chk <- gcheckbox(text = strChkKeep, checked = TRUE, container = option_frm)
glabel(text = strLblKeep, container = option_frm, anchor = c(-1, 0))
# SAVE ######################################################################
save_frame <- gframe(text = strFrmSave, container = g2)
glabel(text = strLblSave, container = save_frame)
save_edt <- gedit(expand = TRUE, fill = TRUE, container = save_frame)
# BUTTON ####################################################################
slim_btn <- gbutton(text = strBtnSlim, container = g2)
addHandlerClicked(slim_btn, handler = function(h, ...) {
# Get new dataset name.
val_name <- svalue(save_edt)
val_data <- .gData
val_data_name <- .gDataName
if (nchar(val_name) > 0) {
# Get values.
fix_val <- svalue(fix_edt)
stack_val <- svalue(stack_edt)
keep_val <- svalue(keep_chk)
# Slim require a vector of strings.
fix_val <- unlist(strsplit(fix_val, "|", fixed = TRUE))
stack_val <- unlist(strsplit(stack_val, "|", fixed = TRUE))
if (debug) {
print("val_data")
print(names(val_data))
print("fix_val")
print(fix_val)
print("stack_val")
print(stack_val)
print("keep_val")
print(keep_val)
}
# Change button.
blockHandlers(slim_btn)
svalue(slim_btn) <- strBtnProcessing
unblockHandlers(slim_btn)
enabled(slim_btn) <- FALSE
datanew <- slim(
data = val_data, fix = fix_val, stack = stack_val,
keep.na = keep_val, debug = debug
)
# Create key-value pairs to log.
keys <- list("data", "fix", "stack", "keep.na")
values <- list(val_data_name, fix_val, stack_val, keep_val)
# 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 = strMsgName,
title = strMsgTitleError,
icon = "error",
parent = w
)
}
})
# INTERNAL FUNCTIONS ########################################################
.refresh_fix_tbl <- function() {
if (debug) {
print(paste("IN:", match.call()[[1]]))
}
# Refresh widget by removing it and...
delete(fix_f, fix_tbl)
# ...creating a new table.
fix_tbl <<- gWidgets2::gtable(
items = names(.gData),
container = fix_f,
expand = TRUE
)
addDropSource(fix_tbl, handler = function(h, ...) svalue(h$obj))
addHandlerDoubleclick(fix_tbl, handler = function(h, ...) {
# Get values.
tbl_val <- svalue(h$obj)
fix_val <- svalue(fix_edt)
# Add new value to selected.
new <- ifelse(nchar(fix_val) > 0,
paste(fix_val, tbl_val, sep = "|"),
tbl_val
)
# Update text box.
svalue(fix_edt) <- new
# Update sample name table.
tmp_tbl <- fix_tbl[, ] # Get all values.
tmp_tbl <- tmp_tbl[tmp_tbl != tbl_val] # Remove value added to selected.
fix_tbl[, ] <- tmp_tbl # Update table.
})
}
.refresh_stack_tbl <- function() {
if (debug) {
print(paste("IN:", match.call()[[1]]))
}
# Refresh widget by removing it and...
delete(stack_f, stack_tbl)
# ...creating a new table.
stack_tbl <<- gWidgets2::gtable(
items = names(.gData),
container = stack_f,
expand = TRUE
)
addDropSource(stack_tbl, handler = function(h, ...) svalue(h$obj))
addHandlerDoubleclick(stack_tbl, handler = function(h, ...) {
# Get values.
tbl_val <- svalue(h$obj)
stack_val <- svalue(stack_edt)
# Add new value to selected.
new <- ifelse(nchar(stack_val) > 0,
paste(stack_val, tbl_val, sep = "|"),
tbl_val
)
# Update text box.
svalue(stack_edt) <- new
# Update column name table.
tmp_tbl <- stack_tbl[, ] # Get all values.
tmp_tbl <- tmp_tbl[tmp_tbl != tbl_val] # Remove value added to selected.
stack_tbl[, ] <- tmp_tbl # Update table.
})
}
.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_slim_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_slim_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_slim_gui_title", envir = env, inherits = FALSE)) {
svalue(keep_chk) <- get(".strvalidator_slim_gui_title", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_slim_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_slim_gui_title", value = svalue(keep_chk), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_slim_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_slim_gui_savegui", envir = env)
}
if (exists(".strvalidator_slim_gui_title", envir = env, inherits = FALSE)) {
remove(".strvalidator_slim_gui_title", 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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