################################################################################
# CHANGE LOG (last 20 changes)
# 08.09.2022: Compacted gui. Fixed narrow dropdowns. Removed destroy workaround.
# 07.03.2020: 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 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'.
# 19.05.2016: Implemented more accurat method and parameter 'quick'.
# 18.05.2016: Changed default of 'Round to nearest (bp)' from 1 to 1.5.
# Also changed min from 1 to 0 and step by from 1 to 0.1.
# 12.10.2015: First version.
#' @title Detect Spike
#'
#' @description
#' GUI wrapper for the \code{\link{calculateSpike}} function.
#'
#' @details Simplifies the use of the \code{\link{calculateSpike}} function
#' by providing a graphical user interface.
#' @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.
#'
#' @return TRUE
#'
#' @export
#'
#' @seealso \code{\link{calculateSpike}}
calculateSpike_gui <- function(env = parent.frame(), savegui = NULL, debug = FALSE, parent = NULL) {
.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 spikes"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Dataset"
strLblDataset <- "Sample dataset:"
strDrpDataset <- "<Select dataset>"
strLblSamples <- "samples"
strLblKit <- "Kit:"
strFrmOptions <- "Options"
strLblThreshold <- "Threshold (number of peaks at similar size):"
strLblTolerance <- "Tolerance (bp):"
strChkQuick <- "Quick and dirty"
strTipQuick <- "NB! The quick method may not catch all spikes since two peaks can be separated by rounding e.g. 200.5 and 200.6 becomes 200 and 201 respectively!"
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"]$value
strFrmOptions <- ifelse(is.na(strtmp), strFrmOptions, strtmp)
strtmp <- dtStrings["strLblThreshold"]$value
strLblThreshold <- ifelse(is.na(strtmp), strLblThreshold, strtmp)
strtmp <- dtStrings["strLblTolerance"]$value
strLblTolerance <- ifelse(is.na(strtmp), strLblTolerance, strtmp)
strtmp <- dtStrings["strChkQuick"]$value
strChkQuick <- ifelse(is.na(strtmp), strChkQuick, strtmp)
strtmp <- dtStrings["strTipQuick"]$value
strTipQuick <- ifelse(is.na(strtmp), strTipQuick, strtmp)
strtmp <- dtStrings["strFrmSave"]$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 ####################################################################
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
)
# 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", "File.Name", "Size")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
slim = TRUE, slimcol = "Size",
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(f2_save_edt) <- paste(.gDataName, "_spikes", 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(f2_save_edt) <- ""
}
})
# FRAME 1 ###################################################################
f1 <- gframe(
text = strFrmOptions,
horizontal = FALSE,
spacing = 1,
container = gv
)
f1g1 <- glayout(container = f1, spacing = 1)
f1g1[1, 1] <- glabel(
text = strLblThreshold,
container = f1g1
)
f1g1[1, 2] <- f1_threshold_spn <- gspinbutton(
from = 1, to = 10, by = 1,
value = 3, container = f1g1
)
f1g1[2, 1] <- glabel(text = strLblTolerance, container = f1g1)
f1g1[2, 2] <- f1_tolerance_spn <- gspinbutton(
from = 0, to = 10, by = 0.1,
value = 2, container = f1g1
)
f1_quick_chk <- gcheckbox(
text = strChkQuick, checked = FALSE,
container = f1
)
tooltip(f1_quick_chk) <- strTipQuick
# FRAME 2 ###################################################################
f2 <- gframe(text = strFrmSave, horizontal = TRUE, spacing = 1, container = gv)
glabel(text = strLblSave, container = f2)
f2_save_edt <- gedit(text = "", container = f2, expand = TRUE, fill = TRUE)
# BUTTON ####################################################################
calculate_btn <- gbutton(text = strBtnCalculate, container = gv)
addHandlerClicked(calculate_btn, handler = function(h, ...) {
# Get values.
val_data <- .gData
val_name_data <- .gDataName
val_threshold <- svalue(f1_threshold_spn)
val_tolerance <- svalue(f1_tolerance_spn)
val_kit <- svalue(kit_drp)
val_name <- svalue(f2_save_edt)
val_quick <- svalue(f1_quick_chk)
if (!is.null(val_data)) {
# Change button.
blockHandlers(calculate_btn)
svalue(calculate_btn) <- strBtnProcessing
unblockHandlers(calculate_btn)
enabled(calculate_btn) <- FALSE
datanew <- calculateSpike(
data = val_data,
threshold = val_threshold,
tolerance = val_tolerance,
kit = val_kit,
quick = val_quick,
debug = debug
)
# Add attributes to result.
attr(datanew, which = "kit") <- val_kit
# Create key-value pairs to log.
keys <- list(
"data", "threshold", "tolerance",
"quick", "kit"
)
values <- list(
val_name_data, val_threshold, val_tolerance,
val_quick, val_kit
)
# 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(str(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_calculateSpike_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculateSpike_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_calculateSpike_gui_threshold", envir = env, inherits = FALSE)) {
svalue(f1_threshold_spn) <- get(".strvalidator_calculateSpike_gui_threshold", envir = env)
}
if (exists(".strvalidator_calculateSpike_gui_tolerance", envir = env, inherits = FALSE)) {
svalue(f1_tolerance_spn) <- get(".strvalidator_calculateSpike_gui_tolerance", envir = env)
}
if (exists(".strvalidator_calculateSpike_gui_quick", envir = env, inherits = FALSE)) {
svalue(f1_quick_chk) <- get(".strvalidator_calculateSpike_gui_quick", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculateSpike_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculateSpike_gui_threshold", value = svalue(f1_threshold_spn), envir = env)
assign(x = ".strvalidator_calculateSpike_gui_tolerance", value = svalue(f1_tolerance_spn), envir = env)
assign(x = ".strvalidator_calculateSpike_gui_quick", value = svalue(f1_quick_chk), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculateSpike_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateSpike_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculateSpike_gui_threshold", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateSpike_gui_threshold", envir = env)
}
if (exists(".strvalidator_calculateSpike_gui_tolerance", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateSpike_gui_tolerance", envir = env)
}
if (exists(".strvalidator_calculateSpike_gui_quick", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateSpike_gui_quick", 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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