# NOTE: As of version 2.2.0 of strvalidator gdf generates an error when gui is closed.
# (R version 3.6.2, gWidgets2RGtk2_1.0-7, gWidgets2_1.0-8, RGtk2_2.20.36)
# (rsession.exe:20768): Gtk-CRITICAL **: gtk_tree_view_unref_tree_helper: assertion `node != NULL' failed
# Issue reported here: https://github.com/jverzani/gWidgets2/issues/11
################################################################################
# CHANGE LOG (last 20 changes)
# 03.09.2022: Compacted gui. Fixed narrow dropdowns. Removed destroy workaround.
# 31.08.2022: Compacted the gui. Fixed Replacement table not expanding.
# 12.08.2022: Changed logical (-> NA in tcltk) to strings in replace-false-stutter df + check for NAs.
# 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'.
# 28.04.2016: 'Save as' textbox expandable.
# 26.10.2015: Added attributes.
# 28.08.2015: Added importFrom.
# 05.05.2015: Changed parameter 'ignoreCase' to 'ignore.case' for 'checkSubset' function.
# 05.01.2015: Added kit dropdown and kit attribute to result.
# 07.10.2014: Added 'focus', added 'parent' parameter.
# 03.08.2014: Added detection of kit and add attribute to result.
# 28.06.2014: Added help button and moved save gui checkbox.
# 08.05.2014: Implemented 'checkDataset'.
# 26.07.2013: Changed parameter 'fixed' to 'word' for 'checkSubset' function.
# 18.07.2013: Check before overwrite object.
# 17.07.2013: Added save GUI settings.
# 17.07.2013: 'false' allele checkboxes replaced by gdf table.
#' @title Calculate Stutter
#'
#' @description
#' GUI wrapper for the \code{\link{calculateStutter}} function.
#'
#' @details
#' Simplifies the use of the \code{\link{calculateStutter}} 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.
#'
#' @export
#'
#' @importFrom utils help head
#' @importFrom graphics title
#'
#' @return TRUE
#'
#' @seealso \code{\link{calculateStutter}}, \code{\link{checkSubset}}
calculateStutter_gui <- function(env = parent.frame(), savegui = NULL, debug = FALSE, parent = NULL) {
# Global variables.
.gData <- NULL
.gRef <- NULL
.gDataName <- NULL
.gRefName <- NULL
# Language ------------------------------------------------------------------
# Get this functions name from call.
fnc <- as.character(match.call()[[1]])
if (debug) {
print(paste("IN:", fnc))
}
# Default strings.
strWinTitle <- "Calculate stutter ratio"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Datasets"
strLblDataset <- "Sample dataset:"
strDrpDataset <- "<Select dataset>"
strLblSamples <- "samples"
strLblRefDataset <- "Reference dataset:"
strLblRef <- "references"
strBtnCheck <- "Check subsetting"
strLblKit <- "Kit:"
strFrmOptions <- "Options"
strLblRange <- "Calculate stutter ratio within the following analysis range:"
strLblBack <- "back stutters to"
strLblForward <- "forward stutters."
strLblNB <- "NB! Additive effects outside the analysis range cannot be controlled.\nA narrow range like 0 to 1 can be greately affected by neighbouring -1 stutters."
strLblInterference <- "Level of interference within the given range:"
strRadNone <- "no overlap between stutters and alleles"
strRadStutter <- "stutter-stutter overlap allowed"
strRadAllele <- "stutter-allele overlap allowed"
strLblReplace <- "Replace 'false' stutters:"
strFrmSave <- "Save as"
strLblSave <- "Name for result:"
strBtnCalculate <- "Calculate"
strBtnProcessing <- "Processing..."
strMsgDataset <- "A sample dataset and a reference dataset must be selected."
strMsgTitleDataset <- "Dataset not selected"
strMsgCheck <- "Data frame is NULL!\n\nMake sure to select a sample dataset."
strWinTitleCheck <- "Check subsetting"
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"]$value
strLblSamples <- ifelse(is.na(strtmp), strLblSamples, strtmp)
strtmp <- dtStrings["strLblRefDataset"]$value
strLblRefDataset <- ifelse(is.na(strtmp), strLblRefDataset, strtmp)
strtmp <- dtStrings["strLblRef"]$value
strLblRef <- ifelse(is.na(strtmp), strLblRef, strtmp)
strtmp <- dtStrings["strBtnCheck"]$value
strBtnCheck <- ifelse(is.na(strtmp), strBtnCheck, 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["strLblRange"]$value
strLblRange <- ifelse(is.na(strtmp), strLblRange, strtmp)
strtmp <- dtStrings["strLblBack"]$value
strLblBack <- ifelse(is.na(strtmp), strLblBack, strtmp)
strtmp <- dtStrings["strLblForward"]$value
strLblForward <- ifelse(is.na(strtmp), strLblForward, strtmp)
strtmp <- dtStrings["strLblNB"]$value
strLblNB <- ifelse(is.na(strtmp), strLblNB, strtmp)
strtmp <- dtStrings["strLblInterference"]$value
strLblInterference <- ifelse(is.na(strtmp), strLblInterference, strtmp)
strtmp <- dtStrings["strRadNone"]$value
strRadNone <- ifelse(is.na(strtmp), strRadNone, strtmp)
strtmp <- dtStrings["strRadStutter"]$value
strRadStutter <- ifelse(is.na(strtmp), strRadStutter, strtmp)
strtmp <- dtStrings["strRadAllele"]$value
strRadAllele <- ifelse(is.na(strtmp), strRadAllele, strtmp)
strtmp <- dtStrings["strLblReplace"]$value
strLblReplace <- ifelse(is.na(strtmp), strLblReplace, strtmp)
strtmp <- dtStrings["strFrmSave"]$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"]$value
strMsgTitleDataset <- ifelse(is.na(strtmp), strMsgTitleDataset, strtmp)
strtmp <- dtStrings["strMsgCheck"]$value
strMsgCheck <- ifelse(is.na(strtmp), strMsgCheck, strtmp)
strtmp <- dtStrings["strWinTitleCheck"]$value
strWinTitleCheck <- ifelse(is.na(strtmp), strWinTitleCheck, strtmp)
strtmp <- dtStrings["strMsgTitleError"]$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 = 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"))
})
# FRAME 0 ###################################################################
f0 <- gframe(
text = strFrmDataset,
horizontal = FALSE,
spacing = 1,
container = gv,
expand = FALSE,
fill = "x"
)
# Datasets ------------------------------------------------------------------
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_dataset_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(f0_dataset_drp, handler = function(h, ...) {
val_obj <- svalue(f0_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$Sample.Name))
svalue(f0_samples_lbl) <- paste("", samples, strLblSamples)
svalue(save_edt) <- paste(val_obj, "_stutter", sep = "")
# Detect kit.
kitIndex <- detectKit(.gData, index = TRUE)
# Select in dropdown.
svalue(kit_drp, index = TRUE) <- kitIndex
} else {
# Reset components.
.gData <<- NULL
.gDataName <<- NULL
svalue(f0_dataset_drp, index = TRUE) <- 1
svalue(f0_samples_lbl) <- paste(" 0", strLblSamples)
svalue(save_edt) <- ""
}
})
f0g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblRefDataset, container = f0g1)
f0_ref_lbl <- glabel(
text = paste(" 0", strLblRef),
container = f0g1
)
f0_refset_drp <- gcombobox(
items = c(
strDrpDataset,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1,
editable = FALSE,
container = f0g1,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(f0_refset_drp, handler = function(h, ...) {
val_obj <- svalue(f0_refset_drp)
# Check if suitable.
requiredCol <- c("Sample.Name", "Marker", "Allele")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
.gRef <<- get(val_obj, envir = env)
.gRefName <<- val_obj
refs <- length(unique(.gRef$Sample.Name))
svalue(f0_ref_lbl) <- paste("", refs, strLblRef)
} else {
# Reset components.
.gRef <<- NULL
.gRefName <<- NULL
svalue(f0_refset_drp, index = TRUE) <- 1
svalue(f0_ref_lbl) <- paste(" 0", strLblRef)
}
})
# Kit -----------------------------------------------------------------------
f0g2 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblKit, container = f0g2)
kit_drp <- gcombobox(
items = getKit(), selected = 1,
editable = FALSE, container = f0g2,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
# CHECK #####################################################################
check_btn <- gbutton(text = strBtnCheck, container = gv)
addHandlerChanged(check_btn, handler = function(h, ...) {
# Get values.
val_data <- .gData
val_ref <- .gRef
if (!is.null(.gData) || !is.null(.gRef)) {
chksubset_w <- gwindow(
title = strWinTitleCheck,
visible = FALSE, name = title,
width = NULL, height = NULL, parent = w,
handler = NULL, action = NULL
)
chksubset_txt <- checkSubset(
data = val_data,
ref = val_ref,
console = FALSE,
ignore.case = TRUE,
word = FALSE
)
gtext(
text = chksubset_txt, width = NULL, height = 300, font.attr = NULL,
wrap = FALSE, container = chksubset_w
)
visible(chksubset_w) <- TRUE
} else {
gmessage(
msg = strMsgCheck,
title = strMsgTitleError,
icon = "error"
)
}
})
# OPTIONS ###################################################################
f1 <- gframe(strFrmOptions,
spacing = 1,
horizontal = FALSE, container = gv,
expand = TRUE, fill = TRUE
)
glabel(text = strLblRange, container = f1, anchor = c(-1, 0))
f1g1 <- ggroup(
horizontal = TRUE,
spacing = 1,
use.scrollwindow = FALSE,
container = f1
)
f1g1_range_b_spb <- gspinbutton(
from = 0, to = 3, by = 1,
value = 1, digits = 0,
container = f1g1
)
glabel(text = strLblBack, container = f1g1, anchor = c(-1, 0))
f1g1_range_f_spb <- gspinbutton(
from = 0, to = 3, by = 1,
value = 1, digits = 0,
container = f1g1
)
glabel(text = strLblForward, container = f1g1, anchor = c(-1, 0))
glabel(text = strLblNB, container = f1, anchor = c(-1, 0))
# INTERFERENCE --------------------------------------------------------------
glabel(text = strLblInterference, container = f1, anchor = c(-1, 0))
options <- c(strRadNone, strRadStutter, strRadAllele)
interference_opt <- gradio(
items = options, selected = 1,
horizontal = FALSE, container = f1
)
# FALSE STUTTERS ------------------------------------------------------------
glabel(text = strLblReplace, container = f1, anchor = c(-1, 0))
# Create default data frame.
replace_val <- c(-1.9, -1.8, -1.7, -0.9, -0.8, -0.7, 0.9, 0.8, 0.7)
by_val <- c(-1.3, -1.2, -1.1, -0.3, -0.2, -0.1, 0.3, 0.2, 0.1)
default <- data.frame(
False.Stutter = replace_val,
True.Stutter = by_val,
Replace = rep("TRUE", length(replace_val)),
stringsAsFactors = FALSE
)
# gdf generates an error when gui is closed.
# (rsession.exe:20768): Gtk-CRITICAL **: gtk_tree_view_unref_tree_helper: assertion `node != NULL' failed
# Issue reported here: https://github.com/jverzani/gWidgets2/issues/11
default_gdf <- gdf(items = default, container = f1, expand = TRUE, fill = TRUE)
# Set initial minimum size.
size(default_gdf) <- c(100, 100)
# 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, ...) {
# Get values.
val_back <- svalue(f1g1_range_b_spb)
val_forward <- svalue(f1g1_range_f_spb)
val_interference <- svalue(interference_opt, index = TRUE) - 1 # NB! range [0-2]
val_data <- .gData
val_ref <- .gRef
val_name_data <- .gDataName
val_name_ref <- .gRefName
val_name <- svalue(save_edt)
val_replace_df <- default_gdf[]
val_chk <- as.logical(val_replace_df$Replace) # Convert strings to logicals.
val_replace <- val_replace_df$False.Stutter
val_by <- val_replace_df$True.Stutter
val_kit <- svalue(kit_drp)
# Check for NAs.
num_na <- sum(is.na(val_chk))
if (num_na > 0) {
val_chk[is.na(val_chk)] <- FALSE
message("Replaced ", num_na, " non TRUE/FALSE strings in column Replace by FALSE")
}
# Get selected values.
val_replace <- val_replace[val_chk]
val_by <- val_by[val_chk]
if (length(val_replace) == 0) {
val_replace <- NULL
}
if (length(val_by) == 0) {
val_by <- NULL
}
if (!is.null(val_data) & !is.null(val_ref)) {
if (debug) {
print("val_data")
print(head(val_data))
print("val_ref")
print(head(val_ref))
print("val_back")
print(val_back)
print("val_forward")
print(val_forward)
print("val_interference")
print(val_interference)
print("val_replace")
print(val_replace)
print("val_by")
print(val_by)
}
# Change button.
blockHandlers(calculate_btn)
svalue(calculate_btn) <- strBtnProcessing
unblockHandlers(calculate_btn)
enabled(calculate_btn) <- FALSE
# Calculate stutter.
datanew <- calculateStutter(
data = val_data, ref = val_ref,
back = val_back, forward = val_forward,
interference = val_interference,
replace.val = val_replace,
by.val = val_by,
debug = debug
)
# Add attributes to result.
attr(datanew, which = "kit") <- val_kit
# Create key-value pairs to log.
keys <- list(
"data", "ref", "back", "forward",
"interference", "replace.val", "by.val"
)
values <- list(
val_name_data, val_name_ref, val_back, val_forward,
val_interference, val_replace, val_by
)
# 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(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_calculateStutter_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculateStutter_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_calculateStutter_gui_back", envir = env, inherits = FALSE)) {
svalue(f1g1_range_b_spb) <- get(".strvalidator_calculateStutter_gui_back", envir = env)
}
if (exists(".strvalidator_calculateStutter_gui_forward", envir = env, inherits = FALSE)) {
svalue(f1g1_range_f_spb) <- get(".strvalidator_calculateStutter_gui_forward", envir = env)
}
if (exists(".strvalidator_calculateStutter_gui_interference", envir = env, inherits = FALSE)) {
svalue(interference_opt) <- get(".strvalidator_calculateStutter_gui_interference", envir = env)
}
if (exists(".strvalidator_calculateStutter_gui_replace", envir = env, inherits = FALSE)) {
default_gdf[, ] <- get(".strvalidator_calculateStutter_gui_replace", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculateStutter_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculateStutter_gui_back", value = svalue(f1g1_range_b_spb), envir = env)
assign(x = ".strvalidator_calculateStutter_gui_forward", value = svalue(f1g1_range_f_spb), envir = env)
assign(x = ".strvalidator_calculateStutter_gui_interference", value = svalue(interference_opt), envir = env)
assign(x = ".strvalidator_calculateStutter_gui_replace", value = default_gdf[], envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculateStutter_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateStutter_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculateStutter_gui_back", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateStutter_gui_back", envir = env)
}
if (exists(".strvalidator_calculateStutter_gui_forward", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateStutter_gui_forward", envir = env)
}
if (exists(".strvalidator_calculateStutter_gui_interference", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateStutter_gui_interference", envir = env)
}
if (exists(".strvalidator_calculateStutter_gui_replace", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateStutter_gui_replace", 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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