################################################################################
# CHANGE LOG (last 20 changes)
# 02.09.2022: Compacted the gui.
# 03.03.2020: Fixed reference to function name.
# 01.03.2020: Added language support.
# 10.01.2020: Changed "LDT" to "AT" following the book.
# 17.02.2019: Fixed Error in if (svalue(savegui_chk)) { : argument is of length zero (tcltk)
# 17.07.2018: 'Save as' textbox expandable.
# 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'.
# 15.08.2016: Implemented new calculateHeight, removed calculateHeterozygous.
# 29.06.2016: Added option to remove sex markers and quality sensor.
# 16.06.2016: 'Save as' textbox expandable.
# 05.10.2015: Added more attributes to result.
# 04.10.2015: Added automatic calculation of average peak height 'H'.
# 28.08.2015: Added importFrom
# 05.05.2015: Changed parameter 'ignoreCase' to 'ignore.case' for 'checkSubset' function.
# 13.12.2014: Added kit dropdown and kit attribute to result.
# 11.10.2014: Added 'focus', added 'parent' parameter.
# 28.06.2014: Added help button and moved save gui checkbox.
#' @title Calculate Dropout Events
#'
#' @description
#' GUI wrapper for the \code{\link{calculateDropout}} function.
#'
#' @details Scores dropouts for a dataset.
#' @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
#' @importFrom graphics title
#'
#' @seealso \code{\link{calculateDropout}}, \code{\link{checkSubset}}
calculateDropout_gui <- function(env = parent.frame(), savegui = NULL,
debug = FALSE, parent = NULL) {
# Global variables.
.gData <- NULL
.gRef <- NULL
# Language ------------------------------------------------------------------
# Get this functions name from call.
fnc <- as.character(match.call()[[1]])
if (debug) {
print(paste("IN:", fnc))
}
# Default strings.
strWinTitle <- "Calculate dropout"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Dataset and kit"
strLblDataset <- "Sample dataset:"
strDrpDefault <- "<Select dataset>"
strLblSamples <- "samples"
strLblRefDataset <- "Reference dataset:"
strLblRef <- "references"
strBtnCheck <- "Check subsetting"
strLblKit <- "Kit:"
strFrmOptions <- "Options"
strChkIgnore <- "Ignore case"
strChkSex <- "Remove sex markers"
strChkSensors <- "Remove quality sensors"
strChkAverage <- "Calculate average peak height"
strLblAt <- "Analytical threshold (AT):"
strLblMethods <- "Select one or more dropout scoring methods:"
strChkMethod1 <- "Score dropout relative to the low molecular weight allele"
strChkMethod2 <- "Score dropout relative to the high molecular weight allele"
strChkMethodX <- "Score dropout relative to a random allele"
strChkMethodL <- "Score dropout per locus"
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"
strWinTitleCheck <- "Check subsetting"
strMsgCheck <- "Data frame is NULL!\n\nMake sure to select a sample dataset and a reference dataset."
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"]$value
strLblDataset <- ifelse(is.na(strtmp), strLblDataset, strtmp)
strtmp <- dtStrings["strDrpDefault"]$value
strDrpDefault <- ifelse(is.na(strtmp), strDrpDefault, 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["strChkIgnore"]$value
strChkIgnore <- ifelse(is.na(strtmp), strChkIgnore, strtmp)
strtmp <- dtStrings["strChkSex"]$value
strChkSex <- ifelse(is.na(strtmp), strChkSex, strtmp)
strtmp <- dtStrings["strChkSensors"]$value
strChkSensors <- ifelse(is.na(strtmp), strChkSensors, strtmp)
strtmp <- dtStrings["strChkAverage"]$value
strChkAverage <- ifelse(is.na(strtmp), strChkAverage, strtmp)
strtmp <- dtStrings["strLblMethods"]$value
strLblMethods <- ifelse(is.na(strtmp), strLblMethods, strtmp)
strtmp <- dtStrings["strChkMethod1"]$value
strChkMethod1 <- ifelse(is.na(strtmp), strChkMethod1, strtmp)
strtmp <- dtStrings["strChkMethod2"]$value
strChkMethod2 <- ifelse(is.na(strtmp), strChkMethod2, strtmp)
strtmp <- dtStrings["strChkMethodX"]$value
strChkMethodX <- ifelse(is.na(strtmp), strChkMethodX, strtmp)
strtmp <- dtStrings["strChkMethodL"]$value
strChkMethodL <- ifelse(is.na(strtmp), strChkMethodL, strtmp)
strtmp <- dtStrings["strFrmSave"]$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)
}
# ---------------------------------------------------------------------------
# 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,
# fill = "x"
)
# Help button group.
gh <- ggroup(container = gv, expand = FALSE, fill = "x")
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 ------------------------------------------------------------------
g0 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblDataset, container = g0)
g0_samples_lbl <- glabel(
text = paste(" 0", strLblSamples),
container = g0
)
dataset_drp <- gcombobox(
items = c(
strDrpDefault,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1,
editable = FALSE,
container = g0,
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", "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)
samples <- length(unique(.gData$Sample.Name))
svalue(g0_samples_lbl) <- paste("", samples, strLblSamples)
svalue(f1g1_at_edt) <- min(as.numeric(.gData$Height), na.rm = TRUE)
# Suggest a name for result.
svalue(f2_save_edt) <- paste(val_obj, "_dropout", sep = "")
# Detect kit.
kitIndex <- detectKit(.gData, index = TRUE)
# Select in dropdown.
svalue(kit_drp, index = TRUE) <- kitIndex
} else {
# Reset components.
.gData <<- NULL
svalue(dataset_drp, index = TRUE) <- 1
svalue(g0_samples_lbl) <- paste(" 0", strLblSamples)
svalue(f1g1_at_edt) <- ""
svalue(f2_save_edt) <- ""
}
})
g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblRefDataset, container = g1)
ref_lbl <- glabel(
text = paste(" 0", strLblRef),
container = g1
)
refset_drp <- gcombobox(
items = c(
strDrpDefault,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1,
editable = FALSE,
container = g1,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(refset_drp, handler = function(h, ...) {
val_obj <- svalue(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)
ref <- length(unique(.gRef$Sample.Name))
svalue(ref_lbl) <- paste("", ref, strLblRef)
} else {
# Reset components.
.gRef <<- NULL
svalue(refset_drp, index = TRUE) <- 1
svalue(ref_lbl) <- paste(" 0", strLblRef)
}
})
# Kit -----------------------------------------------------------------------
g2 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblKit, container = g2)
kit_drp <- gcombobox(
items = getKit(), selected = 1,
editable = FALSE, container = g2,
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
val_ignore <- svalue(f1_ignore_case_chk)
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 = val_ignore,
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"
)
}
})
# FRAME 1 ###################################################################
f1 <- gframe(
text = strFrmOptions,
horizontal = FALSE,
spacing = 1,
container = gv
)
f1_ignore_case_chk <- gcheckbox(
text = strChkIgnore, checked = TRUE,
container = f1
)
f1_sex_chk <- gcheckbox(
text = strChkSex, checked = FALSE,
container = f1
)
f1_qs_chk <- gcheckbox(
text = strChkSensors, checked = TRUE,
container = f1
)
f1_h_chk <- gcheckbox(
text = strChkAverage, checked = TRUE,
container = f1
)
f1g1 <- glayout(container = f1)
f1g1[1, 1] <- glabel(
text = strLblAt,
container = f1g1, anchor = c(-1, 0)
)
f1g1[1, 2] <- f1g1_at_edt <- gedit(text = "", width = 6, container = f1g1)
glabel(
text = strLblMethods,
container = f1, anchor = c(-1, 0)
)
f1_score1_chk <- gcheckbox(
text = strChkMethod1,
checked = TRUE, container = f1
)
f1_score2_chk <- gcheckbox(
text = strChkMethod2,
checked = TRUE, container = f1
)
f1_scorex_chk <- gcheckbox(
text = strChkMethodX,
checked = TRUE, container = f1
)
f1_scorel_chk <- gcheckbox(
text = strChkMethodL,
checked = TRUE, container = f1
)
# FRAME 2 ###################################################################
f2 <- gframe(
text = strFrmSave,
horizontal = TRUE,
spacing = 1,
container = gv
)
glabel(text = strLblSave, container = f2)
f2_save_edt <- gedit(expand = TRUE, fill = "x", container = f2)
# BUTTON ####################################################################
dropout_btn <- gbutton(text = strBtnCalculate, container = gv)
addHandlerClicked(dropout_btn, handler = function(h, ...) {
val_data <- .gData
val_ref <- .gRef
val_name_data <- svalue(dataset_drp)
val_name_ref <- svalue(refset_drp)
val_ignore_case <- svalue(f1_ignore_case_chk)
val_h <- svalue(f1_h_chk)
val_threshold <- as.numeric(svalue(f1g1_at_edt))
val_name <- svalue(f2_save_edt)
val_kit <- svalue(kit_drp)
val_method <- vector()
val_sex <- svalue(f1_sex_chk)
val_qs <- svalue(f1_qs_chk)
# Get methods:
if (svalue(f1_score1_chk)) {
val_method <- c(val_method, "1")
}
if (svalue(f1_score2_chk)) {
val_method <- c(val_method, "2")
}
if (svalue(f1_scorex_chk)) {
val_method <- c(val_method, "X")
}
if (svalue(f1_scorel_chk)) {
val_method <- c(val_method, "L")
}
if (debug) {
print("GUI options:")
print("val_ignore_case")
print(val_ignore_case)
print("val_threshold")
print(val_threshold)
print("val_name")
print(val_name)
print("val_method")
print(val_method)
}
# No threshold is represented by NULL (not needed).
if (length(val_threshold) == 0) {
val_threshold <- NULL
}
if (debug) {
print("Function arguments:")
print("val_ignore_case")
print(val_ignore_case)
print("val_threshold")
print(val_threshold)
print("val_name")
print(val_name)
print("val_sex")
print(val_sex)
print("val_qs")
print(val_qs)
}
if (!is.null(val_data) & !is.null(val_ref)) {
# Change button.
blockHandlers(dropout_btn)
svalue(dropout_btn) <- strBtnProcessing
unblockHandlers(dropout_btn)
enabled(dropout_btn) <- FALSE
datanew <- calculateDropout(
data = val_data,
ref = val_ref,
threshold = val_threshold,
method = val_method,
ignore.case = val_ignore_case,
sex.rm = val_sex,
qs.rm = val_qs,
kit = val_kit,
debug = debug
)
# Add attributes to result.
attr(datanew, which = "kit") <- val_kit
# Create key-value pairs to log.
keys <- list(
"data", "ref", "threshold", "method",
"ignore.case", "sex.rm", "qs.rm", "kit", "calculate.h"
)
values <- list(
val_name_data, val_name_ref, val_threshold, val_method,
val_ignore_case, val_sex, val_qs, val_kit, val_h
)
# Update audit trail.
datanew <- auditTrail(
obj = datanew, key = keys, value = values,
label = fnc, arguments = FALSE,
package = "strvalidator"
)
# Calculate and add average peak height.
if (val_h) {
message("User selected to add average peak height...")
# Calculate average peak height.
dfH <- calculateHeight(
data = val_data, ref = val_ref, na.replace = 0,
add = FALSE, exclude = "OL", sex.rm = val_sex,
qs.rm = val_qs, kit = val_kit,
ignore.case = val_ignore_case, exact = FALSE,
debug = debug
)
message("Average peak height calculated.")
# Add average peak height to dataset.
datanew <- addData(
data = datanew, new.data = dfH,
by.col = "Sample.Name", then.by.col = NULL,
exact = TRUE, ignore.case = val_ignore_case,
debug = debug
)
message("Average peak height added to result.")
}
# Save data.
saveObject(name = val_name, object = datanew, parent = w, env = env)
if (debug) {
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_calculateDropout_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculateDropout_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_calculateDropout_gui_ignore", envir = env, inherits = FALSE)) {
svalue(f1_ignore_case_chk) <- get(".strvalidator_calculateDropout_gui_ignore", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_sex", envir = env, inherits = FALSE)) {
svalue(f1_sex_chk) <- get(".strvalidator_calculateDropout_gui_sex", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_qs", envir = env, inherits = FALSE)) {
svalue(f1_qs_chk) <- get(".strvalidator_calculateDropout_gui_qs", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_h", envir = env, inherits = FALSE)) {
svalue(f1_h_chk) <- get(".strvalidator_calculateDropout_gui_h", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_score1", envir = env, inherits = FALSE)) {
svalue(f1_score1_chk) <- get(".strvalidator_calculateDropout_gui_score1", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_score2", envir = env, inherits = FALSE)) {
svalue(f1_score2_chk) <- get(".strvalidator_calculateDropout_gui_score2", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_scorex", envir = env, inherits = FALSE)) {
svalue(f1_scorex_chk) <- get(".strvalidator_calculateDropout_gui_scorex", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_scorel", envir = env, inherits = FALSE)) {
svalue(f1_scorel_chk) <- get(".strvalidator_calculateDropout_gui_scorel", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculateDropout_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculateDropout_gui_ignore", value = svalue(f1_ignore_case_chk), envir = env)
assign(x = ".strvalidator_calculateDropout_gui_sex", value = svalue(f1_sex_chk), envir = env)
assign(x = ".strvalidator_calculateDropout_gui_qs", value = svalue(f1_qs_chk), envir = env)
assign(x = ".strvalidator_calculateDropout_gui_h", value = svalue(f1_h_chk), envir = env)
assign(x = ".strvalidator_calculateDropout_gui_score1", value = svalue(f1_score1_chk), envir = env)
assign(x = ".strvalidator_calculateDropout_gui_score2", value = svalue(f1_score2_chk), envir = env)
assign(x = ".strvalidator_calculateDropout_gui_scorex", value = svalue(f1_scorex_chk), envir = env)
assign(x = ".strvalidator_calculateDropout_gui_scorel", value = svalue(f1_scorel_chk), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculateDropout_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateDropout_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_ignore", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateDropout_gui_ignore", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_sex", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateDropout_gui_sex", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_qs", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateDropout_gui_qs", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_h", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateDropout_gui_h", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_score1", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateDropout_gui_score1", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_score2", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateDropout_gui_score2", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_scorex", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateDropout_gui_scorex", envir = env)
}
if (exists(".strvalidator_calculateDropout_gui_scorel", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateDropout_gui_scorel", 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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