################################################################################
# CHANGE LOG (last 20 changes)
# 08.09.2022: Compacted gui. Fixed narrow dropdowns. Removed destroy workaround.
# 04.03.2020: Added language support.
# 17.02.2019: Fixed Error in if (svalue(savegui_chk)) { : argument is of length zero (tcltk)
# 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'.
# 10.05.2016: Added new option 'limit' to remove high ratios from the result.
# 10.05.2016: Added attributes to result.
# 10.05.2016: 'Save as' textbox expandable.
# 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.
# 04.12.2014: First version.
#' @title Calculate Spectral Pull-up
#'
#' @description
#' GUI wrapper for the \code{\link{calculatePullup}} function.
#'
#' @details
#' Simplifies the use of the \code{\link{calculatePullup}} 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
#' @importFrom graphics title
#'
#' @seealso \code{\link{calculatePullup}}, \code{\link{checkSubset}}
#'
calculatePullup_gui <- function(env = parent.frame(), savegui = NULL,
debug = FALSE, parent = NULL) {
# Global variables.
.gData <- NULL
.gDataName <- NULL
.gRef <- 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 spectral pull-up"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Datasets"
strLblDataset <- "Sample dataset:"
strDrpDefault <- "<Select dataset>"
strLblSamples <- "samples"
strLblRefDataset <- "Reference dataset:"
strLblRef <- "references"
strBtnCheck <- "Check subsetting"
strFrmOptions <- "Options"
strLblPre <- "Pre-processing:"
strChkOL <- "Remove off-ladder peaks"
strLblMethod <- "Pull-up settings:"
strLblRange <- "Pull-up analysis range (data points) around known alleles:"
strLblBlock <- "Blocking range (data points) around known alleles:"
strLblDiscard <- "Discard pull-ups with ratio >"
strLblMatching <- "Reference sample name matching:"
strChkIgnore <- "Ignore case"
strChkWord <- "Add word boundaries"
strLblPost <- "Post-processing:"
strChkDiscard <- "Discard alleles with no pull-up from the result table"
strFrmSave <- "Save as"
strLblSave <- "Name for result:"
strLblKit <- "Kit attribute:"
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"
strMsgNA <- "'NA' in 'Dye' column. \nUse add dye function to fix."
strMsgTitleNA <- "NA detected!"
# 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["strFrmOptions"]$value
strFrmOptions <- ifelse(is.na(strtmp), strFrmOptions, strtmp)
strtmp <- dtStrings["strLblPre"]$value
strLblPre <- ifelse(is.na(strtmp), strLblPre, strtmp)
strtmp <- dtStrings["strChkOL"]$value
strChkOL <- ifelse(is.na(strtmp), strChkOL, strtmp)
strtmp <- dtStrings["strLblMethod"]$value
strLblMethod <- ifelse(is.na(strtmp), strLblMethod, strtmp)
strtmp <- dtStrings["strLblRange"]$value
strLblRange <- ifelse(is.na(strtmp), strLblRange, strtmp)
strtmp <- dtStrings["strLblBlock"]$value
strLblBlock <- ifelse(is.na(strtmp), strLblBlock, strtmp)
strtmp <- dtStrings["strLblDiscard"]$value
strLblDiscard <- ifelse(is.na(strtmp), strLblDiscard, strtmp)
strtmp <- dtStrings["strLblMatching"]$value
strLblMatching <- ifelse(is.na(strtmp), strLblMatching, strtmp)
strtmp <- dtStrings["strChkIgnore"]$value
strChkIgnore <- ifelse(is.na(strtmp), strChkIgnore, strtmp)
strtmp <- dtStrings["strChkWord"]$value
strChkWord <- ifelse(is.na(strtmp), strChkWord, strtmp)
strtmp <- dtStrings["strLblPost"]$value
strLblPost <- ifelse(is.na(strtmp), strLblPost, strtmp)
strtmp <- dtStrings["strChkDiscard"]$value
strChkDiscard <- ifelse(is.na(strtmp), strChkDiscard, 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["strLblKit"]$value
strLblKit <- ifelse(is.na(strtmp), strLblKit, strtmp)
strtmp <- dtStrings["strBtnCalculate"]$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)
strtmp <- dtStrings["strMsgNA"]$value
strMsgNA <- ifelse(is.na(strtmp), strMsgNA, strtmp)
strtmp <- dtStrings["strMsgTitleNA"]$value
strMsgTitleNA <- ifelse(is.na(strtmp), strMsgTitleNA, 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
)
# Dataset -------------------------------------------------------------------
g0 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblDataset, container = g0)
data_samples_lbl <- glabel(
text = paste(" 0", strLblSamples),
container = g0
)
dfs <- c(strDrpDefault, listObjects(env = env, obj.class = "data.frame"))
g0_data_drp <- gcombobox(
items = dfs,
selected = 1,
editable = FALSE,
container = g0,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(g0_data_drp, handler = function(h, ...) {
val_obj <- svalue(g0_data_drp)
# Check if suitable.
requiredCol <- c("Sample.Name", "Allele", "Marker", "Dye", "Height", "Size", "Data.Point")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
slim = TRUE, slimcol = "Height",
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
# get dataset.
.gData <<- get(val_obj, envir = env)
.gDataName <<- val_obj
svalue(data_samples_lbl) <- paste(
length(unique(.gData$Sample.Name)),
strLblSamples
)
# Suggest a name for result.
svalue(save_edt) <- paste(val_obj, "_pullup", sep = "")
# Detect kit.
kitIndex <- detectKit(.gData, index = TRUE)
# Select in dropdown.
svalue(kit_drp, index = TRUE) <- kitIndex
} else {
# Reset components.
.gData <<- NULL
.gDataName <<- NULL
svalue(g0_data_drp, index = TRUE) <- 1
svalue(data_samples_lbl) <- paste(" 0", strLblSamples)
svalue(save_edt) <- ""
}
})
# Reference -----------------------------------------------------------------
g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblRefDataset, container = g1)
ref_samples_lbl <- glabel(
text = paste(" 0", strLblRef),
container = g1
)
# NB! dfs defined in previous section.
ref_drp <- gcombobox(
items = dfs,
selected = 1,
editable = FALSE,
container = g1,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(ref_drp, handler = function(h, ...) {
val_obj <- svalue(ref_drp)
# Check if suitable.
requiredCol <- c("Sample.Name", "Marker", "Allele")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
slim = TRUE, slimcol = "Allele",
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
.gRef <<- get(val_obj, envir = env)
.gRefName <<- val_obj
svalue(ref_samples_lbl) <- paste(
length(unique(.gRef$Sample.Name)),
strLblRef
)
} else {
# Reset components.
.gRef <<- NULL
.gRefName <<- NULL
svalue(ref_drp, index = TRUE) <- 1
svalue(ref_samples_lbl) <- paste(" 0", strLblRef)
}
})
# 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_chk)
val_word <- svalue(f1_word_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 = val_word
)
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
)
# PRE-PROCESSING ------------------------------------------------------------
glabel(text = strLblPre, anchor = c(-1, 0), container = f1)
f1_ol_chk <- gcheckbox(
text = strChkOL,
checked = FALSE,
container = f1
)
# METHOD --------------------------------------------------------------------
glabel(text = strLblMethod, anchor = c(-1, 0), container = f1)
f1g1 <- glayout(container = f1, anchor = c(-1, 0), spacing = 1)
f1g1[1, 1] <- glabel(text = strLblRange, anchor = c(-1, 0), container = f1g1)
f1g1[1, 2] <- f1_pullup_spb <- gspinbutton(from = 0, to = 1000, by = 10, value = 6, container = f1g1)
f1g1[2, 1] <- glabel(text = strLblBlock, anchor = c(-1, 0), container = f1g1)
f1g1[2, 2] <- f1_block_spb <- gspinbutton(from = 0, to = 1000, by = 10, value = 70, container = f1g1)
f1g1[3, 1] <- glabel(text = strLblDiscard, anchor = c(-1, 0), container = f1g1)
f1g1[3, 2] <- f1_limit_spb <- gspinbutton(from = 0, to = 10, by = 0.1, value = 1, container = f1g1)
# MATCHING ------------------------------------------------------------------
glabel(text = strLblMatching, anchor = c(-1, 0), container = f1)
f1_ignore_chk <- gcheckbox(
text = strChkIgnore,
checked = TRUE,
container = f1
)
f1_word_chk <- gcheckbox(
text = strChkWord,
checked = FALSE,
container = f1
)
# POST-PROCESSING -----------------------------------------------------------
glabel(text = strLblPost, anchor = c(-1, 0), container = f1)
f1_discard_chk <- gcheckbox(
text = strChkDiscard,
checked = FALSE,
container = f1
)
# SAVE ######################################################################
save_frame <- gframe(text = strFrmSave, container = gv)
glabel(text = strLblSave, container = save_frame)
save_edt <- gedit(expand = TRUE, fill = TRUE, container = save_frame)
glabel(text = strLblKit, container = save_frame)
kit_drp <- gcombobox(
items = getKit(), container = save_frame,
ellipsize = "none"
)
# BUTTON ####################################################################
calculate_btn <- gbutton(text = strBtnCalculate, container = gv)
addHandlerClicked(calculate_btn, handler = function(h, ...) {
# Get values.
val_data <- .gData
val_ref <- .gRef
val_name_data <- .gDataName
val_name_ref <- .gRefName
val_ignore <- svalue(f1_ignore_chk)
val_word <- svalue(f1_word_chk)
val_ol <- svalue(f1_ol_chk)
val_pullup <- svalue(f1_pullup_spb)
val_block <- svalue(f1_block_spb)
val_limit <- svalue(f1_limit_spb)
val_discard <- svalue(f1_discard_chk)
val_name <- svalue(save_edt)
val_kit <- svalue(kit_drp)
if (debug) {
print("Read Values:")
print("val_data")
print(head(val_data))
print("val_ref")
print(head(val_ref))
print("val_ignore")
print(val_ignore)
print("val_word")
print(val_word)
print("val_ol")
print(val_ol)
print("val_pullup")
print(val_pullup)
print("val_block")
print(val_block)
print("val_limit")
print(val_limit)
print("val_name")
print(val_name)
}
# Check if data.
if (!is.null(.gData) & !is.null(.gRef)) {
# Check for NA's in dye column.
if (!any(is.na(.gData$Dye))) {
# Change button.
blockHandlers(calculate_btn)
svalue(calculate_btn) <- strBtnProcessing
unblockHandlers(calculate_btn)
enabled(calculate_btn) <- FALSE
datanew <- calculatePullup(
data = val_data,
ref = val_ref,
pullup.range = val_pullup,
block.range = val_block,
ol.rm = val_ol,
ignore.case = val_ignore,
word = val_word,
discard = val_discard,
limit = val_limit,
debug = debug
)
# Add attributes to result.
attr(datanew, which = "kit") <- val_kit
# Create key-value pairs to log.
keys <- list(
"data", "ref", "pullup.range", "block.range", "ol.rm",
"ignore.case", "word", "discard", "limit"
)
values <- list(
val_name_data, val_name_ref, val_pullup, val_block, val_ol,
val_ignore, val_word, val_discard, val_limit
)
# 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(head(datanew))
print(paste("EXIT:", fnc))
}
# Close GUI.
.saveSettings()
dispose(w)
} else {
gmessage(
msg = strMsgNA,
title = strMsgTitleNA,
icon = "error",
parent = 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_calculatePullup_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculatePullup_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_calculatePullup_gui_window", envir = env, inherits = FALSE)) {
svalue(f1_pullup_spb) <- get(".strvalidator_calculatePullup_gui_window", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_block", envir = env, inherits = FALSE)) {
svalue(f1_block_spb) <- get(".strvalidator_calculatePullup_gui_block", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_limit", envir = env, inherits = FALSE)) {
svalue(f1_limit_spb) <- get(".strvalidator_calculatePullup_gui_limit", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_ol", envir = env, inherits = FALSE)) {
svalue(f1_ol_chk) <- get(".strvalidator_calculatePullup_gui_ol", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_ignore", envir = env, inherits = FALSE)) {
svalue(f1_ignore_chk) <- get(".strvalidator_calculatePullup_gui_ignore", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_word", envir = env, inherits = FALSE)) {
svalue(f1_word_chk) <- get(".strvalidator_calculatePullup_gui_word", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_discard", envir = env, inherits = FALSE)) {
svalue(f1_discard_chk) <- get(".strvalidator_calculatePullup_gui_discard", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculatePullup_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculatePullup_gui_window", value = svalue(f1_pullup_spb), envir = env)
assign(x = ".strvalidator_calculatePullup_gui_block", value = svalue(f1_block_spb), envir = env)
assign(x = ".strvalidator_calculatePullup_gui_limit", value = svalue(f1_limit_spb), envir = env)
assign(x = ".strvalidator_calculatePullup_gui_ol", value = svalue(f1_ol_chk), envir = env)
assign(x = ".strvalidator_calculatePullup_gui_ignore", value = svalue(f1_ignore_chk), envir = env)
assign(x = ".strvalidator_calculatePullup_gui_word", value = svalue(f1_word_chk), envir = env)
assign(x = ".strvalidator_calculatePullup_gui_discard", value = svalue(f1_discard_chk), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculatePullup_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculatePullup_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_window", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculatePullup_gui_window", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_block", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculatePullup_gui_block", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_limit", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculatePullup_gui_limit", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_ol", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculatePullup_gui_ol", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_ignore", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculatePullup_gui_ignore", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_word", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculatePullup_gui_word", envir = env)
}
if (exists(".strvalidator_calculatePullup_gui_discard", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculatePullup_gui_discard", 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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