Nothing
################################################################################
# CHANGE LOG (last 20 changes)
# 05.09.2022: Compacted gui. Fixed narrow dropdowns. Removed destroy workaround.
# 07.07.2022: Fixed "...URLs which should use \doi (with the DOI name only)".
# 03.03.2020: Fixed reference to function name.
# 02.03.2020: Added language support.
# 03.03.2019: Compacted and tweaked widgets under tcltk.
# 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'.
# 15.08.2016: Implemented new calculateHeight, selection of reference, and check subsetting.
# 08.07.2016: Fixed options 'sex.rm' and 'qs.rm' not saved.
# 29.06.2016: Implement 'checkDataset'.
# 29.06.2016: Added option to remove sex markers and quality sensor.
# 29.04.2016: 'Save as' textbox expandable.
# 06.01.2016: Added attributes to result.
# 28.08.2015: Added importFrom
# 11.10.2014: Added 'focus', added 'parent' parameter.
# 26.09.2014: Implemented text field for 'exclude'.
#' @title Calculate Peak Height
#'
#' @description
#' GUI wrapper for the \code{\link{calculateHeight}} function.
#'
#' @details
#' Simplifies the use of the \code{\link{calculateHeight}} 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
#'
#' @references
#' Torben Tvedebrink, Poul Svante Eriksen, Helle Smidt Mogensen, Niels Morling,
#' Evaluating the weight of evidence by using quantitative short tandem repeat data in DNA mixtures
#' Journal of the Royal Statistical Society: Series C (Applied Statistics),
#' Volume 59, Issue 5, 2010,
#' Pages 855-874, 10.1111/j.1467-9876.2010.00722.x.
#' \doi{10.1111/j.1467-9876.2010.00722.x}
#'
#' @seealso \code{\link{calculateHeight}}
calculateHeight_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 peak height"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Datasets"
strLblDataset <- "Sample dataset:"
strDrpDefault <- "<Select dataset>"
strLblSamples <- "samples"
strLblRefDataset <- "Reference dataset:"
strLblRef <- "references"
strBtnCheck <- "Check subsetting"
strLblKit <- "Kit:"
strFrmOptions <- "Options"
strLblPre <- "Pre-processing:"
strChkSex <- "Remove sex markers"
strChkSensors <- "Remove quality sensors"
strChkExclude <- "Exclude values in 'Allele' column"
strChkExcludeInfo <- "Case sensitive values separated by comma:"
strLblMatching <- "Reference sample name matching:"
strChkIgnore <- "Ignore case"
strChkExact <- "Exact matching"
strLblPost <- "Post-processing:"
strChkReplace <- "Replace NA in the result with 0"
strChkAdd <- "Add result to dataset"
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 and a reference 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"]$value
strLblDataset <- ifelse(is.na(strtmp), strLblDataset, strtmp)
strtmp <- dtStrings["strDrpDefault"]$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["strLblPre"]$value
strLblPre <- ifelse(is.na(strtmp), strLblPre, strtmp)
strtmp <- dtStrings["strChkSex"]$value
strChkSex <- ifelse(is.na(strtmp), strChkSex, strtmp)
strtmp <- dtStrings["strChkSensors"]$value
strChkSensors <- ifelse(is.na(strtmp), strChkSensors, strtmp)
strtmp <- dtStrings["strChkExclude"]$value
strChkExclude <- ifelse(is.na(strtmp), strChkExclude, strtmp)
strtmp <- dtStrings["strChkExcludeInfo"]$value
strChkExcludeInfo <- ifelse(is.na(strtmp), strChkExcludeInfo, strtmp)
strtmp <- dtStrings["strLblMatching"]$value
strLblMatching <- ifelse(is.na(strtmp), strLblMatching, strtmp)
strtmp <- dtStrings["strChkIgnore"]$value
strChkIgnore <- ifelse(is.na(strtmp), strChkIgnore, strtmp)
strtmp <- dtStrings["strChkExact"]$value
strChkExact <- ifelse(is.na(strtmp), strChkExact, strtmp)
strtmp <- dtStrings["strLblPost"]$value
strLblPost <- ifelse(is.na(strtmp), strLblPost, strtmp)
strtmp <- dtStrings["strChkReplace"]$value
strChkReplace <- ifelse(is.na(strtmp), strChkReplace, strtmp)
strtmp <- dtStrings["strChkAdd"]$value
strChkAdd <- ifelse(is.na(strtmp), strChkAdd, strtmp)
strtmp <- dtStrings["strFrmSave"]$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 = 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
)
# Samples -------------------------------------------------------------------
f0g0 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblDataset, container = f0g0)
samples_lbl <- glabel(
text = paste(" 0", strLblSamples),
container = f0g0
)
dataset_drp <- gcombobox(
items = c(
strDrpDefault,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1, editable = FALSE,
container = f0g0,
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", "Height")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
slim = TRUE, slimcol = "Height",
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$Sample.Name))
svalue(samples_lbl) <- paste("", samples, strLblSamples)
# Suggest name for the result.
svalue(save_edt) <- paste(val_obj, "_height", sep = "")
# Detect kit.
kitIndex <- detectKit(data = .gData, index = TRUE)
# Select in dropdown.
svalue(kit_drp, index = TRUE) <- kitIndex
} else {
# Reset components.
.gData <<- NULL
.gDataName <<- NULL
svalue(dataset_drp, index = TRUE) <- 1
svalue(samples_lbl) <- paste(" 0", strLblSamples)
svalue(save_edt) <- ""
}
})
# References ----------------------------------------------------------------
f0g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblRefDataset, container = f0g1)
ref_lbl <- glabel(
text = paste(" 0", strLblRef),
container = f0g1
)
refset_drp <- gcombobox(
items = c(
strDrpDefault,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1, editable = FALSE,
container = f0g1,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(refset_drp, handler = function(h, ...) {
val_obj <- svalue(refset_drp)
# Check if suitable.
requiredCol <- c("Sample.Name", "Marker", "Allele")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
slim = TRUE, slimcol = "Allele",
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
.gRef <<- get(val_obj, envir = env)
.gRefName <<- val_obj
ref <- length(unique(.gRef$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 -----------------------------------------------------------------------
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
val_ignore <- svalue(f1_ignore_chk)
val_exact <- svalue(f1_exact_chk)
val_word <- FALSE
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,
exact = val_exact,
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
)
glabel(text = strLblPre, anchor = c(-1, 0), container = f1)
f1_sex_chk <- gcheckbox(
text = strChkSex,
checked = FALSE, container = f1
)
f1_qs_chk <- gcheckbox(
text = strChkSensors,
checked = TRUE, container = f1
)
f1_exclude_chk <- gcheckbox(
text = strChkExclude,
checked = TRUE, container = f1
)
f1_exclude_lbl <- glabel(
text = strChkExcludeInfo,
anchor = c(-1, 0), container = f1
)
f1_exclude_edt <- gedit(text = "OL", container = f1)
glabel(text = strLblMatching, anchor = c(-1, 0), container = f1)
f1_ignore_chk <- gcheckbox(
text = strChkIgnore,
checked = TRUE, container = f1
)
f1_exact_chk <- gcheckbox(
text = strChkExact,
checked = FALSE, container = f1
)
glabel(text = strLblPost, anchor = c(-1, 0), container = f1)
f1_replace_chk <- gcheckbox(
text = strChkReplace,
checked = TRUE, container = f1
)
f1_add_chk <- gcheckbox(
text = strChkAdd,
checked = TRUE, container = f1
)
addHandlerChanged(f1_exclude_chk, handler = function(h, ...) {
if (svalue(f1_exclude_chk)) {
enabled(f1_exclude_lbl) <- TRUE
enabled(f1_exclude_edt) <- TRUE
} else {
enabled(f1_exclude_lbl) <- FALSE
enabled(f1_exclude_edt) <- FALSE
}
})
# 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, ...) {
val_data <- .gData
val_data_name <- .gDataName
val_ref <- .gRef
val_ref_name <- .gRefName
val_name <- svalue(save_edt)
val_add <- svalue(f1_add_chk)
val_sex <- svalue(f1_sex_chk)
val_qs <- svalue(f1_qs_chk)
val_kit <- svalue(kit_drp)
val_ignore <- svalue(f1_ignore_chk)
val_exact <- svalue(f1_exact_chk)
val_replace <- svalue(f1_replace_chk)
val_exclude <- svalue(f1_exclude_chk)
val_ex_values <- svalue(f1_exclude_edt)
val_na <- NULL
val_ex <- NULL
if (val_replace) {
val_na <- 0
} else {
val_na <- NULL
}
if (val_exclude) {
val_ex <- unlist(strsplit(val_ex_values, ",", fixed = TRUE))
} else {
val_ex <- NULL
}
if (!is.null(val_data)) {
# Change button.
blockHandlers(calculate_btn)
svalue(calculate_btn) <- strBtnProcessing
unblockHandlers(calculate_btn)
enabled(calculate_btn) <- FALSE
datanew <- calculateHeight(
data = val_data, ref = val_ref, na.replace = val_na,
add = val_add, sex.rm = val_sex, qs.rm = val_qs,
kit = val_kit, exclude = val_ex,
ignore.case = val_ignore, exact = val_exact,
debug = debug
)
# Add attributes to result.
attr(datanew, which = "kit") <- val_kit
# Create key-value pairs to log.
keys <- list(
"data", "ref", "na.replace", "add", "sex.rm",
"qs.rm", "kit", "exclude", "ignore.case", "exact"
)
values <- list(
val_data_name, val_ref_name, val_na, val_add, val_sex,
val_qs, val_kit, val_ex, val_ignore, val_exact
)
# 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(paste("EXIT:", fnc))
}
# Close GUI.
.saveSettings()
dispose(w)
} else {
gmessage(
msg = strMsgDataset,
title = strMsgTitleDataset,
icon = "error",
parent = w
)
}
})
.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_calculateHeight_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculateHeight_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_calculateHeight_gui_sex", envir = env, inherits = FALSE)) {
svalue(f1_sex_chk) <- get(".strvalidator_calculateHeight_gui_sex", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_qs", envir = env, inherits = FALSE)) {
svalue(f1_qs_chk) <- get(".strvalidator_calculateHeight_gui_qs", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_ignore", envir = env, inherits = FALSE)) {
svalue(f1_ignore_chk) <- get(".strvalidator_calculateHeight_gui_ignore", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_exact", envir = env, inherits = FALSE)) {
svalue(f1_exact_chk) <- get(".strvalidator_calculateHeight_gui_exact", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_replace", envir = env, inherits = FALSE)) {
svalue(f1_replace_chk) <- get(".strvalidator_calculateHeight_gui_replace", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_add", envir = env, inherits = FALSE)) {
svalue(f1_add_chk) <- get(".strvalidator_calculateHeight_gui_add", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_exclude", envir = env, inherits = FALSE)) {
svalue(f1_exclude_chk) <- get(".strvalidator_calculateHeight_gui_exclude", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_exclude_edt", envir = env, inherits = FALSE)) {
svalue(f1_exclude_edt) <- get(".strvalidator_calculateHeight_gui_exclude_edt", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculateHeight_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculateHeight_gui_sex", value = svalue(f1_sex_chk), envir = env)
assign(x = ".strvalidator_calculateHeight_gui_qs", value = svalue(f1_qs_chk), envir = env)
assign(x = ".strvalidator_calculateHeight_gui_ignore", value = svalue(f1_ignore_chk), envir = env)
assign(x = ".strvalidator_calculateHeight_gui_exact", value = svalue(f1_exact_chk), envir = env)
assign(x = ".strvalidator_calculateHeight_gui_replace", value = svalue(f1_replace_chk), envir = env)
assign(x = ".strvalidator_calculateHeight_gui_add", value = svalue(f1_add_chk), envir = env)
assign(x = ".strvalidator_calculateHeight_gui_exclude", value = svalue(f1_exclude_chk), envir = env)
assign(x = ".strvalidator_calculateHeight_gui_exclude_edt", value = svalue(f1_exclude_edt), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculateHeight_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateHeight_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_sex", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateHeight_gui_sex", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_qs", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateHeight_gui_qs", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_ignore", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateHeight_gui_ignore", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_exact", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateHeight_gui_exact", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_replace", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateHeight_gui_replace", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_add", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateHeight_gui_add", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_exclude", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateHeight_gui_exclude", envir = env)
}
if (exists(".strvalidator_calculateHeight_gui_exclude_edt", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateHeight_gui_exclude_edt", 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)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.