Nothing
################################################################################
# CHANGE LOG (last 20 changes)
# 05.09.2022: Compacted gui. Fixed narrow dropdowns. Removed destroy workaround.
# 03.03.2020: Added language support.
# 03.05.2019: Compacted gui and expand text field under tcltk.
# 17.02.2019: Fixed Error in if (svalue(savegui_chk)) { : argument is of length zero (tcltk)
# 12.09.2018: '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'.
# 28.08.2015: Added importFrom.
# 05.05.2015: Changed parameter 'ignoreCase' to 'ignore.case' for 'checkSubset' function.
# 11.10.2014: Added 'focus', added 'parent' parameter.
# 28.08.2014: Fixed bug in 'Check subsetting' showing extra combinations in many cases.
# 08.07.2014: First version.
#' @title Calculate Mixture
#'
#' @description
#' GUI wrapper for the \code{\link{calculateMixture}} function.
#'
#' @details
#' Simplifies the use of the \code{\link{calculateMixture}} 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{calculateMixture}}, \code{\link{checkSubset}}
calculateMixture_gui <- function(env = parent.frame(), savegui = NULL,
debug = FALSE, parent = NULL) {
# Global variables.
.gData <- NULL
.gRef1 <- NULL
.gRef2 <- NULL
.gNameData <- NULL
.gNameRef1 <- NULL
.gNameRef2 <- NULL
# Language ------------------------------------------------------------------
# Get this functions name from call.
fnc <- as.character(match.call()[[1]])
if (debug) {
print(paste("IN:", fnc))
}
# Default strings.
strWinTitle <- "Calculate Mixture"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Datasets"
strLblDataset <- "Sample dataset:"
strDrpDefault <- "<Select dataset>"
strLblSamples <- "samples"
strLblRefMajor <- "Reference dataset (major):"
strLblRefMinor <- "Reference dataset (minor):"
strLblRef <- "references"
strBtnCheck <- "Check subsetting"
strFrmOptions <- "Options"
strChkOL <- "Remove off-ladder alleles (affects number of drop-in)"
strChkDrop <- "Ignore drop-out (calculate Mx anyway)"
strFrmSave <- "Save as"
strLblSave <- "Name for result:"
strBtnCalculate <- "Calculate"
strBtnProcessing <- "Processing..."
strMsgDataset <- "A sample dataset and two reference datasets 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"]$value
strLblDataset <- ifelse(is.na(strtmp), strLblDataset, strtmp)
strtmp <- dtStrings["strDrpDefault"]$value
strDrpDefault <- ifelse(is.na(strtmp), strDrpDefault, strtmp)
strtmp <- dtStrings["strLblSamples"]$value
strLblSamples <- ifelse(is.na(strtmp), strLblSamples, strtmp)
strtmp <- dtStrings["strLblRefMajor"]$value
strLblRefMajor <- ifelse(is.na(strtmp), strLblRefMajor, strtmp)
strtmp <- dtStrings["strLblRefMinor"]$value
strLblRefMinor <- ifelse(is.na(strtmp), strLblRefMinor, strtmp)
strtmp <- dtStrings["strLblRef"]$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["strChkOL"]$value
strChkOL <- ifelse(is.na(strtmp), strChkOL, strtmp)
strtmp <- dtStrings["strChkDrop"]$value
strChkDrop <- ifelse(is.na(strtmp), strChkDrop, 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)
})
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,
expand = FALSE,
fill = "x"
)
# 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"))
data_drp <- gcombobox(
items = dfs,
selected = 1,
editable = FALSE,
container = g0,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(data_drp, handler = function(h, ...) {
val_obj <- svalue(data_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.
# get dataset.
.gData <<- get(val_obj, envir = env)
.gNameData <<- val_obj
svalue(data_samples_lbl) <- paste(
length(unique(.gData$Sample.Name)),
strLblSamples
)
svalue(save_edt) <- paste(val_obj, "_mixture", sep = "")
} else {
# Reset components.
.gData <<- NULL
.gNameData <<- NULL
svalue(data_drp, index = TRUE) <- 1
svalue(data_samples_lbl) <- paste(" 0", strLblSamples)
svalue(save_edt) <- ""
}
})
# Reference 1 ---------------------------------------------------------------
g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblRefMajor, container = g1)
ref1_samples_lbl <- glabel(
text = paste(" 0", strLblRef),
container = g1
)
# NB! dfs defined in previous section.
ref1_drp <- gcombobox(
items = dfs,
selected = 1,
editable = FALSE,
container = g1,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(ref1_drp, handler = function(h, ...) {
val_obj <- svalue(ref1_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.
.gRef1 <<- get(val_obj, envir = env)
.gNameRef1 <<- val_obj
svalue(ref1_samples_lbl) <- paste(
length(unique(.gRef1$Sample.Name)),
strLblRef
)
} else {
# Reset components.
.gRef1 <<- NULL
.gNameRef1 <<- NULL
svalue(ref1_drp, index = TRUE) <- 1
svalue(ref1_samples_lbl) <- paste(" 0", strLblRef)
}
})
# Reference 2 ---------------------------------------------------------------
g2 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblRefMinor, container = g2)
ref2_samples_lbl <- glabel(
text = paste(" 0", strLblRef),
container = g2
)
# NB! dfs defined in previous section.
ref2_drp <- gcombobox(
items = dfs,
selected = 1,
editable = FALSE,
container = g2,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(ref2_drp, handler = function(h, ...) {
val_obj <- svalue(ref2_drp)
# Check if suitable.
requiredCol <- c("Sample.Name", "Marker", "Allele")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
slim = TRUE, slimcol = "Allele",
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
.gRef2 <<- get(val_obj, envir = env)
.gNameRef2 <<- val_obj
svalue(ref2_samples_lbl) <- paste(
length(unique(.gRef2$Sample.Name)),
strLblRef
)
} else {
# Reset components.
.gRef2 <<- NULL
.gNameRef2 <<- NULL
svalue(ref2_drp, index = TRUE) <- 1
svalue(ref2_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_ref1 <- .gRef1
val_ref2 <- .gRef2
val_ignore <- FALSE
val_word <- FALSE
if (!is.null(.gData) || !is.null(.gRef1) || !is.null(.gRef2)) {
chksubset_w <- gwindow(
title = strWinTitleCheck,
visible = FALSE, name = title,
width = NULL, height = NULL, parent = w,
handler = NULL, action = NULL
)
# Create pattern.
tmp <- paste(".*", unique(.gRef1$Sample.Name), ".*",
unique(.gRef2$Sample.Name), ".*",
sep = ""
)
# Save as dataframe.
val_pattern <- data.frame(Sample.Name = tmp, stringsAsFactors = FALSE)
if (debug) {
print("Pattern")
print(val_pattern)
}
chksubset_txt <- checkSubset(
data = val_data,
ref = val_pattern,
console = FALSE,
ignore.case = val_ignore,
word = val_word,
debug = debug
)
gtext(
text = chksubset_txt, width = NULL, height = 300, font.attr = NULL,
wrap = FALSE, container = chksubset_w
)
visible(chksubset_w) <- TRUE
} else {
gmessage(
msg = strMsgDataset,
title = strMsgTitleError,
icon = "error"
)
}
})
# FRAME 1 ###################################################################
f1 <- gframe(
text = strFrmOptions, horizontal = FALSE,
spacing = 1, container = gv
)
f1_ol_chk <- gcheckbox(
text = strChkOL,
checked = TRUE, container = f1
)
f1_drop_chk <- gcheckbox(
text = strChkDrop,
checked = TRUE, 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)
# BUTTON ####################################################################
calculate_btn <- gbutton(text = strBtnCalculate, container = gv)
addHandlerClicked(calculate_btn, handler = function(h, ...) {
# Get values.
val_data <- .gData
val_ref1 <- .gRef1
val_ref2 <- .gRef2
val_name_data <- .gNameData
val_name_ref1 <- .gNameRef1
val_name_ref2 <- .gNameRef2
val_name <- svalue(save_edt)
val_ol <- svalue(f1_ol_chk)
val_drop <- svalue(f1_drop_chk)
if (debug) {
print("Read Values:")
print("val_data")
print(head(val_data))
print("val_ref1")
print(head(val_ref1))
print("val_ref2")
print(head(val_ref2))
print("val_ol")
print(val_ol)
print("val_drop")
print(val_drop)
print("val_name")
print(val_name)
}
# Check if data.
if (!is.null(.gData) & !is.null(.gRef1) & !is.null(.gRef2)) {
# Change button.
blockHandlers(calculate_btn)
svalue(calculate_btn) <- strBtnProcessing
unblockHandlers(calculate_btn)
enabled(calculate_btn) <- FALSE
datanew <- calculateMixture(
data = val_data,
ref1 = val_ref1,
ref2 = val_ref2,
ol.rm = val_ol,
ignore.dropout = val_drop,
debug = debug
)
# Create key-value pairs to log.
keys <- list(
"data", "ref1", "ref2",
"ol.rm", "ignore.dropout"
)
values <- list(
val_name_data, val_name_ref1, val_name_ref2,
val_ol, val_drop
)
# 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 = 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_calculateMixture_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculateMixture_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_calculateMixture_gui_ol", envir = env, inherits = FALSE)) {
svalue(f1_ol_chk) <- get(".strvalidator_calculateMixture_gui_ol", envir = env)
}
if (exists(".strvalidator_calculateMixture_gui_dropout", envir = env, inherits = FALSE)) {
svalue(f1_drop_chk) <- get(".strvalidator_calculateMixture_gui_dropout", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculateMixture_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculateMixture_gui_ol", value = svalue(f1_ol_chk), envir = env)
assign(x = ".strvalidator_calculateMixture_gui_dropout", value = svalue(f1_drop_chk), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculateMixture_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateMixture_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculateMixture_gui_ol", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateMixture_gui_ol", envir = env)
}
if (exists(".strvalidator_calculateMixture_gui_dropout", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateMixture_gui_dropout", 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.