################################################################################
# CHANGE LOG (last 20 changes)
# 20.06.2023: Fixed Error in !is.null(val_data) && !is.na(val_data) in coercion to 'logical(1)
# 10.09.2022: Compacted the gui. Fixed narrow dropdowns. Removed destroy workaround.
# 09.07.2022: Fixed "...URLs which should use \doi (with the DOI name only)".
# 18.04.2020: Added language support.
# 23.02.2019: Compacted and tweaked gui for tcltk.
# 17.02.2019: Fixed Error in if (svalue(savegui_chk)) { : argument is of length zero (tcltk)
# 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'.
# 04.08.2016: First version.
#' @title Plot Contamination
#'
#' @description
#' GUI simplifying the creation of plots from negative control data.
#'
#' @details Select data to plot in the drop-down menu.
#' Automatic plot titles can be replaced by custom titles.
#' A name for the result is automatically suggested.
#' The resulting plot can be saved as either a plot object or as an image.
#' @param env environment in which to search for data frames.
#' @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
#' @importFrom data.table data.table
#' @importFrom stats dpois
#' @importFrom MASS fitdistr
#' @importFrom ggplot2 ggplot aes_string theme_gray theme_bw
#' theme_linedraw theme_light theme_dark theme_minimal theme_classic
#' theme_void scale_y_log10 scale_colour_manual coord_cartesian geom_point
#' geom_line
#'
#' @references
#' Duncan Taylor et.al.,
#' Validating multiplexes for use in conjunction with modern interpretation strategies,
#' Forensic Science International: Genetics, Volume 20, January 2016,
#' Pages 6-19, ISSN 1872-4973, 10.1016/j.fsigen.2015.09.011.
#' \doi{10.1016/j.fsigen.2015.09.011}
plotContamination_gui <- function(env = parent.frame(), savegui = NULL, debug = FALSE, parent = NULL) {
# Global variables.
.gData <- NULL
.gPlot <- NULL
# Language ------------------------------------------------------------------
# Get this functions name from call.
fnc <- as.character(match.call()[[1]])
if (debug) {
print(paste("IN:", fnc))
}
# Default strings.
strWinTitle <- "Plot contamination"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Dataset"
strLblDataset <- "Contamination dataset:"
strDrpDataset <- "<Select dataset>"
strLblSamples <- "samples"
strFrmOptions <- "Options"
strChkOverride <- "Override automatic titles"
strLblTitlePlot <- "Plot title:"
strLblTitleX <- "X title:"
strLblTitleY <- "Y title:"
strLblTheme <- "Plot theme:"
strBtnPlot <- "Plot"
strBtnProcessing <- "Processing..."
strFrmSave <- "Save as"
strLblSave <- "Name for result:"
strBtnSaveObject <- "Save as object"
strBtnSaveImage <- "Save as image"
strBtnObjectSaved <- "Object saved"
strLblMainTitle <- "Observed and expected number of peaks per profile (n="
strLblXTitle <- "Number of peaks per control"
strLblYTitle <- "Relative occurance"
strMsgNotDf <- "Data set must be a data.frame!"
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"]$value
strLblSamples <- ifelse(is.na(strtmp), strLblSamples, strtmp)
strtmp <- dtStrings["strFrmOptions"]$value
strFrmOptions <- ifelse(is.na(strtmp), strFrmOptions, strtmp)
strtmp <- dtStrings["strChkOverride"]$value
strChkOverride <- ifelse(is.na(strtmp), strChkOverride, strtmp)
strtmp <- dtStrings["strLblTitlePlot"]$value
strLblTitlePlot <- ifelse(is.na(strtmp), strLblTitlePlot, strtmp)
strtmp <- dtStrings["strLblTitleX"]$value
strLblTitleX <- ifelse(is.na(strtmp), strLblTitleX, strtmp)
strtmp <- dtStrings["strLblTitleY"]$value
strLblTitleY <- ifelse(is.na(strtmp), strLblTitleY, strtmp)
strtmp <- dtStrings["strLblTheme"]$value
strLblTheme <- ifelse(is.na(strtmp), strLblTheme, strtmp)
strtmp <- dtStrings["strBtnPlot"]$value
strBtnPlot <- ifelse(is.na(strtmp), strBtnPlot, strtmp)
strtmp <- dtStrings["strBtnProcessing"]$value
strBtnProcessing <- ifelse(is.na(strtmp), strBtnProcessing, strtmp)
strtmp <- dtStrings["strFrmSave"]$value
strFrmSave <- ifelse(is.na(strtmp), strFrmSave, strtmp)
strtmp <- dtStrings["strLblSave"]$value
strLblSave <- ifelse(is.na(strtmp), strLblSave, strtmp)
strtmp <- dtStrings["strBtnSaveObject"]$value
strBtnSaveObject <- ifelse(is.na(strtmp), strBtnSaveObject, strtmp)
strtmp <- dtStrings["strBtnSaveImage"]$value
strBtnSaveImage <- ifelse(is.na(strtmp), strBtnSaveImage, strtmp)
strtmp <- dtStrings["strBtnObjectSaved"]$value
strBtnObjectSaved <- ifelse(is.na(strtmp), strBtnObjectSaved, strtmp)
strtmp <- dtStrings["strLblMainTitle"]$value
strLblMainTitle <- ifelse(is.na(strtmp), strLblMainTitle, strtmp)
strtmp <- dtStrings["strLblXTitle"]$value
strLblXTitle <- ifelse(is.na(strtmp), strLblXTitle, strtmp)
strtmp <- dtStrings["strLblYTitle"]$value
strLblYTitle <- ifelse(is.na(strtmp), strLblYTitle, strtmp)
strtmp <- dtStrings["strMsgNotDf"]$value
strMsgNotDf <- ifelse(is.na(strtmp), strMsgNotDf, strtmp)
strtmp <- dtStrings["strMsgTitleError"]$value
strMsgTitleError <- ifelse(is.na(strtmp), strMsgTitleError, strtmp)
}
# WINDOW ####################################################################
# Main window.
w <- gwindow(title = strWinTitle, visible = FALSE)
# Runs when window is closed.
addHandlerUnrealize(w, handler = function(h, ...) {
# Save GUI state.
.saveSettings()
# Focus on parent window.
if (!is.null(parent)) {
focus(parent)
}
# Destroy window.
return(FALSE)
})
# Vertical main group.
gv <- ggroup(
horizontal = FALSE,
spacing = 1,
use.scrollwindow = FALSE,
container = w,
expand = TRUE
)
# Help button group.
gh <- ggroup(container = gv, expand = FALSE, fill = "both")
savegui_chk <- gcheckbox(text = strChkGui, checked = FALSE, container = gh)
addSpring(gh)
help_btn <- gbutton(text = strBtnHelp, container = gh)
addHandlerChanged(help_btn, handler = function(h, ...) {
# Open help page for function.
print(help(fnc, help_type = "html"))
})
# FRAME 0 ###################################################################
f0 <- gframe(
text = strFrmDataset,
horizontal = TRUE,
spacing = 1,
container = gv
)
glabel(text = strLblDataset, container = f0)
samples_lbl <- glabel(
text = paste(" 0 ", strLblSamples),
container = f0
)
dataset_drp <- gcombobox(
items = c(
strDrpDataset,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1,
editable = FALSE,
container = f0,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(dataset_drp, handler = function(h, ...) {
val_obj <- svalue(dataset_drp)
# Check if suitable.
requiredCol <- c("Peaks", "Id")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
# Get data.
.gData <<- get(val_obj, envir = env)
# Suggest name.
svalue(f5_save_edt) <- paste(val_obj, "_ggplot", sep = "")
svalue(samples_lbl) <- paste(" ",
length(unique(.gData$Sample.Name)),
" ", strLblSamples,
sep = ""
)
# Enable buttons.
enabled(plot_poiss_btn) <- TRUE
} else {
# Reset components.
.gData <<- NULL
svalue(f5_save_edt) <- ""
svalue(dataset_drp, index = TRUE) <- 1
svalue(samples_lbl) <- paste(" 0 ", strLblSamples)
}
})
# FRAME 1 ###################################################################
f1 <- gframe(
text = strFrmOptions,
horizontal = FALSE,
spacing = 1,
container = gv
)
titles_chk <- gcheckbox(
text = strChkOverride,
checked = FALSE, container = f1
)
addHandlerChanged(titles_chk, handler = function(h, ...) {
.updateGui()
})
titles_group <- ggroup(
container = f1, spacing = 1, horizontal = FALSE,
expand = TRUE, fill = TRUE
)
# Legends
glabel(text = strLblTitlePlot, container = titles_group, anchor = c(-1, 0))
title_edt <- gedit(expand = TRUE, fill = TRUE, container = titles_group)
glabel(text = strLblTitleX, container = titles_group, anchor = c(-1, 0))
x_title_edt <- gedit(expand = TRUE, fill = TRUE, container = titles_group)
glabel(text = strLblTitleY, container = titles_group, anchor = c(-1, 0))
y_title_edt <- gedit(expand = TRUE, fill = TRUE, container = titles_group)
f1g2 <- glayout(container = f1)
f1g2[1, 1] <- glabel(text = strLblTheme, anchor = c(-1, 0), container = f1g2)
items_theme <- c(
"theme_grey()", "theme_bw()", "theme_linedraw()",
"theme_light()", "theme_dark()", "theme_minimal()",
"theme_classic()", "theme_void()"
)
f1g2[1, 2] <- f1_theme_drp <- gcombobox(
items = items_theme,
selected = 1,
container = f1g2,
ellipsize = "none"
)
# BUTTON ####################################################################
plot_poiss_btn <- gbutton(
text = strBtnPlot, container = gv,
expand = TRUE, fill = TRUE
)
tooltip(plot_poiss_btn) <- "Plot observed and expected contamination rate"
addHandlerChanged(plot_poiss_btn, handler = function(h, ...) {
enabled(plot_poiss_btn) <- FALSE
.plot()
enabled(plot_poiss_btn) <- TRUE
})
# FRAME 5 ###################################################################
f5 <- gframe(
text = strFrmSave,
horizontal = TRUE,
spacing = 1,
container = gv
)
glabel(text = strLblSave, container = f5)
f5_save_edt <- gedit(expand = TRUE, fill = TRUE, container = f5)
f5_save_btn <- gbutton(text = strBtnSaveObject, container = f5)
f5_ggsave_btn <- gbutton(text = strBtnSaveImage, container = f5)
addHandlerClicked(f5_save_btn, handler = function(h, ...) {
val_name <- svalue(f5_save_edt)
# Change button.
blockHandlers(f5_save_btn)
svalue(f5_save_btn) <- strBtnProcessing
unblockHandlers(f5_save_btn)
enabled(f5_save_btn) <- FALSE
# Save data.
saveObject(
name = val_name, object = .gPlot,
parent = w, env = env, debug = debug
)
# Change button.
blockHandlers(f5_save_btn)
svalue(f5_save_btn) <- strBtnObjectSaved
unblockHandlers(f5_save_btn)
})
addHandlerChanged(f5_ggsave_btn, handler = function(h, ...) {
val_name <- svalue(f5_save_edt)
# Save data.
ggsave_gui(
ggplot = .gPlot, name = val_name,
parent = w, env = env, savegui = savegui, debug = debug
)
})
# FUNCTIONS #################################################################
.plot <- function() {
# Get values.
val_data <- .gData
val_titles <- svalue(titles_chk)
val_title <- svalue(title_edt)
val_xtitle <- svalue(x_title_edt)
val_ytitle <- svalue(y_title_edt)
val_theme <- svalue(f1_theme_drp)
if (is.data.frame(val_data)) {
# Convert to data table.
DT <- data.table(val_data)
# Get number of peaks per sample (one row per sample).
DTsample <- DT[, list(Peaks = unique(Peaks)), by = list(Id)]
# Get count of samples with N peaks and sort by # peaks.
DTtable <- DTsample[, list(Samples = .N), keyby = list(Peaks)]
# Calculate total number of sampels.
totalSamples <- sum(DTtable$Samples)
# Calculate and add proportion (relative occurance).
DTtable[, Proportion := Samples / totalSamples]
# Add method.
DTtable$Method <- "Observed"
# Print some output.
print("Observed:")
print(DTtable)
# Fit a poisson distribution (estimate lambda parameter)
maxpeaks <- max(DTsample$Peaks)
parms <- MASS::fitdistr(DTsample$Peaks, "poisson")
lambda <- parms$estimate
sd_x <- as.numeric(parms$sd)
model <- paste("Pois(", signif(lambda, 3), "), sd=", signif(sd_x, 3), sep = "")
message("Best fit: ", model)
# Create data frame with expected observations.
expected <- data.frame(
Peaks = seq(0, maxpeaks),
Proportion = stats::dpois(seq(0, maxpeaks),
lambda = lambda
),
Method = "Poisson"
)
# Print some output.
print("Expected:")
print(expected)
# Prepare some plot settings.
title <- paste(strLblMainTitle, totalSamples, ")", sep = "")
legend <- model
ymin <- floor(log10(min(DTtable$Proportion)))
breaks <- 10^seq(1, ymin) # Pretty breaks.
# Create plot.
gp <- ggplot(data = expected)
gp <- gp + geom_line(aes_string(x = "Peaks", y = "Proportion", colour = "Method"))
gp <- gp + scale_y_log10(breaks = breaks)
gp <- gp + coord_cartesian(ylim = c(1, min(breaks)))
gp <- gp + geom_point(data = DTtable, aes_string(x = "Peaks", y = "Proportion", colour = "Method"))
gp <- gp + scale_colour_manual(
name = NULL,
values = c("black", "black"),
labels = c(legend, "Observed"),
guide = guide_legend(override.aes = list(
linetype = c("solid", "blank"),
shape = c(NA, 16)
))
)
# Add titles.
if (val_titles) {
# User defined titles.
gp <- .applyPlotSettings(
gp = gp, theme = val_theme,
main.title = val_title,
x.title = val_xtitle, y.title = val_ytitle
)
} else {
# Automatic titles.
gp <- .applyPlotSettings(
gp = gp, theme = val_theme,
main.title = title,
x.title = strLblXTitle,
y.title = strLblYTitle
)
}
# Show plot.
print(gp)
# Store in global variable.
.gPlot <<- gp
# Change save button.
svalue(f5_save_btn) <- strBtnSaveObject
enabled(f5_save_btn) <- TRUE
} else {
gmessage(
msg = strMsgNotDf,
title = strMsgTitleError,
icon = "error"
)
}
}
# INTERNAL FUNCTIONS ########################################################
.updateGui <- function() {
# Override titles.
val <- svalue(titles_chk)
if (val) {
enabled(titles_group) <- TRUE
} else {
enabled(titles_group) <- FALSE
}
}
.applyPlotSettings <- function(gp, theme = "theme_grey()",
main.title = NULL, x.title = NULL, y.title = NULL) {
# Apply theme.
gp <- gp + eval(parse(text = theme))
gp <- gp + theme(legend.justification = c(1, 1), legend.position = c(1, 1))
# Apply titles.
gp <- gp + labs(title = main.title)
gp <- gp + xlab(x.title)
gp <- gp + ylab(y.title)
return(gp)
}
.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_plotContamination_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_plotContamination_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_plotContamination_gui_title", envir = env, inherits = FALSE)) {
svalue(title_edt) <- get(".strvalidator_plotContamination_gui_title", envir = env)
}
if (exists(".strvalidator_plotContamination_gui_title_chk", envir = env, inherits = FALSE)) {
svalue(titles_chk) <- get(".strvalidator_plotContamination_gui_title_chk", envir = env)
}
if (exists(".strvalidator_plotContamination_gui_x_title", envir = env, inherits = FALSE)) {
svalue(x_title_edt) <- get(".strvalidator_plotContamination_gui_x_title", envir = env)
}
if (exists(".strvalidator_plotContamination_gui_y_title", envir = env, inherits = FALSE)) {
svalue(y_title_edt) <- get(".strvalidator_plotContamination_gui_y_title", envir = env)
}
if (exists(".strvalidator_plotContamination_gui_theme", envir = env, inherits = FALSE)) {
svalue(f1_theme_drp) <- get(".strvalidator_plotContamination_gui_theme", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_plotContamination_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_plotContamination_gui_title", value = svalue(title_edt), envir = env)
assign(x = ".strvalidator_plotContamination_gui_title_chk", value = svalue(titles_chk), envir = env)
assign(x = ".strvalidator_plotContamination_gui_x_title", value = svalue(x_title_edt), envir = env)
assign(x = ".strvalidator_plotContamination_gui_y_title", value = svalue(y_title_edt), envir = env)
assign(x = ".strvalidator_plotContamination_gui_theme", value = svalue(f1_theme_drp), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_plotContamination_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_plotContamination_gui_savegui", envir = env)
}
if (exists(".strvalidator_plotContamination_gui_title", envir = env, inherits = FALSE)) {
remove(".strvalidator_plotContamination_gui_title", envir = env)
}
if (exists(".strvalidator_plotContamination_gui_title_chk", envir = env, inherits = FALSE)) {
remove(".strvalidator_plotContamination_gui_title_chk", envir = env)
}
if (exists(".strvalidator_plotContamination_gui_x_title", envir = env, inherits = FALSE)) {
remove(".strvalidator_plotContamination_gui_x_title", envir = env)
}
if (exists(".strvalidator_plotContamination_gui_y_title", envir = env, inherits = FALSE)) {
remove(".strvalidator_plotContamination_gui_y_title", envir = env)
}
if (exists(".strvalidator_plotContamination_gui_theme", envir = env, inherits = FALSE)) {
remove(".strvalidator_plotContamination_gui_theme", envir = env)
}
if (debug) {
print("Settings cleared!")
}
}
if (debug) {
print("Settings saved!")
}
}
# END GUI ###################################################################
# Load GUI settings.
.loadSavedSettings()
.updateGui()
# Show GUI.
visible(w) <- TRUE
focus(w)
}
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