Nothing
# NOTE: Column names used for calculations with data.table is declared
# in globals.R to avoid NOTES in R CMD CHECK.
################################################################################
# CHANGE LOG (last 20 changes)
# 01.09.2022: Compacted gui. Fixed narrow dropdowns. Removed destroy workaround.
# 03.03.2020: Fixed reference to function name.
# 29.02.2020: Added language support.
# 17.02.2019: Fixed Error in if (svalue(savegui_chk)) { : argument is of length zero (tcltk)
# 20.07.2018: Fixed dropdown gets blank when dataset is selected.
# 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'.
# 27.06.2016: Added kit drop-down to fix hardcoded kit in mask plot.
# 27.06.2016: Removed check for reference sample if masking is selected (no harm).
# 16.06.2016: Fixed bug in plot sample masking range.
# 16.06.2016: Now all excluded peaks are marked (not only high peaks).
# 15.06.2016: Prepare button and drop-down menu now disabled while processing.
# 22.05.2016: Added masked data to result for manual investigation.
# 20.05.2016: 'Blocked' changed to 'masked' throughout.
# 25.04.2016: 'Save as' textbox expandable.
# 11.11.2015: Added importFrom ggplot2.
# 21.10.2015: Added attributes.
# 28.08.2015: Added importFrom
#' @title Calculate Analytical Threshold
#'
#' @description
#' GUI wrapper for the \code{\link{maskAT}} and \code{\link{calculateAT}} function.
#'
#' @details
#' Simplifies the use of the \code{\link{calculateAT}} and
#' \code{\link{calculateAT}} function by providing a graphical user interface.
#' In addition there are integrated control functions.
#'
#' @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
#' @importFrom ggplot2 ggtitle scale_shape_discrete ggplot facet_wrap geom_point
#' aes_string scale_colour_manual geom_rect
#'
#' @seealso \code{\link{calculateAT}}, \code{\link{maskAT}},
#' \code{\link{checkSubset}}
calculateAT_gui <- function(env = parent.frame(), savegui = NULL,
debug = FALSE, parent = NULL) {
# Global variables.
.gData <- NULL
.gSamples <- NULL
.gDataPrep <- NULL
.gPlot <- 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 analytical threshold"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Datasets"
strLblDataset <- "Sample dataset:"
strDrpDefault <- "<Select dataset>"
strLblSamples <- "samples"
strLblDatasetRef <- "Reference dataset:"
strLblRef <- "references"
strBtnCheck <- "Check subsetting"
strLblKit <- "Kit:"
strTipKit <- "Only used to shade masked ranges in plot."
strFrmOptions <- "Options"
strChkIgnore <- "Ignore case"
strChkWord <- "Add word boundaries"
strChkMaskHigh <- "Mask high peaks"
strLblMaskHigh <- "Mask all peaks above (RFU): "
strChkMaskAllele <- "Mask sample alleles"
strLblDpAllele <- "Range (data points) around known alleles:"
strChkMaskDye <- "Mask sample alleles per dye channel"
strChkILS <- "Mask ILS peaks"
strLblDpPeak <- "Range (data points) around known peak: "
strLblConf <- "Confidence level 'k' (AT1, AT7): "
strLblRank <- "Percentile rank threshold (AT2): "
strLblAlpha <- "Upper confidence 'alpha' (AT4): "
strFrmPrepare <- "Prepare data and check masking"
strBtnMask <- "Prepare and mask"
strDrpDefault2 <- "<Select sample>"
strBtnSave <- "Save plot"
strFrmSave <- "Save as"
strLblSave <- "Name for result:"
strLblSaveRank <- "Name for percentile rank list:"
strLblSaveMasked <- "Name for masked raw data:"
strBtnCalculate <- "Calculate"
strBtnProcessing <- "Processing..."
strWinCheck <- "Check subsetting"
strMsgPlot <- "Click 'Prepare and mask' and select a sample before saving."
strMsgTitlePlot <- "No plot!"
strMsgTitleError <- "Error"
strMsgCheck <- "Data frame is NULL!\n\nMake sure to select a dataset and a reference set"
strMsgDataset <- "A dataset and a reference dataset must be selected."
strMsgTitleDataset <- "Datasets not selected"
# 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"]$value
strLblSamples <- ifelse(is.na(strtmp), strLblSamples, strtmp)
strtmp <- dtStrings["strLblDatasetRef"]$value
strLblDatasetRef <- ifelse(is.na(strtmp), strLblDatasetRef, 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"]$value
strLblKit <- ifelse(is.na(strtmp), strLblKit, strtmp)
strtmp <- dtStrings["strTipKit"]$value
strTipKit <- ifelse(is.na(strtmp), strTipKit, 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["strChkWord"]$value
strChkWord <- ifelse(is.na(strtmp), strChkWord, strtmp)
strtmp <- dtStrings["strChkMaskHigh"]$value
strChkMaskHigh <- ifelse(is.na(strtmp), strChkMaskHigh, strtmp)
strtmp <- dtStrings["strLblMaskHigh"]$value
strLblMaskHigh <- ifelse(is.na(strtmp), strLblMaskHigh, strtmp)
strtmp <- dtStrings["strChkMaskAllele"]$value
strChkMaskAllele <- ifelse(is.na(strtmp), strChkMaskAllele, strtmp)
strtmp <- dtStrings["strLblDpAllele"]$value
strLblDpAllele <- ifelse(is.na(strtmp), strLblDpAllele, strtmp)
strtmp <- dtStrings["strChkMaskDye"]$value
strChkMaskDye <- ifelse(is.na(strtmp), strChkMaskDye, strtmp)
strtmp <- dtStrings["strChkILS"]$value
strChkILS <- ifelse(is.na(strtmp), strChkILS, strtmp)
strtmp <- dtStrings["strLblDpPeak"]$value
strLblDpPeak <- ifelse(is.na(strtmp), strLblDpPeak, strtmp)
strtmp <- dtStrings["strLblConf"]$value
strLblConf <- ifelse(is.na(strtmp), strLblConf, strtmp)
strtmp <- dtStrings["strLblRank"]$value
strLblRank <- ifelse(is.na(strtmp), strLblRank, strtmp)
strtmp <- dtStrings["strLblAlpha"]$value
strLblAlpha <- ifelse(is.na(strtmp), strLblAlpha, strtmp)
strtmp <- dtStrings["strFrmPrepare"]$value
strFrmPrepare <- ifelse(is.na(strtmp), strFrmPrepare, strtmp)
strtmp <- dtStrings["strBtnMask"]$value
strBtnMask <- ifelse(is.na(strtmp), strBtnMask, strtmp)
strtmp <- dtStrings["strDrpDefault2"]$value
strDrpDefault2 <- ifelse(is.na(strtmp), strDrpDefault2, strtmp)
strtmp <- dtStrings["strBtnSave"]$value
strBtnSave <- ifelse(is.na(strtmp), strBtnSave, strtmp)
strtmp <- dtStrings["strFrmSave"]$value
strFrmSave <- ifelse(is.na(strtmp), strFrmSave, strtmp)
strtmp <- dtStrings["strLblSave"]$value
strLblSave <- ifelse(is.na(strtmp), strLblSave, strtmp)
strtmp <- dtStrings["strLblSaveRank"]$value
strLblSaveRank <- ifelse(is.na(strtmp), strLblSaveRank, strtmp)
strtmp <- dtStrings["strLblSaveMasked"]$value
strLblSaveMasked <- ifelse(is.na(strtmp), strLblSaveMasked, strtmp)
strtmp <- dtStrings["strBtnCalculate"]$value
strBtnCalculate <- ifelse(is.na(strtmp), strBtnCalculate, strtmp)
strtmp <- dtStrings["strBtnProcessing"]$value
strBtnProcessing <- ifelse(is.na(strtmp), strBtnProcessing, strtmp)
strtmp <- dtStrings["strMsgTitlePlot"]$value
strMsgTitlePlot <- ifelse(is.na(strtmp), strMsgTitlePlot, strtmp)
strtmp <- dtStrings["strMsgPlot"]$value
strMsgPlot <- ifelse(is.na(strtmp), strMsgPlot, strtmp)
strtmp <- dtStrings["strWinCheck"]$value
strWinCheck <- ifelse(is.na(strtmp), strWinCheck, strtmp)
strtmp <- dtStrings["strMsgTitleError"]$value
strMsgTitleError <- ifelse(is.na(strtmp), strMsgTitleError, strtmp)
strtmp <- dtStrings["strMsgCheck"]$value
strMsgCheck <- ifelse(is.na(strtmp), strMsgCheck, strtmp)
strtmp <- dtStrings["strMsgDataset"]$value
strMsgDataset <- ifelse(is.na(strtmp), strMsgDataset, strtmp)
strtmp <- dtStrings["strMsgTitleDataset"]$value
strMsgTitleDataset <- ifelse(is.na(strtmp), strMsgTitleDataset, 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)
g0_data_samples_lbl <- glabel(
text = paste(" 0", strLblSamples),
container = g0
)
# Create default dropdown.
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(
"Dye.Sample.Peak", "Sample.File.Name", "Marker", "Allele",
"Marker", "Height", "Data.Point"
)
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
slim = TRUE, slimcol = c("Allele", "Height", "Data.Point"),
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
# get dataset.
.gData <<- get(val_obj, envir = env)
svalue(g0_data_samples_lbl) <- paste(
length(unique(.gData$Sample.File.Name)),
strLblSamples
)
.refresh_sample_drp()
.gDataPrep <- NULL # Erase any previously prepared data.
# Suggest a name for result.
svalue(f4_save1_edt) <- paste(val_obj, "_at", sep = "")
svalue(f4_save2_edt) <- paste(val_obj, "_rank", sep = "")
svalue(f4_save3_edt) <- paste(val_obj, "_masked", sep = "")
# Detect kit.
kitIndex <- detectKit(data = .gData, index = TRUE, debug = debug)
# Select in dropdown.
svalue(g2_kit_drp, index = TRUE) <- kitIndex
} else {
# Reset components.
.gData <<- NULL
svalue(g0_data_drp, index = TRUE) <- 1
svalue(g0_data_samples_lbl) <- paste(" 0", strLblSamples)
svalue(f4_save1_edt) <- ""
svalue(f4_save2_edt) <- ""
svalue(f4_save3_edt) <- ""
.refresh_sample_drp()
.gDataPrep <- NULL # Erase any previously prepared data.
}
})
# Reference -----------------------------------------------------------------
g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")
glabel(text = strLblDatasetRef, container = g1)
g1_ref_samples_lbl <- glabel(
text = paste(" 0", strLblRef),
container = g1
)
# NB! dfs defined in previous section.
g1_ref_drp <- gcombobox(
items = dfs,
selected = 1,
editable = FALSE,
container = g1,
ellipsize = "none", expand = TRUE, fill = "x"
)
addHandlerChanged(g1_ref_drp, handler = function(h, ...) {
val_obj <- svalue(g1_ref_drp)
# Check if suitable.
requiredCol <- c("Sample.Name", "Marker", "Allele")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
slim = TRUE, slimcol = "Allele",
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
.gRef <<- get(val_obj, envir = env)
svalue(g1_ref_samples_lbl) <- paste(
length(unique(.gRef$Sample.Name)),
strLblSamples
)
} else {
# Reset components.
.gRef <<- NULL
svalue(g1_ref_drp, index = TRUE) <- 1
svalue(g1_ref_samples_lbl) <- paste(" 0", strLblRef)
}
})
# Kit -----------------------------------------------------------------------
g2 <- ggroup(container = f0, expand = TRUE, fill = "x")
glabel(text = strLblKit, container = g2)
g2_kit_drp <- gcombobox(
items = getKit(),
selected = 1,
editable = FALSE,
container = g2,
ellipsize = "none", expand = TRUE, fill = "x"
)
tooltip(g2_kit_drp) <- strTipKit
# CHECK #####################################################################
check_btn <- gbutton(text = strBtnCheck, expande = TRUE, 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 = strWinCheck,
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
)
f1_ignore_chk <- gcheckbox(
text = strChkIgnore,
checked = TRUE,
container = f1
)
f1_word_chk <- gcheckbox(
text = strChkWord,
checked = FALSE,
container = f1
)
# LAYOUT --------------------------------------------------------------------
f1g1 <- glayout(container = f1, spacing = 1)
f1g1[1, 1] <- f1_mask_h_chk <- gcheckbox(
text = strChkMaskHigh,
checked = TRUE, container = f1g1
)
f1g1[1, 2] <- glabel(text = strLblMaskHigh, anchor = c(-1, 0), container = f1g1)
f1g1[1, 3] <- f1_mask_h_edt <- gedit(text = "200", width = 6, container = f1g1)
f1g1[2, 1] <- f1_mask_chk <- gcheckbox(
text = strChkMaskAllele,
checked = TRUE, container = f1g1
)
f1g1[3, 1] <- f1_mask_d_chk <- gcheckbox(
text = strChkMaskDye,
checked = TRUE, container = f1g1
)
f1g1[2, 2] <- glabel(text = strLblDpAllele, anchor = c(-1, 0), container = f1g1)
f1g1[2, 3] <- f1_mask_spb <- gspinbutton(from = 0, to = 100, by = 10, value = 50, container = f1g1)
f1g1[4, 1] <- f1_mask_ils_chk <- gcheckbox(
text = strChkILS,
checked = TRUE, container = f1g1
)
f1g1[4, 2] <- glabel(text = strLblDpPeak, anchor = c(-1, 0), container = f1g1)
f1g1[4, 3] <- f1_mask_ils_spb <- gspinbutton(from = 0, to = 100, by = 20, value = 10, container = f1g1)
# LAYOUT --------------------------------------------------------------------
f1g2 <- glayout(container = f1, spacing = 1)
f1g2[1, 1] <- glabel(text = strLblConf, container = f1g2)
f1g2[1, 2] <- f1_k_spb <- gspinbutton(from = 0, to = 100, by = 1, value = 3, container = f1g2)
f1g2[2, 1] <- glabel(text = strLblRank, container = f1g2)
f1g2[2, 2] <- f1_t_spb <- gspinbutton(from = 0, to = 1, by = 0.01, value = 0.99, container = f1g2)
f1g2[3, 1] <- glabel(text = strLblAlpha, container = f1g2)
f1g2[3, 2] <- f1_a_spb <- gspinbutton(from = 0, to = 1, by = 0.01, value = 0.01, container = f1g2)
# Handlers ------------------------------------------------------------------
addHandlerChanged(f1_mask_h_chk, handler = function(h, ...) {
# Update otions.
.refresh_options()
})
addHandlerChanged(f1_mask_chk, handler = function(h, ...) {
# Update otions.
.refresh_options()
})
addHandlerChanged(f1_mask_ils_chk, handler = function(h, ...) {
# Update otions.
.refresh_options()
})
# FRAME 3 ###################################################################
f3 <- gframe(
text = strFrmPrepare,
horizontal = TRUE,
spacing = 1,
container = gv,
expand = TRUE,
fill = "x"
)
mask_btn <- gbutton(text = strBtnMask, container = f3)
f3_sample_drp <- gcombobox(
items = strDrpDefault2, selected = 1,
editable = FALSE, container = f3, ellipsize = "none", expand = TRUE, fill = "x"
)
save_btn <- gbutton(text = strBtnSave, container = f3)
addHandlerClicked(mask_btn, handler = function(h, ...) {
# Get values.
val_data <- .gData
val_ref <- .gRef
val_mask_h <- svalue(f1_mask_h_chk)
val_mask <- svalue(f1_mask_chk)
val_mask_d <- svalue(f1_mask_d_chk)
val_mask_ils <- svalue(f1_mask_ils_chk)
val_height <- as.numeric(svalue(f1_mask_h_edt))
val_range <- svalue(f1_mask_spb)
val_range_ils <- svalue(f1_mask_ils_spb)
val_ignore <- svalue(f1_ignore_chk)
val_word <- svalue(f1_word_chk)
if (debug) {
print("Read Values:")
print("val_data")
print(head(val_data))
print("val_mask_h")
print(val_mask_h)
print("val_mask")
print(val_mask)
print("val_range")
print(val_range)
print("val_mask_d")
print(val_mask_d)
print("val_mask_ils")
print(val_mask_ils)
print("val_range_ils")
print(val_range_ils)
print("val_ignore")
print(val_ignore)
print("val_word")
print(val_word)
}
# Change button.
blockHandlers(mask_btn)
svalue(mask_btn) <- strBtnProcessing
unblockHandlers(mask_btn)
enabled(mask_btn) <- FALSE
enabled(f3_sample_drp) <- FALSE
# Prepare data.
.gDataPrep <<- maskAT(
data = val_data, ref = val_ref,
mask.height = val_mask_h,
height = val_height,
mask.sample = val_mask,
per.dye = val_mask_d,
range.sample = val_range,
mask.ils = val_mask_ils,
range.ils = val_range_ils,
ignore.case = val_ignore,
word = val_word,
debug = debug
)
# Change button.
blockHandlers(mask_btn)
svalue(mask_btn) <- strBtnMask
unblockHandlers(mask_btn)
enabled(mask_btn) <- TRUE
enabled(f3_sample_drp) <- TRUE
# Unselect sample.
svalue(f3_sample_drp, index = TRUE) <- 1
})
addHandlerChanged(f3_sample_drp, handler = function(h, ...) {
# Get values.
val_sample <- svalue(f3_sample_drp)
if (!is.null(.gDataPrep) & !is.null(val_sample)) {
# Get values.
val_mask_h <- svalue(f1_mask_h_chk)
val_mask <- svalue(f1_mask_chk)
val_mask_d <- svalue(f1_mask_d_chk)
val_mask_ils <- svalue(f1_mask_ils_chk)
val_range <- svalue(f1_mask_spb)
val_range_ils <- svalue(f1_mask_ils_spb)
val_kit <- svalue(g2_kit_drp)
if (val_sample %in% unique(.gDataPrep$Sample.File.Name)) {
# Must come after 'val_sample'.
val_data <- subset(.gDataPrep, Sample.File.Name == val_sample)
if (debug) {
print("Read Values:")
print("val_data")
print(head(val_data))
print("val_sample")
print(val_sample)
print("val_mask_h")
print(val_mask_h)
print("val_mask")
print(val_mask)
print("val_range")
print(val_range)
print("val_mask_d")
print(val_mask_d)
print("val_mask_ils")
print(val_mask_ils)
print("val_range_ils")
print(val_range_ils)
print("val_kit")
print(val_kit)
}
# Get all dyes.
dyes <- as.character(unique(val_data$Dye))
colorsKit <- unique(getKit(val_kit, what = "Color")$Color)
dyesKit <- addColor(colorsKit, have = "Color", need = "Dye")
dyeILS <- setdiff(dyes, dyesKit)
# Refactor and keep order of levels.
val_data$Dye <- factor(val_data$Dye, levels = unique(val_data$Dye))
# Create plot.
gp <- ggplot(data = val_data)
gp <- gp + ggtitle(paste("Masked data for", val_sample))
gp <- gp + facet_wrap(~Dye, ncol = 1, scales = "fixed", drop = FALSE)
if (any(val_mask, val_mask_h, val_mask_ils, val_mask_d)) {
# Change shape, color, and legend.
gp <- gp + geom_point(aes_string(
x = "Data.Point", y = "Height",
colour = "Masked", shape = "Masked"
))
gp <- gp + scale_shape_discrete(
name = "Peaks",
breaks = c(FALSE, TRUE),
labels = c("Included", "Excluded")
)
gp <- gp + scale_colour_manual(
values = c("black", "red"),
name = "Peaks",
breaks = c(FALSE, TRUE),
labels = c("Included", "Excluded")
)
} else {
# Use default color and shape.
gp <- gp + geom_point(aes_string(x = "Data.Point", y = "Height"))
}
if (val_mask_ils) {
# ILS masking data frame for plot:
dfIls <- val_data[val_data$ILS == TRUE, ]
ilsDye <- unique(dfIls$Dye)
dpMask <- dfIls$Data.Point
dyeMask <- rep(unique(val_data$Dye), each = length(dpMask))
dpMask <- rep(dpMask, length(unique(val_data$Dye)))
dfMask <- data.frame(
Dye = dyeMask, Data.Point = dpMask,
Xmin = dpMask - val_range_ils,
Xmax = dpMask + val_range_ils
)
if (nrow(dfMask) > 0) {
# Add masking range to plot.
gp <- gp + geom_rect(
data = dfMask,
aes_string(
ymin = -Inf, ymax = Inf,
xmin = "Xmin", xmax = "Xmax"
),
alpha = 0.2,
fill = addColor(ilsDye, have = "Dye", need = "Color")
)
}
}
if (val_mask) {
# Sample masking data frame for plot:
dfSample <- val_data[!is.na(val_data$Min), ]
if (val_mask_d) {
# Loop over dyes and add mask ranges.
for (d in seq(along = dyesKit)) {
# Get data points for selected sample.
dpMask <- dfSample$Data.Point[dfSample$Dye == dyesKit[d]]
dpMin <- dfSample$Min[dfSample$Dye == dyesKit[d]]
dpMax <- dfSample$Max[dfSample$Dye == dyesKit[d]]
# Create mask data.frame.
dyeMask <- rep(dyesKit[d], length(dpMask))
dfMask <- data.frame(
Dye = dyeMask, Data.Point = dpMask,
Xmin = dpMin, Xmax = dpMax
)
if (nrow(dfMask) > 0) {
# Add masking range to plot.
gp <- gp + geom_rect(
data = dfMask,
aes_string(
ymin = -Inf, ymax = Inf,
xmin = "Xmin", xmax = "Xmax"
),
alpha = 0.2, fill = colorsKit[d]
)
}
}
} else {
# Get data points for selected sample.
dpMask <- dfSample$Data.Point
dpMin <- dfSample$Min
dpMax <- dfSample$Max
# Create mask data.frame.
dyeMask <- rep(dyesKit, each = length(dpMask))
dpMask <- rep(dpMask, length(dyesKit))
dpMin <- rep(dpMin, length(dyesKit))
dpMax <- rep(dpMax, length(dyesKit))
dfMask <- data.frame(
Dye = dyeMask, Data.Point = dpMask,
Xmin = dpMin, Xmax = dpMax
)
if (nrow(dfMask) > 0) {
# Add masking range to plot.
gp <- gp + geom_rect(
data = dfMask,
aes_string(
ymin = -Inf, ymax = Inf,
xmin = "Xmin", xmax = "Xmax"
),
alpha = 0.2, fill = "red"
)
}
}
}
# Show plot.
print(gp)
# Save plot object.
.gPlot <<- gp
} # End 'sample exist' if.
} # End 'data exist' if.
})
addHandlerChanged(save_btn, handler = function(h, ...) {
# Get sample name.
val_name <- svalue(f3_sample_drp)
if (!is.null(.gPlot)) {
# Save data.
ggsave_gui(
ggplot = .gPlot, name = val_name, parent = w, env = env,
savegui = savegui, debug = debug
)
} else {
gmessage(
msg = strMsgPlot,
title = strMsgTitlePlot,
icon = "info", parent = w
)
}
})
# FRAME 4 ###################################################################
f4 <- gframe(
text = strFrmSave,
horizontal = FALSE,
spacing = 1,
container = gv
)
glabel(text = strLblSave, anchor = c(-1, 0), container = f4)
f4_save1_edt <- gedit(text = "", container = f4, expand = TRUE)
glabel(text = strLblSaveRank, anchor = c(-1, 0), container = f4)
f4_save2_edt <- gedit(text = "", container = f4, expand = TRUE)
glabel(text = strLblSaveMasked, anchor = c(-1, 0), container = f4)
f4_save3_edt <- gedit(text = "", container = f4, expand = TRUE)
# BUTTON ####################################################################
calculate_btn <- gbutton(text = strBtnCalculate, container = gv)
addHandlerClicked(calculate_btn, handler = function(h, ...) {
# Get values.
if (is.null(.gDataPrep)) {
val_data <- .gData
} else {
val_data <- .gDataPrep
}
val_ref <- .gRef
val_name_data <- svalue(g0_data_drp)
val_name_ref <- svalue(g1_ref_drp)
val_ignore <- svalue(f1_ignore_chk)
val_word <- svalue(f1_word_chk)
val_mask_h <- svalue(f1_mask_h_chk)
val_mask <- svalue(f1_mask_chk)
val_mask_d <- svalue(f1_mask_d_chk)
val_mask_ils <- svalue(f1_mask_ils_chk)
val_height <- as.numeric(svalue(f1_mask_h_edt))
val_range <- svalue(f1_mask_spb)
val_range_ils <- svalue(f1_mask_ils_spb)
val_k <- svalue(f1_k_spb)
val_t <- svalue(f1_t_spb)
val_a <- svalue(f1_a_spb)
val_name1 <- svalue(f4_save1_edt)
val_name2 <- svalue(f4_save2_edt)
val_name3 <- svalue(f4_save3_edt)
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_mask_h")
print(val_mask_h)
print("val_height")
print(val_height)
print("val_mask")
print(val_mask)
print("val_range")
print(val_range)
print("val_mask_d")
print(val_mask_d)
print("val_mask_ils")
print(val_mask_ils)
print("val_range_ils")
print(val_range_ils)
print("val_k")
print(val_k)
print("val_t")
print(val_t)
print("val_a")
print(val_a)
print("val_name1")
print(val_name1)
print("val_name2")
print(val_name2)
}
# Check if data.
if (!is.null(val_data)) {
# Change button.
blockHandlers(calculate_btn)
svalue(calculate_btn) <- strBtnProcessing
unblockHandlers(calculate_btn)
enabled(calculate_btn) <- FALSE
datanew <- calculateAT(
data = val_data,
ref = val_ref,
mask.height = val_mask_h,
height = val_height,
mask.sample = val_mask,
per.dye = val_mask_d,
range.sample = val_range,
mask.ils = val_mask_ils,
range.ils = val_range_ils,
k = val_k,
rank.t = val_t,
alpha = val_a,
ignore.case = val_ignore,
word = val_word,
debug = debug
)
# Create key-value pairs to log.
keys <- list(
"data", "ref", "k", "rank.t", "alpha",
"mask.height", "height", "mask", "range.sample",
"mask.ils", "range.ils", "per.dye", "ignore.case",
"word"
)
values <- list(
val_name_data, val_name_ref, val_k, val_t,
val_a, val_mask_h, val_height, val_mask, val_range,
val_mask_ils, val_range_ils, val_mask_d, val_ignore,
val_word
)
# Update audit trail.
datanew[[1]] <- auditTrail(
obj = datanew[[1]], key = keys, value = values,
label = fnc, arguments = FALSE,
package = "strvalidator"
)
datanew[[2]] <- auditTrail(
obj = datanew[[2]], key = keys, value = values,
label = fnc, arguments = FALSE,
package = "strvalidator"
)
datanew[[3]] <- auditTrail(
obj = datanew[[3]], key = keys, value = values,
label = fnc, arguments = FALSE,
package = "strvalidator"
)
# Save data.
saveObject(name = val_name1, object = datanew[[1]], parent = w, env = env)
saveObject(name = val_name2, object = datanew[[2]], parent = w, env = env)
saveObject(name = val_name3, object = datanew[[3]], parent = w, env = env)
if (debug) {
print(str(datanew))
print(head(datanew))
print(paste("EXIT:", fnc))
}
# Close GUI.
.saveSettings()
dispose(w)
} else {
message <- strMsgDataset
gmessage(message,
title = strMsgTitleDataset,
icon = "error",
parent = w
)
}
})
# INTERNAL FUNCTIONS ########################################################
.refresh_sample_drp <- function() {
# Get data frames in global workspace.
samples <- unique(.gData$Sample.File.Name)
if (!is.null(samples)) {
# Populate drop list.
f3_sample_drp[] <- c(strDrpDefault2, samples)
svalue(f3_sample_drp, index = TRUE) <- 1
} else {
# Populate drop list.
f3_sample_drp[] <- c(strDrpDefault2)
svalue(f3_sample_drp, index = TRUE) <- 1
}
}
.refresh_options <- function() {
val_mask_h <- svalue(f1_mask_h_chk)
val_mask <- svalue(f1_mask_chk)
val_mask_d <- svalue(f1_mask_d_chk)
val_mask_ils <- svalue(f1_mask_ils_chk)
# Update dependent widgets.
if (val_mask_h) {
enabled(f1_mask_h_edt) <- TRUE
} else {
enabled(f1_mask_h_edt) <- FALSE
}
# Update dependent widgets.
if (val_mask) {
enabled(f1_mask_d_chk) <- TRUE
enabled(f1_mask_spb) <- TRUE
} else {
enabled(f1_mask_d_chk) <- FALSE
enabled(f1_mask_spb) <- FALSE
}
# Update dependent widgets.
if (val_mask_ils) {
enabled(f1_mask_ils_spb) <- TRUE
} else {
enabled(f1_mask_ils_spb) <- FALSE
}
}
.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_calculateAT_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculateAT_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_calculateAT_gui_mask_h", envir = env, inherits = FALSE)) {
svalue(f1_mask_h_chk) <- get(".strvalidator_calculateAT_gui_mask_h", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_mask", envir = env, inherits = FALSE)) {
svalue(f1_mask_chk) <- get(".strvalidator_calculateAT_gui_mask", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_mask_ils", envir = env, inherits = FALSE)) {
svalue(f1_mask_ils_chk) <- get(".strvalidator_calculateAT_gui_mask_ils", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_dye", envir = env, inherits = FALSE)) {
svalue(f1_mask_d_chk) <- get(".strvalidator_calculateAT_gui_dye", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_height", envir = env, inherits = FALSE)) {
svalue(f1_mask_h_edt) <- get(".strvalidator_calculateAT_gui_height", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_range", envir = env, inherits = FALSE)) {
svalue(f1_mask_spb) <- get(".strvalidator_calculateAT_gui_range", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_range_ils", envir = env, inherits = FALSE)) {
svalue(f1_mask_ils_spb) <- get(".strvalidator_calculateAT_gui_range_ils", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_k", envir = env, inherits = FALSE)) {
svalue(f1_k_spb) <- get(".strvalidator_calculateAT_gui_k", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_t", envir = env, inherits = FALSE)) {
svalue(f1_t_spb) <- get(".strvalidator_calculateAT_gui_t", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_a", envir = env, inherits = FALSE)) {
svalue(f1_a_spb) <- get(".strvalidator_calculateAT_gui_a", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_ignore", envir = env, inherits = FALSE)) {
svalue(f1_ignore_chk) <- get(".strvalidator_calculateAT_gui_ignore", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_word", envir = env, inherits = FALSE)) {
svalue(f1_word_chk) <- get(".strvalidator_calculateAT_gui_word", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculateAT_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculateAT_gui_mask_h", value = svalue(f1_mask_h_chk), envir = env)
assign(x = ".strvalidator_calculateAT_gui_mask", value = svalue(f1_mask_chk), envir = env)
assign(x = ".strvalidator_calculateAT_gui_mask_ils", value = svalue(f1_mask_ils_chk), envir = env)
assign(x = ".strvalidator_calculateAT_gui_dye", value = svalue(f1_mask_d_chk), envir = env)
assign(x = ".strvalidator_calculateAT_gui_height", value = svalue(f1_mask_h_edt), envir = env)
assign(x = ".strvalidator_calculateAT_gui_range", value = svalue(f1_mask_spb), envir = env)
assign(x = ".strvalidator_calculateAT_gui_range_ils", value = svalue(f1_mask_ils_spb), envir = env)
assign(x = ".strvalidator_calculateAT_gui_k", value = svalue(f1_k_spb), envir = env)
assign(x = ".strvalidator_calculateAT_gui_t", value = svalue(f1_t_spb), envir = env)
assign(x = ".strvalidator_calculateAT_gui_a", value = svalue(f1_a_spb), envir = env)
assign(x = ".strvalidator_calculateAT_gui_ignore", value = svalue(f1_ignore_chk), envir = env)
assign(x = ".strvalidator_calculateAT_gui_word", value = svalue(f1_word_chk), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculateAT_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_mask_h", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_mask_h", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_mask", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_mask", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_mask_ils", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_mask_ils", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_dye", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_dye", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_height", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_height", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_range", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_range", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_range_ils", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_range_ils", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_k", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_k", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_t", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_t", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_a", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_a", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_ignore", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_ignore", envir = env)
}
if (exists(".strvalidator_calculateAT_gui_word", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateAT_gui_word", envir = env)
}
if (debug) {
print("Settings cleared!")
}
}
if (debug) {
print("Settings saved!")
}
}
# END GUI ###################################################################
# Load GUI settings.
.loadSavedSettings()
# Update otions.
.refresh_options()
# Show GUI.
visible(w) <- TRUE
focus(w)
}
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