R/plotStutter_gui.r

In strvalidator: Process Control and Validation of Forensic STR Kits

################################################################################
# CHANGE LOG (last 20 changes)
# 07.07.2023: Fixed Error in !is.na(.gData) && !is.null(.gData) in coercion to 'logical(1)
# 10.09.2022: Compacted the gui. Fixed narrow dropdowns. Removed destroy workaround.
# 02.05.2020: Added language support.
# 07.09.2019: Added option to override labels and titles.
# 24.02.2019: 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 expanded 'gexpandgroup'.
# 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'.
# 10.01.2017: Added option to drop unused levels.
# 10.05.2016: 'Save as' textbox expandable.
# 10.05.2016: Fixed some plot error and included check for missing values.
# 10.05.2016: New method '.enablePlotButtons' and called when changing plot options.
# 06.01.2016: Fixed theme methods not found and added more themes.
# 11.11.2015: Added importFrom grid and gridExtra arrangeGrob, and ggplot2.
# 11.11.2015: Added more themes.
# 29.08.2015: Added importFrom.
# 05.01.2015: 'Save as object' now disabled when complex plot.

#' @title Plot Stutter
#'
#' @description
#' GUI simplifying the creation of plots from stutter data.
#'
#' @details Select data to plot in the drop-down menu. Check that the correct
#' kit has been detected. Plot stutter data by parent allele or by peak height.
#' 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 gridExtra arrangeGrob
# @importFrom gtable gtable_add_grob gtable gtable_filter
#' @importFrom grid unit textGrob grid.newpage grid.draw
#' @importFrom plyr rbind.fill
#' @importFrom scales pretty_breaks
#' @importFrom utils help str
#' @importFrom stats as.formula
#' @importFrom grDevices hcl
#' @importFrom ggplot2 ggplot aes_string scale_x_continuous geom_point position_jitter
#'  facet_grid facet_wrap coord_cartesian guides guide_legend theme element_text
#'  labs xlab ylab ggplotGrob scale_colour_manual element_blank theme_gray
#'  theme_bw theme_linedraw theme_light theme_dark theme_minimal theme_classic
#'  theme_void
#' @importFrom  data.table data.table
#'
#' @seealso \url{https://ggplot2.tidyverse.org/} for details on plot settings.

plotStutter_gui <- function(env = parent.frame(), savegui = NULL, debug = FALSE, parent = NULL) {
  # Global variables.
  .gData <- NULL
  .gDataName <- NULL
  .gPlot <- NULL
  .theme <- c(
    "theme_grey()", "theme_bw()", "theme_linedraw()",
    "theme_light()", "theme_dark()", "theme_minimal()",
    "theme_classic()", "theme_void()"
  )
  .scales <- c("fixed", "free_x", "free_y", "free")


  # Language ------------------------------------------------------------------

  # Get this functions name from call.
  fnc <- as.character(match.call()[[1]])

  if (debug) {
    print(paste("IN:", fnc))
  }

  # Default strings.
  strWinTitle <- "Plot stutter ratios"
  strChkGui <- "Save GUI settings"
  strBtnHelp <- "Help"
  strFrmDataset <- "Dataset and kit"
  strLblDataset <- "Stutter dataset:"
  strDrpDataset <- "<Select dataset>"
  strLblSamples <- "samples"
  strLblKit <- "Kit:"
  strFrmOptions <- "Options"
  strChkOverride <- "Override automatic titles"
  strExpTitles <- "Titles"
  strLblTitlePlot <- "Plot title:"
  strLblTitleX <- "X title:"
  strLblTitleY <- "Y title:"
  strLblNB <- "NB! Title size, angle, vjust, and hjust does not always work as expected with different number of facets per row."
  strLblTitleSettings <- "Main title size, angle, vjust, hjust:"
  strLblXTitleSettings <- "X title size, angle, vjust, hjust:"
  strLblYTitleSettings <- "Y title size, angle, vjust, hjust:"
  strLblTheme <- "Plot theme:"
  strChkSex <- "Exclude sex markers"
  strChkMarker <- "Exclude markers with no data"
  strExpPoints <- "Data points"
  strLblShape <- "Shape:"
  strLblAlpha <- "Alpha:"
  strLblJitter <- "Jitter (width):"
  strExpAxes <- "Axes"
  strLblLimitY <- "Limit Y axis (min-max)"
  strLblLimitX <- "Limit X axis (min-max)"
  strLblScales <- "Scales:"
  strChkOverrideLabels <- "Override default x/y/facet labels"
  strExpXLabels <- "X labels"
  strLblSize <- "Text size (pts):"
  strLblAngle <- "Angle:"
  strLblJustification <- "Justification (v/h):"
  strExpYLabels <- "Y labels"
  strExpFacets <- "Facets"
  strLblSizeX <- "Text size X (pts):"
  strLblSizeY <- "Text size Y (pts):"
  strFrmPlot <- "Plot stutter data"
  strBtnAllele <- "Ratio vs. Allele"
  strBtnHeight <- "Ratio vs. Height"
  strBtnProcessing <- "Processing..."
  strFrmSave <- "Save as"
  strLblSave <- "Name for result:"
  strBtnSaveObject <- "Save as object"
  strBtnSaveImage <- "Save as image"
  strBtnObjectSaved <- "Object saved"
  strLblMainTitle <- "Stutter ratios"
  strLblXTitleAllele <- "True allele"
  strLblXTitleHeight <- "True allele (RFU)"
  strLblYTitleRatio <- "Ratio"
  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["strLblKit"]$value
    strLblKit <- ifelse(is.na(strtmp), strLblKit, 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["strExpTitles"]$value
    strExpTitles <- ifelse(is.na(strtmp), strExpTitles, 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["strLblNB"]$value
    strLblNB <- ifelse(is.na(strtmp), strLblNB, strtmp)

    strtmp <- dtStrings["strLblTitleSettings"]$value
    strLblTitleSettings <- ifelse(is.na(strtmp), strLblTitleSettings, strtmp)

    strtmp <- dtStrings["strLblXTitleSettings"]$value
    strLblXTitleSettings <- ifelse(is.na(strtmp), strLblXTitleSettings, strtmp)

    strtmp <- dtStrings["strLblYTitleSettings"]$value
    strLblYTitleSettings <- ifelse(is.na(strtmp), strLblYTitleSettings, strtmp)

    strtmp <- dtStrings["strLblTheme"]$value
    strLblTheme <- ifelse(is.na(strtmp), strLblTheme, strtmp)

    strtmp <- dtStrings["strChkSex"]$value
    strChkSex <- ifelse(is.na(strtmp), strChkSex, strtmp)

    strtmp <- dtStrings["strChkMarker"]$value
    strChkMarker <- ifelse(is.na(strtmp), strChkMarker, strtmp)

    strtmp <- dtStrings["strExpPoints"]$value
    strExpPoints <- ifelse(is.na(strtmp), strExpPoints, strtmp)

    strtmp <- dtStrings["strLblShape"]$value
    strLblShape <- ifelse(is.na(strtmp), strLblShape, strtmp)

    strtmp <- dtStrings["strLblAlpha"]$value
    strLblAlpha <- ifelse(is.na(strtmp), strLblAlpha, strtmp)

    strtmp <- dtStrings["strLblJitter"]$value
    strLblJitter <- ifelse(is.na(strtmp), strLblJitter, strtmp)

    strtmp <- dtStrings["strExpAxes"]$value
    strExpAxes <- ifelse(is.na(strtmp), strExpAxes, strtmp)

    strtmp <- dtStrings["strLblLimitY"]$value
    strLblLimitY <- ifelse(is.na(strtmp), strLblLimitY, strtmp)

    strtmp <- dtStrings["strLblLimitX"]$value
    strLblLimitX <- ifelse(is.na(strtmp), strLblLimitX, strtmp)

    strtmp <- dtStrings["strLblScales"]$value
    strLblScales <- ifelse(is.na(strtmp), strLblScales, strtmp)

    strtmp <- dtStrings["strChkOverrideLabels"]$value
    strChkOverrideLabels <- ifelse(is.na(strtmp), strChkOverrideLabels, strtmp)

    strtmp <- dtStrings["strExpXLabels"]$value
    strExpXLabels <- ifelse(is.na(strtmp), strExpXLabels, strtmp)

    strtmp <- dtStrings["strLblSize"]$value
    strLblSize <- ifelse(is.na(strtmp), strLblSize, strtmp)

    strtmp <- dtStrings["strLblAngle"]$value
    strLblAngle <- ifelse(is.na(strtmp), strLblAngle, strtmp)

    strtmp <- dtStrings["strLblJustification"]$value
    strLblJustification <- ifelse(is.na(strtmp), strLblJustification, strtmp)

    strtmp <- dtStrings["strExpYLabels"]$value
    strExpYLabels <- ifelse(is.na(strtmp), strExpYLabels, strtmp)

    strtmp <- dtStrings["strExpFacets"]$value
    strExpFacets <- ifelse(is.na(strtmp), strExpFacets, strtmp)

    strtmp <- dtStrings["strLblSizeX"]$value
    strLblSizeX <- ifelse(is.na(strtmp), strLblSizeX, strtmp)

    strtmp <- dtStrings["strLblSizeY"]$value
    strLblSizeY <- ifelse(is.na(strtmp), strLblSizeY, strtmp)

    strtmp <- dtStrings["strFrmPlot"]$value
    strFrmPlot <- ifelse(is.na(strtmp), strFrmPlot, strtmp)

    strtmp <- dtStrings["strBtnAllele"]$value
    strBtnAllele <- ifelse(is.na(strtmp), strBtnAllele, strtmp)

    strtmp <- dtStrings["strBtnHeight"]$value
    strBtnHeight <- ifelse(is.na(strtmp), strBtnHeight, 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["strLblXTitleAllele"]$value
    strLblXTitleAllele <- ifelse(is.na(strtmp), strLblXTitleAllele, strtmp)

    strtmp <- dtStrings["strLblXTitleHeight"]$value
    strLblXTitleHeight <- ifelse(is.na(strtmp), strLblXTitleHeight, strtmp)

    strtmp <- dtStrings["strLblYTitleRatio"]$value
    strLblYTitleRatio <- ifelse(is.na(strtmp), strLblYTitleRatio, 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 = FALSE,
    spacing = 1,
    container = gv
  )

  # Dataset -------------------------------------------------------------------

  g0 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")

  glabel(text = strLblDataset, container = g0)

  samples_lbl <- glabel(
    text = paste(" 0 ", strLblSamples, sep = ""),
    container = g0
  )

  dataset_drp <- gcombobox(
    items = c(
      strDrpDataset,
      listObjects(
        env = env,
        obj.class = "data.frame"
      )
    ),
    selected = 1,
    editable = FALSE,
    container = g0,
    ellipsize = "none",
    expand = TRUE,
    fill = "x"
  )

  # Kit -----------------------------------------------------------------------

  g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")

  glabel(text = strLblKit, container = g1)

  kit_drp <- gcombobox(
    items = getKit(),
    selected = 1,
    editable = FALSE,
    container = g1,
    ellipsize = "none",
    expand = TRUE,
    fill = "x"
  )

  # Handlers ------------------------------------------------------------------

  addHandlerChanged(dataset_drp, handler = function(h, ...) {
    val_obj <- svalue(dataset_drp)

    # Check if suitable.
    requiredCol <- c("Marker", "Allele", "HeightA", "Stutter", "Type")
    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 = ""
      )

      # Detect kit.
      kitIndex <- detectKit(.gData, index = TRUE)
      # Select in dropdown.
      svalue(kit_drp, index = TRUE) <- kitIndex

      # Enable buttons.
      .enablePlotButtons()
    } else {
      # Reset components.
      .gData <<- NULL
      svalue(f5_save_edt) <- ""
      svalue(dataset_drp, index = TRUE) <- 1
      svalue(samples_lbl) <- paste(" 0 ", strLblSamples, sep = "")
    }
  })

  # 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 --------------------------------------------------------------------

  titles_group <- gexpandgroup(
    text = strExpTitles,
    horizontal = FALSE,
    container = f1
  )

  # Start collapsed.
  visible(titles_group) <- FALSE

  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)

  glabel(
    text = strLblNB,
    anchor = c(-1, 0), container = titles_group
  )

  titles_layout <- glayout(container = titles_group)

  title_lbl <- glabel(
    text = strLblTitleSettings,
    anchor = c(-1, 0), container = titles_layout
  )
  title_size_txt <- gedit(
    text = "14", width = 2,
    container = titles_layout
  )
  title_angle_spb <- gspinbutton(
    from = 0, to = 360, by = 1, value = 0,
    container = titles_layout
  )
  title_vjust_spb <- gspinbutton(
    from = 0, to = 1, by = 0.1, value = 0.5,
    container = titles_layout
  )

  title_hjust_spb <- gspinbutton(
    from = 0, to = 1, by = 0.1, value = 0.5,
    container = titles_layout
  )

  titles_layout[1, 1] <- title_lbl
  titles_layout[1, 2] <- title_size_txt
  titles_layout[1, 3] <- title_angle_spb
  titles_layout[1, 4] <- title_vjust_spb
  titles_layout[1, 5] <- title_hjust_spb

  x_title_lbl <- glabel(
    text = strLblXTitleSettings,
    anchor = c(-1, 0), container = titles_layout
  )
  x_title_size_txt <- gedit(
    text = "12", width = 2,
    container = titles_layout
  )
  x_title_angle_spb <- gspinbutton(
    from = 0, to = 360, by = 1, value = 0,
    container = titles_layout
  )
  x_title_vjust_spb <- gspinbutton(
    from = 0, to = 1, by = 0.1, value = 0.5,
    container = titles_layout
  )

  x_title_hjust_spb <- gspinbutton(
    from = 0, to = 1, by = 0.1, value = 0.5,
    container = titles_layout
  )
  titles_layout[2, 1] <- x_title_lbl
  titles_layout[2, 2] <- x_title_size_txt
  titles_layout[2, 3] <- x_title_angle_spb
  titles_layout[2, 4] <- x_title_vjust_spb
  titles_layout[2, 5] <- x_title_hjust_spb

  y_title_lbl <- glabel(
    text = strLblYTitleSettings,
    anchor = c(-1, 0), container = titles_layout
  )
  y_title_size_txt <- gedit(
    text = "12", width = 2,
    container = titles_layout
  )
  y_title_angle_spb <- gspinbutton(
    from = 0, to = 360, by = 1, value = 90,
    container = titles_layout
  )
  y_title_vjust_spb <- gspinbutton(
    from = 0, to = 1, by = 0.1, value = 0.5,
    container = titles_layout
  )

  y_title_hjust_spb <- gspinbutton(
    from = 0, to = 1, by = 0.1, value = 0.5,
    container = titles_layout
  )
  titles_layout[3, 1] <- y_title_lbl
  titles_layout[3, 2] <- y_title_size_txt
  titles_layout[3, 3] <- y_title_angle_spb
  titles_layout[3, 4] <- y_title_vjust_spb
  titles_layout[3, 5] <- y_title_hjust_spb

  # Theme ---------------------------------------------------------------------

  f1g2 <- glayout(container = f1)
  f1g2[1, 1] <- glabel(text = strLblTheme, anchor = c(-1, 0), container = f1g2)
  f1g2[1, 2] <- f1_theme_drp <- gcombobox(
    items = .theme,
    selected = 1,
    container = f1g2,
    ellipsize = "none"
  )

  f1_drop_chk <- gcheckbox(
    text = strChkSex,
    checked = TRUE,
    container = f1
  )

  f1_levels_chk <- gcheckbox(
    text = strChkMarker,
    checked = FALSE,
    container = f1
  )

  addHandlerChanged(f1_drop_chk, handler = function(h, ...) {
    # Enable buttons.
    .enablePlotButtons()
  })

  # FRAME 7 ###################################################################

  f7 <- gframe(
    text = strFrmPlot,
    horizontal = TRUE,
    container = gv
  )

  plot_allele_btn <- gbutton(text = strBtnAllele, container = f7)

  plot_height_btn <- gbutton(text = strBtnHeight, container = f7)

  addHandlerChanged(plot_allele_btn, handler = function(h, ...) {
    enabled(plot_allele_btn) <- FALSE
    .plotStutter(what = "allele")
    enabled(plot_allele_btn) <- TRUE
  })

  addHandlerChanged(plot_height_btn, handler = function(h, ...) {
    enabled(plot_height_btn) <- FALSE
    .plotStutter(what = "height")
    enabled(plot_height_btn) <- TRUE
  })

  # FRAME 5 ###################################################################

  f5 <- gframe(
    text = strFrmSave,
    horizontal = TRUE,
    spacing = 1,
    container = gv
  )

  glabel(text = strLblSave, container = f5)

  f5_save_edt <- gedit(container = f5, expand = TRUE, fill = TRUE)

  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
    )
  })

  # ADVANCED OPTIONS ##########################################################

  e2 <- gexpandgroup(
    text = strExpPoints,
    horizontal = FALSE,
    container = f1
  )

  # Start collapsed.
  visible(e2) <- FALSE

  grid2 <- glayout(container = e2)

  grid2[1, 1] <- glabel(text = strLblShape, container = grid2)
  grid2[1, 2] <- shape_spb <- gspinbutton(
    from = 0, to = 25,
    by = 1, value = 18,
    container = grid2
  )

  grid2[1, 3] <- glabel(text = strLblAlpha, container = grid2)
  grid2[1, 4] <- alpha_spb <- gspinbutton(
    from = 0, to = 1,
    by = 0.01, value = 0.60,
    container = grid2
  )

  grid2[1, 5] <- glabel(text = strLblJitter, container = grid2)
  grid2[1, 6] <- jitter_txt <- gedit(text = "0.1", width = 4, container = grid2)

  # FRAME 3 ###################################################################

  e3 <- gexpandgroup(
    text = strExpAxes,
    horizontal = FALSE,
    container = f1
  )

  # Start collapsed.
  visible(e3) <- FALSE

  grid3 <- glayout(container = e3, spacing = 1)

  grid3[1, 1:2] <- glabel(text = strLblLimitY, container = grid3)
  grid3[2, 1] <- y_min_txt <- gedit(text = "", width = 5, container = grid3)
  grid3[2, 2] <- y_max_txt <- gedit(text = "", width = 5, container = grid3)

  grid3[3, 1:2] <- glabel(text = strLblLimitX, container = grid3)
  grid3[4, 1] <- x_min_txt <- gedit(text = "", width = 5, container = grid3)
  grid3[4, 2] <- x_max_txt <- gedit(text = "", width = 5, container = grid3)

  grid3[1, 3] <- glabel(text = "    ", container = grid3) # Add some space.

  grid3[1, 4] <- glabel(text = strLblScales, container = grid3)
  grid3[2:4, 4] <- scales_opt <- gradio(
    items = .scales,
    selected = 2,
    horizontal = FALSE,
    container = grid3
  )

  addHandlerChanged(scales_opt, handler = function(h, ...) {
    # Enable buttons.
    .enablePlotButtons()
  })


  # FRAME 4 ###################################################################

  labels_chk <- gcheckbox(
    text = strChkOverrideLabels,
    checked = FALSE,
    container = f1
  )

  addHandlerChanged(labels_chk, handler = function(h, ...) {
    # Enable buttons.
    .updateGui()
  })

  e4 <- gexpandgroup(
    text = strExpXLabels,
    horizontal = FALSE,
    container = f1
  )

  # Start collapsed.
  visible(e4) <- FALSE

  grid4 <- glayout(container = e4)

  grid4[1, 1] <- glabel(text = strLblSize, container = grid4)
  grid4[1, 2] <- size_txt <- gedit(text = "8", width = 4, container = grid4)

  grid4[1, 3] <- glabel(text = strLblAngle, container = grid4)
  grid4[1, 4] <- angle_spb <- gspinbutton(
    from = 0, to = 360, by = 1,
    value = 270,
    container = grid4
  )

  grid4[2, 1] <- glabel(text = strLblJustification, container = grid4)
  grid4[2, 2] <- vjust_spb <- gspinbutton(
    from = 0, to = 1, by = 0.1,
    value = 0.5,
    container = grid4
  )

  grid4[2, 3] <- hjust_spb <- gspinbutton(
    from = 0, to = 1, by = 0.1,
    value = 0,
    container = grid4
  )

  # FRAME 5 ###################################################################

  e5 <- gexpandgroup(
    text = strExpYLabels,
    horizontal = FALSE,
    container = f1
  )

  # Start collapsed.
  visible(e5) <- FALSE

  grid5 <- glayout(container = e5)

  grid5[1, 1] <- glabel(text = strLblSize, container = grid5)
  grid5[1, 2] <- size_txt_y <- gedit(text = "8", width = 4, container = grid5)

  grid5[1, 3] <- glabel(text = strLblAngle, container = grid5)
  grid5[1, 4] <- angle_spb_y <- gspinbutton(
    from = 0, to = 360, by = 1,
    value = 0,
    container = grid5
  )

  grid5[2, 1] <- glabel(text = strLblJustification, container = grid5)
  grid5[2, 2] <- vjust_spb_y <- gspinbutton(
    from = 0, to = 1, by = 0.1,
    value = 0.5,
    container = grid5
  )

  grid5[2, 3] <- hjust_spb_y <- gspinbutton(
    from = 0, to = 1, by = 0.1,
    value = 0,
    container = grid5
  )

  # FRAME 6 ###################################################################

  e6 <- gexpandgroup(
    text = strExpFacets,
    horizontal = FALSE,
    container = f1
  )

  # Start collapsed.
  visible(e6) <- FALSE

  grid6 <- glayout(container = e6)

  grid6[1, 1] <- glabel(text = strLblSizeX, container = grid6)
  grid6[1, 2] <- size_txt_sx <- gedit(text = "10", width = 4, container = grid6)

  grid6[1, 3] <- glabel(text = strLblAngle, container = grid6)
  grid6[1, 4] <- angle_spb_sx <- gspinbutton(
    from = 0, to = 360, by = 1,
    value = 0,
    container = grid6
  )

  grid6[2, 1] <- glabel(text = strLblSizeY, container = grid6)
  grid6[2, 2] <- size_txt_sy <- gedit(text = "10", width = 4, container = grid6)

  grid6[2, 3] <- glabel(text = strLblAngle, container = grid6)
  grid6[2, 4] <- angle_spb_sy <- gspinbutton(
    from = 0, to = 360, by = 1,
    value = 0,
    container = grid6
  )

  # FUNCTIONS #################################################################


  .plotStutter <- function(what) {
    # Get values.
    val_titles <- svalue(titles_chk)
    val_title <- svalue(title_edt)
    val_title_size <- svalue(title_size_txt)
    val_title_angle <- svalue(title_angle_spb)
    val_title_vjust <- svalue(title_vjust_spb)
    val_title_hjust <- svalue(title_hjust_spb)
    val_xtitle <- svalue(x_title_edt)
    val_xtitle_size <- svalue(x_title_size_txt)
    val_xtitle_angle <- svalue(x_title_angle_spb)
    val_xtitle_vjust <- svalue(x_title_vjust_spb)
    val_xtitle_hjust <- svalue(x_title_hjust_spb)
    val_ytitle <- svalue(y_title_edt)
    val_ytitle_size <- svalue(y_title_size_txt)
    val_ytitle_angle <- svalue(y_title_angle_spb)
    val_ytitle_vjust <- svalue(y_title_vjust_spb)
    val_ytitle_hjust <- svalue(y_title_hjust_spb)
    val_shape <- as.numeric(svalue(shape_spb))
    val_alpha <- as.numeric(svalue(alpha_spb))
    val_jitter <- as.numeric(svalue(jitter_txt))
    val_ymin <- as.numeric(svalue(y_min_txt))
    val_ymax <- as.numeric(svalue(y_max_txt))
    val_xmin <- as.numeric(svalue(x_min_txt))
    val_xmax <- as.numeric(svalue(x_max_txt))
    val_labels <- svalue(labels_chk)
    val_angle <- as.numeric(svalue(angle_spb))
    val_angle_y <- as.numeric(svalue(angle_spb_y))
    val_angle_sx <- as.numeric(svalue(angle_spb_sx))
    val_angle_sy <- as.numeric(svalue(angle_spb_sy))
    val_vjust <- as.numeric(svalue(vjust_spb))
    val_vjust_y <- as.numeric(svalue(vjust_spb_y))
    val_hjust <- as.numeric(svalue(hjust_spb))
    val_hjust_y <- as.numeric(svalue(hjust_spb_y))
    val_size <- as.numeric(svalue(size_txt))
    val_size_y <- as.numeric(svalue(size_txt_y))
    val_size_sx <- as.numeric(svalue(size_txt_sx))
    val_size_sy <- as.numeric(svalue(size_txt_sy))
    val_scales <- svalue(scales_opt)
    val_kit <- svalue(kit_drp)
    val_theme <- svalue(f1_theme_drp)
    val_drop <- svalue(f1_drop_chk)
    val_levels <- svalue(f1_levels_chk)

    # Declare variables.
    ymax <- NULL # For complex plots.
    ymin <- NULL # For complex plots.

    if (debug) {
      print("str(.gData)")
      print(str(.gData))
      print("levels(.gData$Allele)")
      print(levels(.gData$Allele))
      print("levels(.gData$Stutter)")
      print(levels(.gData$Stutter))
      print("levels(.gData$Marker)")
      print(levels(.gData$Marker))
    }

    if (is.data.frame(.gData)) {
      # Call functions.
      # Add color information.
      if (!"Dye" %in% names(.gData)) {
        .gData <- addColor(data = .gData, kit = val_kit, need = "Dye", debug = debug)
        message("'Dye' added to dataset!")
      }

      # Sort by marker in kit
      .gData <- sortMarker(
        data = .gData,
        kit = val_kit,
        add.missing.levels = TRUE
      )

      # Drop sex markers.
      if (val_drop) {
        # Get sex markers.
        sexMarkers <- getKit(val_kit, what = "Sex.Marker")
        if (length(sexMarkers) > 0) {
          # Drop sex markers.
          n0 <- nrow(.gData)
          for (m in seq(along = sexMarkers)) {
            .gData <- .gData[.gData$Marker != sexMarkers[m], ]
          }
          n1 <- nrow(.gData)
          message(paste(n1, " rows after removing ", n0 - n1, " sex marker rows.", sep = ""))

          # Refactor and keep order of levels.
          .gData$Marker <- factor(.gData$Marker,
            levels = levels(.gData$Marker)[!levels(.gData$Marker) %in% sexMarkers]
          )
        }
      }

      # Create factors and round. IMPORTANT!
      .gData$Type <- factor(round(.gData$Type, 2))

      # Sort stutter/allele factors. IMPORTANT!
      .gData$Stutter <- factor(.gData$Stutter, levels = sort(unique(as.numeric(as.character(.gData$Stutter)))))
      .gData$Allele <- factor(.gData$Allele, levels = sort(unique(as.numeric(as.character(.gData$Allele)))))

      # Height must be numeric (not string).
      .gData$HeightA <- as.numeric(as.character(.gData$HeightA))

      if (debug) {
        print("BEFORE PLOTTING:")
        print("str(.gData)")
        print(str(.gData))
        print("levels(.gData$Allele)")
        print(levels(.gData$Allele))
        print("levels(.gData$Stutter)")
        print(levels(.gData$Stutter))
        print("levels(.gData$Marker)")
        print(levels(.gData$Marker))
      }

      # Check if 'simple' or 'complex' plotting:
      # Make data frame from dataset marker levels.
      markerDye <- data.frame(Marker = levels(.gData$Marker))
      # Add colors.
      markerDye <- addColor(data = markerDye, kit = val_kit)
      # Get Marker and Dye column.
      markerDye <- markerDye[c("Marker", "Dye")]
      # Extract unique elements.
      uniqueMarkerDye <- markerDye[!duplicated(markerDye), ]
      # Calculate number of unique columns per dye.
      val_ncol <- unique(table(uniqueMarkerDye$Dye))

      # Create data.table to check for facet error caused by all NA's.
      dt <- data.table::data.table(.gData)
      # Check for facet error caused by all NA's.
      tmp <- dt[, list(Sum = sum(Ratio)), by = Marker]
      if (any(tmp$Sum == 0) || !all(levels(dt$Marker) %in% unique(dt$Marker))) {
        message(
          "Empty facets detected!",
          "If this leads to plot error try another scale for axes,",
          "or drop markers with no data."
        )
      }

      # Plotting alleles for observed stutters per marker.
      if (what == "allele") {
        if (val_titles) {
          mainTitle <- val_title
          xTitle <- val_xtitle
          yTitle <- val_ytitle
        } else {
          mainTitle <- strLblMainTitle
          xTitle <- strLblXTitleAllele
          yTitle <- strLblYTitleRatio
        }

        gp <- ggplot(.gData, aes_string(x = "Allele", y = "Ratio", colour = "Type"))
      } else if (what == "height") {
        if (val_titles) {
          mainTitle <- val_title
          xTitle <- val_xtitle
          yTitle <- val_ytitle
        } else {
          mainTitle <- strLblMainTitle
          xTitle <- strLblXTitleHeight
          yTitle <- strLblYTitleRatio
        }

        gp <- ggplot(.gData, aes_string(x = "HeightA", y = "Ratio", colour = "Type"))
        gp <- gp + scale_x_continuous(breaks = scales::pretty_breaks())
      }

      # Apply theme.
      gp <- gp + eval(parse(text = val_theme))

      # Plot settings.
      gp <- gp + geom_point(
        shape = val_shape, alpha = val_alpha,
        position = position_jitter(height = 0, width = val_jitter)
      )

      # Facet and keep all levels.
      gp <- gp + facet_grid("Dye ~ Marker", drop = val_levels)

      # Restrict y axis.
      if (!is.na(val_ymin) && !is.na(val_ymax)) {
        val_y <- c(val_ymin, val_ymax)
      } else {
        val_y <- NULL
      }
      # Restrict x axis.
      if (!is.na(val_xmin) && !is.na(val_xmax)) {
        val_x <- c(val_xmin, val_xmax)
      } else {
        val_x <- NULL
      }
      # Zoom in without dropping observations.
      gp <- gp + coord_cartesian(xlim = val_x, ylim = val_y)

      if (debug) {
        print(paste("Plot zoomed to xlim:", val_x, "ylim:", val_y))
      }

      # Titles and legends.
      gp <- gp + guides(fill = guide_legend(reverse = TRUE))

      # Override default labels.
      if (val_labels) {
        gp <- gp + theme(
          axis.text.x = element_text(
            angle = val_angle,
            hjust = val_hjust,
            vjust = val_vjust,
            size = val_size
          ), axis.text.y = element_text(
            angle = val_angle_y,
            hjust = val_hjust_y,
            vjust = val_vjust_y,
            size = val_size_y
          ), strip.text.x = element_text(size = val_size_sx, angle = val_angle_sx),
          strip.text.y = element_text(size = val_size_sy, angle = val_angle_sy)
        )
      }

      # Add titles.
      gp <- gp + labs(title = mainTitle)
      gp <- gp + xlab(xTitle)
      gp <- gp + ylab(yTitle)

      # Override default theme for titles.
      if (val_titles) {
        gp <- gp + theme(
          plot.title = element_text(
            angle = val_title_angle,
            hjust = val_title_hjust,
            vjust = val_title_vjust,
            size = val_title_size
          ), axis.title.x = element_text(
            angle = val_xtitle_angle,
            hjust = val_xtitle_hjust,
            vjust = val_xtitle_vjust,
            size = val_xtitle_size
          ), axis.title.y = element_text(
            angle = val_ytitle_angle,
            hjust = val_ytitle_hjust,
            vjust = val_ytitle_vjust,
            size = val_ytitle_size
          )
        )
      }

      # Check plot type.
      if (length(val_ncol) == 1) {
        # Simple plot, equal number of markers per dye.

        if (debug) {
          print(paste(
            "Simple plot, val_ncol:",
            paste(val_ncol, collapse = ", ")
          ))
        }
        # NB! 'facet_wrap' does not seem to support strings.
        #     Use 'as.formula(paste("string1", "string2"))' as a workaround.
        gp <- gp + facet_wrap(as.formula(paste("~ Marker")),
          ncol = val_ncol,
          drop = val_levels, scales = val_scales
        )

        # Restrict y axis.
        if (!is.na(val_ymin) && !is.na(val_ymax)) {
          val_y <- c(val_ymin, val_ymax)
        } else {
          val_y <- NULL
        }
        # Restrict x axis.
        if (!is.na(val_xmin) && !is.na(val_xmax)) {
          val_x <- c(val_xmin, val_xmax)
        } else {
          val_x <- NULL
        }
        # Zoom in without dropping observations.
        gp <- gp + coord_cartesian(xlim = val_x, ylim = val_y)

        if (debug) {
          print(paste("Plot zoomed to xlim:", val_x, "ylim:", val_y))
        }

        # Show plot.
        print(gp)

        # Change save button.
        svalue(f5_save_btn) <- strBtnSaveObject
        enabled(f5_save_btn) <- TRUE
      } else if (length(val_ncol) > 1) {
        # Complex plot, unequal number of markers per dye.

        if (debug) {
          print(paste(
            "Complex plot, val_ncol:",
            paste(val_ncol, collapse = ", ")
          ))
        }

        # Extract the legend from the 'simple' plot.
        guide <- gtable::gtable_filter(ggplotGrob(gp), pattern = "guide")

        # Get y max to be able to use same scale across plots.
        ymax <- max(.gData$Ratio, na.rm = TRUE) * 1.05
        ymin <- min(.gData$Ratio, na.rm = TRUE) * 0.95

        if (debug) {
          print("ymax:")
          print(ymax)
          print("ymin:")
          print(ymin)
        }

        # Get kit colors and convert to dyes.
        dyes <- unique(getKit(val_kit, what = "Color")$Color)
        dyes <- addColor(dyes, have = "Color", need = "Dye")
        # Number of dyes.
        noDyes <- length(dyes)
        # Number of rows in table object (one per dye + title + x title).
        noRows <- length(dyes) + 2

        # Create table object.
        # Note: width(1.5 for y-title, and the rest for plots + guides)
        #       height(1.5 for plot title, equal for each plot, and 1.5 for x-title)
        g <- gtable::gtable(
          widths = grid::unit.c(
            grid::unit(1.5, "lines"),
            grid::unit(1, "null"),
            sum(guide$widths)
          ),
          heights = grid::unit(
            c(1.5, rep(1, noDyes), 1.5),
            c("line", rep("null", noDyes), "line")
          )
        )

        # Add titles.
        if (val_titles) {
          g <- gtable::gtable_add_grob(g,
            grid::textGrob(mainTitle,
              vjust = val_title_vjust,
              hjust = val_title_hjust,
              rot = val_title_angle
            ),
            t = 1, b = 1, l = 2, r = 2
          )
          g <- gtable::gtable_add_grob(g, grid::textGrob(xTitle,
            vjust = val_xtitle_vjust,
            hjust = val_xtitle_hjust,
            rot = val_xtitle_angle
          ),
          t = noRows, b = noRows, l = 2, r = 2
          )
          g <- gtable::gtable_add_grob(g, grid::textGrob(yTitle,
            vjust = val_ytitle_vjust,
            hjust = val_ytitle_hjust,
            rot = val_ytitle_angle
          ), t = 1, b = noRows, l = 1, r = 1)
        } else {
          # Add default titles.

          g <- gtable::gtable_add_grob(g, grid::textGrob(mainTitle), t = 1, b = 1, l = 2, r = 2)
          g <- gtable::gtable_add_grob(g, grid::textGrob(xTitle), t = noRows, b = noRows, l = 2, r = 2)
          g <- gtable::gtable_add_grob(g, grid::textGrob(yTitle, rot = 90), t = 1, b = noRows, l = 1, r = 1)
        }

        # Add the legend to the table object.
        g <- gtable::gtable_add_grob(g, guide, t = 1, b = noRows, l = 3, r = 3)

        # Get all markers to be plotted and add dye for subsetting.
        gLevel <- data.frame(Marker = levels(.gData$Marker))
        gLevel <- addColor(gLevel, kit = val_kit)

        # Make palette.
        gTypeLevel <- levels(.gData$Type)
        val_palette <- .gg_color_hue(length(gTypeLevel))
        names(val_palette) <- gTypeLevel

        # Loop over all dyes.
        for (d in seq(along = dyes)) {
          # Get data for current dye.
          gDataSub <- .gData[.gData$Dye == dyes[d], ]

          # Get current markers/levels.
          gDyeLevel <- as.character(gLevel$Marker[gLevel$Dye == dyes[d]])

          # Can't handle zero rows.
          if (nrow(gDataSub) == 0) {
            tmp <- data.frame(Marker = gDyeLevel, Allele = NA, HeightA = 0, Ratio = 0, Type = -1)
            gDataSub <- plyr::rbind.fill(gDataSub, tmp)
          }

          # Refactor to levels of current dye (and maintain order).
          gDataSub$Marker <- factor(gDataSub$Marker, levels = gDyeLevel)
          gDataSub$Dye <- factor(dyes[d])

          # Create a plot for the current subset.
          # Select what to plot.
          if (what == "allele") {
            # Plotting alleles for observed stutters per marker.

            # Create a plot for the current subset.
            gp <- ggplot(gDataSub, aes_string(x = "Allele", y = "Ratio", color = "Type"))
          } else if (what == "height") {
            # Plotting true allele height for observed stutters per marker.

            # Create a plot for the current subset.
            gp <- ggplot(gDataSub, aes_string(x = "HeightA", y = "Ratio", color = "Type"))
            gp <- gp + scale_x_continuous(breaks = scales::pretty_breaks())
          }

          # Apply theme.
          gp <- gp + eval(parse(text = val_theme))

          # Plot settings.
          gp <- gp + geom_point(
            shape = val_shape, alpha = val_alpha,
            position = position_jitter(height = 0, width = val_jitter)
          )

          # Add custom color palette (use same for all sub plots).
          gp <- gp + scale_colour_manual(values = val_palette)

          # Facet plot and keep all levels (in current dye).
          gp <- gp + facet_grid("Dye ~ Marker", scales = val_scales, drop = val_levels) # Keep dye labels.
          # gp <- gp + facet_grid("~ Marker", scales=val_scales, drop = FALSE) # No dye labels.

          # Set margin around each plot. Note: top, right, bottom, left.
          gp <- gp + theme(plot.margin = grid::unit(c(0.25, 0, 0, 0), "lines"))

          # Restrict y axis.
          if (!is.na(val_ymin) && !is.na(val_ymax)) {
            val_y <- c(val_ymin, val_ymax)
          } else {
            if (val_scales %in% c("fixed", "free_x")) {
              # Keep Y fixed.
              val_y <- c(ymin, ymax)
            }
            val_y <- NULL
          }
          # Restrict x axis.
          if (!is.na(val_xmin) && !is.na(val_xmax)) {
            val_x <- c(val_xmin, val_xmax)
          } else {
            if (val_scales %in% c("fixed", "free_x")) {
              # Keep Y fixed.
              val_y <- c(ymin, ymax)
            }
            val_x <- NULL
          }
          # Zoom in without dropping observations.
          gp <- gp + coord_cartesian(xlim = val_x, ylim = val_y)

          if (debug) {
            print(paste("Plot zoomed to xlim:", val_x, "ylim:", val_y))
          }

          # Remove titles, axis labels and legend on current subplot.
          gp <- gp + labs(title = element_blank())
          gp <- gp + theme(axis.title.x = element_blank())

          # Override default labels.
          if (val_labels) {
            gp <- gp + theme(
              axis.text.x = element_text(
                angle = val_angle,
                hjust = val_hjust,
                vjust = val_vjust,
                size = val_size
              ), axis.text.y = element_text(
                angle = val_angle_y,
                hjust = val_hjust_y,
                vjust = val_vjust_y,
                size = val_size_y
              ), strip.text.x = element_text(
                size = val_size_sx,
                angle = val_angle_sx
              ), strip.text.y = element_text(
                size = val_size_sy,
                angle = val_angle_sy
              )
            )
          }

          gp <- gp + theme(axis.title.y = element_blank())

          gp <- gp + theme(legend.position = "none")

          # Add plot panel to table object.
          g <- gtable::gtable_add_grob(g, ggplotGrob(gp),
            t = (d + 1), b = (d + 1), l = 2, r = 2
          )
        }

        # Plot.
        grid::grid.newpage()
        grid::grid.draw(g)

        # This is step 1 in workaround to save 'complex plots':
        # Step 1: http://stackoverflow.com/a/20433318/2173340
        # Step 2: http://stackoverflow.com/a/18407452/2173340
        gp <- gridExtra::arrangeGrob(g)

        # Change save button.
        svalue(f5_save_btn) <- strBtnSaveObject
        enabled(f5_save_btn) <- FALSE
      } else {
        # Not supported!
        stop(paste("Unsupported number of columns:", val_ncol))
      }


      # Store in global variable.
      .gPlot <<- gp
    } 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
    }

    # Override labels.
    val <- svalue(labels_chk)
    if (val) {
      enabled(e4) <- TRUE
      enabled(e5) <- TRUE
      enabled(e6) <- TRUE
    } else {
      enabled(e4) <- FALSE
      enabled(e5) <- FALSE
      enabled(e6) <- FALSE
    }
  }

  .enablePlotButtons <- function() {
    enabled(plot_allele_btn) <- TRUE
    enabled(plot_height_btn) <- TRUE
  }

  # Return a number of ggplot default colors.
  .gg_color_hue <- function(n) {
    hues <- seq(15, 375, length = n + 1)
    hcl(h = hues, l = 65, c = 100)[1:n]
  }

  .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_plotStutter_gui_savegui", envir = env, inherits = FALSE)) {
        svalue(savegui_chk) <- get(".strvalidator_plotStutter_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_plotStutter_gui_title_chk", envir = env, inherits = FALSE)) {
        svalue(titles_chk) <- get(".strvalidator_plotStutter_gui_title_chk", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title", envir = env, inherits = FALSE)) {
        svalue(title_edt) <- get(".strvalidator_plotStutter_gui_title", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_x_title", envir = env, inherits = FALSE)) {
        svalue(x_title_edt) <- get(".strvalidator_plotStutter_gui_x_title", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_y_title", envir = env, inherits = FALSE)) {
        svalue(y_title_edt) <- get(".strvalidator_plotStutter_gui_y_title", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title_size", envir = env, inherits = FALSE)) {
        svalue(title_size_txt) <- get(".strvalidator_plotStutter_gui_title_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_x_title_size", envir = env, inherits = FALSE)) {
        svalue(x_title_size_txt) <- get(".strvalidator_plotStutter_gui_x_title_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_y_title_size", envir = env, inherits = FALSE)) {
        svalue(y_title_size_txt) <- get(".strvalidator_plotStutter_gui_y_title_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title_angle", envir = env, inherits = FALSE)) {
        svalue(title_angle_spb) <- get(".strvalidator_plotStutter_gui_title_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_x_title_angle", envir = env, inherits = FALSE)) {
        svalue(x_title_angle_spb) <- get(".strvalidator_plotStutter_gui_x_title_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_y_title_angle", envir = env, inherits = FALSE)) {
        svalue(y_title_angle_spb) <- get(".strvalidator_plotStutter_gui_y_title_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title_vjust", envir = env, inherits = FALSE)) {
        svalue(title_vjust_spb) <- get(".strvalidator_plotStutter_gui_title_vjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_x_title_vjust", envir = env, inherits = FALSE)) {
        svalue(x_title_vjust_spb) <- get(".strvalidator_plotStutter_gui_x_title_vjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_y_title_vjust", envir = env, inherits = FALSE)) {
        svalue(y_title_vjust_spb) <- get(".strvalidator_plotStutter_gui_y_title_vjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title_hjust", envir = env, inherits = FALSE)) {
        svalue(title_hjust_spb) <- get(".strvalidator_plotStutter_gui_title_hjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_x_title_hjust", envir = env, inherits = FALSE)) {
        svalue(x_title_hjust_spb) <- get(".strvalidator_plotStutter_gui_x_title_hjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_y_title_hjust", envir = env, inherits = FALSE)) {
        svalue(y_title_hjust_spb) <- get(".strvalidator_plotStutter_gui_y_title_hjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_points_shape", envir = env, inherits = FALSE)) {
        svalue(shape_spb) <- get(".strvalidator_plotStutter_gui_points_shape", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_points_alpha", envir = env, inherits = FALSE)) {
        svalue(alpha_spb) <- get(".strvalidator_plotStutter_gui_points_alpha", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_points_jitter", envir = env, inherits = FALSE)) {
        svalue(jitter_txt) <- get(".strvalidator_plotStutter_gui_points_jitter", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_axes_y_min", envir = env, inherits = FALSE)) {
        svalue(y_min_txt) <- get(".strvalidator_plotStutter_gui_axes_y_min", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_axes_y_max", envir = env, inherits = FALSE)) {
        svalue(y_max_txt) <- get(".strvalidator_plotStutter_gui_axes_y_max", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_axes_x_min", envir = env, inherits = FALSE)) {
        svalue(x_min_txt) <- get(".strvalidator_plotStutter_gui_axes_x_min", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_axes_x_max", envir = env, inherits = FALSE)) {
        svalue(x_max_txt) <- get(".strvalidator_plotStutter_gui_axes_x_max", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_axes_scales", envir = env, inherits = FALSE)) {
        svalue(scales_opt) <- get(".strvalidator_plotStutter_gui_axes_scales", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_labels_chk", envir = env, inherits = FALSE)) {
        svalue(labels_chk) <- get(".strvalidator_plotStutter_gui_labels_chk", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_xlabel_size", envir = env, inherits = FALSE)) {
        svalue(size_txt) <- get(".strvalidator_plotStutter_gui_xlabel_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_ylabel_size", envir = env, inherits = FALSE)) {
        svalue(size_txt_y) <- get(".strvalidator_plotStutter_gui_ylabel_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_sxlabel_size", envir = env, inherits = FALSE)) {
        svalue(size_txt_sx) <- get(".strvalidator_plotStutter_gui_sxlabel_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_sylabel_size", envir = env, inherits = FALSE)) {
        svalue(size_txt_sy) <- get(".strvalidator_plotStutter_gui_sylabel_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_xlabel_angle", envir = env, inherits = FALSE)) {
        svalue(angle_spb) <- get(".strvalidator_plotStutter_gui_xlabel_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_ylabel_angle", envir = env, inherits = FALSE)) {
        svalue(angle_spb_y) <- get(".strvalidator_plotStutter_gui_ylabel_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_sxlabel_angle", envir = env, inherits = FALSE)) {
        svalue(angle_spb_sx) <- get(".strvalidator_plotStutter_gui_sxlabel_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_sylabel_angle", envir = env, inherits = FALSE)) {
        svalue(angle_spb_sy) <- get(".strvalidator_plotStutter_gui_sylabel_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_xlabel_justh", envir = env, inherits = FALSE)) {
        svalue(hjust_spb) <- get(".strvalidator_plotStutter_gui_xlabel_justh", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_ylabel_justh", envir = env, inherits = FALSE)) {
        svalue(hjust_spb_y) <- get(".strvalidator_plotStutter_gui_ylabel_justh", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_xlabel_justv", envir = env, inherits = FALSE)) {
        svalue(vjust_spb) <- get(".strvalidator_plotStutter_gui_xlabel_justv", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_ylabel_justv", envir = env, inherits = FALSE)) {
        svalue(vjust_spb_y) <- get(".strvalidator_plotStutter_gui_ylabel_justv", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_theme", envir = env, inherits = FALSE)) {
        svalue(f1_theme_drp) <- get(".strvalidator_plotStutter_gui_theme", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_sex", envir = env, inherits = FALSE)) {
        svalue(f1_drop_chk) <- get(".strvalidator_plotStutter_gui_sex", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_levels", envir = env, inherits = FALSE)) {
        svalue(f1_levels_chk) <- get(".strvalidator_plotStutter_gui_levels", envir = env)
      }

      if (debug) {
        print("Saved settings loaded!")
      }
    }
  }

  .saveSettings <- function() {
    # Then save settings if true.
    if (svalue(savegui_chk)) {
      assign(x = ".strvalidator_plotStutter_gui_savegui", value = svalue(savegui_chk), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_title_chk", value = svalue(titles_chk), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_title", value = svalue(title_edt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_x_title", value = svalue(x_title_edt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_y_title", value = svalue(y_title_edt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_title_size", value = svalue(title_size_txt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_x_title_size", value = svalue(x_title_size_txt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_y_title_size", value = svalue(y_title_size_txt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_title_angle", value = svalue(title_angle_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_x_title_angle", value = svalue(x_title_angle_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_y_title_angle", value = svalue(y_title_angle_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_title_vjust", value = svalue(title_vjust_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_x_title_vjust", value = svalue(x_title_vjust_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_y_title_vjust", value = svalue(y_title_vjust_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_title_hjust", value = svalue(title_hjust_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_x_title_hjust", value = svalue(x_title_hjust_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_y_title_hjust", value = svalue(y_title_hjust_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_points_shape", value = svalue(shape_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_points_alpha", value = svalue(alpha_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_points_jitter", value = svalue(jitter_txt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_axes_y_min", value = svalue(y_min_txt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_axes_y_max", value = svalue(y_max_txt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_axes_x_min", value = svalue(x_min_txt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_axes_x_max", value = svalue(x_max_txt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_axes_scales", value = svalue(scales_opt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_labels_chk", value = svalue(labels_chk), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_xlabel_size", value = svalue(size_txt), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_ylabel_size", value = svalue(size_txt_y), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_sxlabel_size", value = svalue(size_txt_sx), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_sylabel_size", value = svalue(size_txt_sy), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_xlabel_angle", value = svalue(angle_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_ylabel_angle", value = svalue(angle_spb_y), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_sxlabel_angle", value = svalue(angle_spb_sx), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_sylabel_angle", value = svalue(angle_spb_sy), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_xlabel_justh", value = svalue(hjust_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_xlabel_justv", value = svalue(vjust_spb), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_ylabel_justh", value = svalue(hjust_spb_y), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_ylabel_justv", value = svalue(vjust_spb_y), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_theme", value = svalue(f1_theme_drp), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_sex", value = svalue(f1_drop_chk), envir = env)
      assign(x = ".strvalidator_plotStutter_gui_levels", value = svalue(f1_levels_chk), envir = env)
    } else { # or remove all saved values if false.

      if (exists(".strvalidator_plotStutter_gui_savegui", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_savegui", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title_chk", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_title_chk", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_title", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_x_title", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_x_title", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_y_title", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_y_title", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title_size", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_title_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_x_title_size", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_x_title_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_y_title_size", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_y_title_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title_angle", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_title_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_x_title_angle", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_x_title_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_y_title_angle", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_y_title_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title_vjust", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_title_vjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_x_title_vjust", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_x_title_vjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_y_title_vjust", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_y_title_vjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_title_hjust", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_title_hjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_x_title_hjust", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_x_title_hjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_y_title_hjust", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_y_title_hjust", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_points_shape", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_points_shape", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_points_alpha", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_points_alpha", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_points_jitter", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_points_jitter", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_axes_y_min", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_axes_y_min", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_axes_y_max", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_axes_y_max", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_axes_x_min", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_axes_x_min", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_axes_x_max", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_axes_x_max", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_axes_scales", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_axes_scales", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_labels_chk", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_labels_chk", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_xlabel_size", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_xlabel_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_ylabel_size", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_ylabel_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_sxlabel_size", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_sxlabel_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_sylabel_size", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_sylabel_size", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_xlabel_angle", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_xlabel_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_ylabel_angle", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_ylabel_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_sxlabel_angle", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_sxlabel_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_sylabel_angle", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_sylabel_angle", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_xlabel_justh", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_xlabel_justh", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_xlabel_justv", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_xlabel_justv", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_ylabel_justh", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_ylabel_justh", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_ylabel_justv", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_ylabel_justv", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_theme", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_theme", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_sex", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_sex", envir = env)
      }
      if (exists(".strvalidator_plotStutter_gui_levels", envir = env, inherits = FALSE)) {
        remove(".strvalidator_plotStutter_gui_levels", 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)
}