diff --git a/CITATION.cff b/CITATION.cff
index 13bbc10..f04509a 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: vertesy/ggExpress - the fastest way to create, annotate and and save plots in R.
-version: v0.9.0
+version: v0.9.5
 message: >-
   If you use this software, please cite it using these metadata.
 type: software
diff --git a/DESCRIPTION b/DESCRIPTION
index ae6d9b1..42fce17 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ggExpress
 Title: ggExpress is the fastest way to create, annotate and export plots
     in R
-Version: 0.9.0
+Version: 0.9.5
 Authors@R: 
     person("Abel", "Vertesy", , "av@imba.oeaw.ac.at", role = c("aut", "cre"))
 Author: Abel Vertesy <av@imba.oeaw.ac.at> [aut, cre]
@@ -30,9 +30,12 @@ Imports:
     cowplot,
     ggVennDiagram,
     MarkdownReports,
+    qs,
     RColorBrewer,
-    tibble
+    tibble,
+    tictoc,
+    tidyr
 Encoding: UTF-8
-Packaged: 2023-11-27 00:15:29.839722
+Packaged: 2024-10-24 15:50:59.849277
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
diff --git a/Development/Dependencies.R b/Development/Dependencies.R
index 72c711f..5fa9ada 100644
--- a/Development/Dependencies.R
+++ b/Development/Dependencies.R
@@ -1,51 +1,120 @@
-Dependency file generated on Mon Nov 27 00:06:14 2023 
+Dependency file generated on Thu Oct 24 15:20:01 2024 
 
 #################################################################################################### 
 ggExpress.R
 #################################################################################################### 
-$`character(0)`
-[1] "as_tibble"     "ggVennDiagram" "iround"        "is.list2"      "plot_grid"     "save_plot"    
+$`c("package:Connectome.tools", "package:MarkdownHelpers")`
+[1] "unless.specified"
+
+$`c("package:Connectome.tools", "package:Seurat.utils", "package:ggExpress", "package:CodeAndRoll2", "package:dplyr", "package:tidyr", "package:tibble")`
+[1] "as_tibble"
+
+$`c("package:dplyr", "package:ggplot2")`
+[1] "sym"
+
+$`c("package:MarkdownHelpers", "package:CodeAndRoll2")`
+[1] "iround"
+
+$`c("package:MarkdownReports", "package:CodeAndRoll2", "package:stats")`
+[1] "median"
+
+$`c("package:ReadWriter", "package:Stringendo")`
+[1] "sppp"
+
+$`c("package:Seurat.utils", "package:ggExpress", "package:cowplot")`
+[1] "plot_grid" "save_plot"
+
+$`c("package:Seurat.utils", "package:ggExpress", "package:MarkdownHelpers")`
+[1] "llogit"
+
+$`c("package:Seurat.utils", "package:ggExpress")`
+[1] "qqSave" "qsave" 
+
+$`c("package:Seurat.utils", "package:ggplot2")`
+[1] "coord_polar"   "element_text"  "geom_hline"    "geom_vline"    "labs"         
+[6] "scale_x_log10" "scale_y_log10" "theme"        
+
+$`c("package:Seurat.utils", "package:MarkdownHelpers", "package:Stringendo")`
+[1] "percentage_formatter"
+
+$`c("package:Seurat.utils", "package:MarkdownReports", "package:MarkdownHelpers", "package:Stringendo")`
+[1] "iprint"
+
+$`c("package:Seurat.utils", "package:Stringendo")`
+[1] "kpp"
+
+$`c("package:UVI.tools", "package:ggpubr")`
+[1] "ggbarplot"
+
+$`c("package:UVI.tools", "package:Seurat.utils", "package:ggExpress", "package:tictoc")`
+[1] "tic" "toc"
+
+$`c("package:UVI.tools", "package:Seurat.utils", "package:tibble")`
+[1] "rownames_to_column"
+
+$`c("package:UVI.tools", "package:tidyr")`
+[1] "pivot_longer"
 
 $`package:base`
- [1] "as.character"  "as.data.frame" "as.numeric"    "c"             "cat"           "cbind"         "colnames"     
- [8] "factor"        "getwd"         "is.matrix"     "is.null"       "is.numeric"    "isFALSE"       "length"       
-[15] "make.unique"   "max"           "names"         "ncol"          "paste"         "paste0"        "print"        
-[22] "rep"           "rev"           "round"         "signif"        "sort"          "stopifnot"     "substitute"   
-[29] "sum"           "unique"        "unlist"        "which"        
+ [1] "as.character"  "as.data.frame" "as.factor"     "as.numeric"    "c"            
+ [6] "cat"           "cbind"         "colnames"      "factor"        "getwd"        
+[11] "is.character"  "is.data.frame" "is.logical"    "is.matrix"     "is.null"      
+[16] "is.numeric"    "isFALSE"       "length"        "make.names"    "make.unique"  
+[21] "max"           "message"       "names"         "ncol"          "nrow"         
+[26] "paste"         "paste0"        "print"         "rep"           "rev"          
+[31] "round"         "sapply"        "signif"        "sort"          "stop"         
+[36] "stopifnot"     "substitute"    "sum"           "unique"        "unlist"       
+[41] "which"        
+
+$`package:CodeAndRoll2`
+[1] "is.list2"
 
 $`package:ggExpress`
-[1] "qMarkdownImageLink"  "qqqAxisLength"       "qqqList.2.DF.ggplot" "qqqNamed.Vec.2.Tbl"  "qqSave"             
+[1] ".assertMaxCategories" "ggVennDiagram"        "qMarkdownImageLink"   "qqqAxisLength"       
+[5] "qqqList.2.DF.ggplot"  "qqqNamed.Vec.2.Tbl"  
 
 $`package:ggplot2`
- [1] "annotation_logticks" "coord_polar"         "element_rect"        "element_text"        "geom_abline"        
- [6] "geom_density_2d"     "geom_hline"          "geom_vline"          "guides"              "labs"               
-[11] "scale_fill_gradient" "scale_x_log10"       "scale_y_log10"       "theme"              
+ [1] "annotation_logticks" "element_rect"        "expansion"           "geom_abline"        
+ [5] "geom_density_2d"     "guide_legend"        "guides"              "position_fill"      
+ [9] "position_stack"      "scale_fill_gradient" "scale_x_continuous"  "ylab"               
 
 $`package:ggpubr`
- [1] "ggbarplot"          "ggboxplot"          "ggdensity"          "gghistogram"        "ggpar"             
- [6] "ggpie"              "ggscatter"          "ggstripchart"       "ggviolin"           "grids"             
-[11] "stat_compare_means" "stat_cor"          
+ [1] "ggboxplot"          "ggdensity"          "gghistogram"        "ggpar"             
+ [5] "ggpie"              "ggscatter"          "ggstripchart"       "ggviolin"          
+ [9] "grids"              "stat_compare_means" "stat_cor"          
 
 $`package:MarkdownHelpers`
-[1] "llogit"                "stopif"                "unless.specified"      "ww.FnP_parser"        
-[5] "ww.set.file.extension" "ww.ttl_field"         
-
-$`package:stats`
-[1] "median"
+[1] "ww.FnP_parser"         "ww.set.file.extension" "ww.ttl_field"         
 
 $`package:Stringendo`
-[1] "FixPlotName"          "flag.nameiftrue"      "iprint"               "percentage_formatter"
-[5] "sppp"                
+[1] "FixPlotName"            "flag.nameiftrue"        "parseParamStringWNames"
+[4] "stopif"                
 
 $`package:utils`
-[1] "stack"
+[1] "head"  "stack"
 
-character(0)
+c("Connectome.tools", "MarkdownHelpers")
+c("Connectome.tools", "Seurat.utils", "ggExpress", "CodeAndRoll2", "dplyr", "tidyr", "tibble")
+c("dplyr", "ggplot2")
+c("MarkdownHelpers", "CodeAndRoll2")
+c("MarkdownReports", "CodeAndRoll2", "stats")
+c("ReadWriter", "Stringendo")
+c("Seurat.utils", "ggExpress", "cowplot")
+c("Seurat.utils", "ggExpress", "MarkdownHelpers")
+c("Seurat.utils", "ggExpress")
+c("Seurat.utils", "ggplot2")
+c("Seurat.utils", "MarkdownHelpers", "Stringendo")
+c("Seurat.utils", "MarkdownReports", "MarkdownHelpers", "Stringendo")
+c("Seurat.utils", "Stringendo")
+c("UVI.tools", "ggpubr")
+c("UVI.tools", "Seurat.utils", "ggExpress", "tictoc")
+c("UVI.tools", "Seurat.utils", "tibble")
+c("UVI.tools", "tidyr")
 base
+CodeAndRoll2
 ggExpress
 ggplot2
 ggpubr
 MarkdownHelpers
-stats
 Stringendo
 utils
diff --git a/Development/config.R b/Development/config.R
index 0c8dda7..49372bb 100644
--- a/Development/config.R
+++ b/Development/config.R
@@ -1,7 +1,9 @@
 # Configuration for the Package
+# file.edit("~/GitHub/Packages/ggExpress/Development/config.R")
+
 DESCRIPTION <- list(
   package.name = "ggExpress",
-  version = "0.9.0",
+  version = "0.9.5",
   title = "ggExpress is the fastest way to create, annotate and export plots in R",
   description = "ggExpress is a set of R functions that allows you to generate precise figures easily,
     and create clean markdown reports about what you just discovered with your analysis script. It is ggplot-based smaller brother of vertesy/MarkdownReports. It helps you to:
@@ -12,7 +14,7 @@ DESCRIPTION <- list(
     5. Share your report, by exporting your report to .pdf, .html or .docx, or via Github or a personal website.",
 
   depends = "Stringendo, MarkdownHelpers, ggplot2, ggpubr",
-  imports = "cowplot, tibble, RColorBrewer, MarkdownReports, CodeAndRoll2, ggVennDiagram",
+  imports = "cowplot, tibble, tidyr, RColorBrewer, MarkdownReports, CodeAndRoll2, ggVennDiagram, qs, tictoc",
 
   author.given = "Abel",
   author.family = "Vertesy",
diff --git a/NAMESPACE b/NAMESPACE
index 4df1369..690c974 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -17,6 +17,7 @@ export(qscatter)
 export(qstripchart)
 export(qvenn)
 export(qviolin)
+importFrom(CodeAndRoll2,is.list2)
 importFrom(MarkdownHelpers,llogit)
 importFrom(cowplot,plot_grid)
 importFrom(cowplot,save_plot)
diff --git a/R/ggExpress.R b/R/ggExpress.R
index 6825d34..d16cb47 100644
--- a/R/ggExpress.R
+++ b/R/ggExpress.R
@@ -131,7 +131,6 @@ qhistogram <- function(
 #' @param ext File extension (.pdf / .png).
 #' @param also.pdf Save plot in both png and pdf formats.
 #' @param save.obj Save the ggplot object to a file. Default: FALSE.
-#' @param xlab X-axis label.
 #' @param plot Display the plot.
 #' @param plotname The title of the plot and the name of the file (unless specified in `filename`).
 #' @param subtitle Optional subtitle text added below the title. Default is NULL.
@@ -141,6 +140,7 @@ qhistogram <- function(
 #' @param save Save the plot into a file.
 #' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "path_of_report".
 #' @param logX Make X axis log10-scale.
+#' @param xlab X-axis label. Default: FALSE.
 #' @param xlab.angle Rotate X-axis labels by N degree. Default: 90
 #' @param palette_use GGpubr Color palette to use.
 #' @param hide.legend hide legend
@@ -160,6 +160,7 @@ qdensity <- function(
     also.pdf = FALSE, save.obj = FALSE,
     ext = MarkdownHelpers::ww.set.file.extension(default = "png", also_pdf = also.pdf),
     xlab = FALSE, plot = TRUE,
+    xlab.angle = 90,
     plotname = FixPlotName(substitute(vec)),
     subtitle = NULL,
     suffix = NULL,
@@ -168,10 +169,9 @@ qdensity <- function(
     save = TRUE, mdlink = MarkdownHelpers::unless.specified("b.mdlink", def = FALSE),
     logX = FALSE, logY = FALSE,
     palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4],
-    xlab.angle = 90,
     hide.legend = TRUE,
     max.names = 50,
-    grid = F,
+    grid = FALSE,
     w = 5, h = w, ...) {
   if (isFALSE(xlab)) xlab <- plotname
   df <- qqqNamed.Vec.2.Tbl(namedVec = vec, thr = max.names)
@@ -233,7 +233,7 @@ qdensity <- function(
 #' @param custom.order custom.order
 #' @param palette_use GGpubr Color palette to use.
 #' @param max.names The maximum number of names still to be shown on the axis.
-#' @param label Slice labels. Set to NULL to remove slice names.
+#' @param labels Slice labels. Set to NULL to remove slice names.
 #' @param w Width of the plot.
 #' @param h Height of the plot.
 #' @param ... Pass any other parameter of the corresponding plotting function(most of them should work).
@@ -318,7 +318,7 @@ qpie <- function(
   print(nrCategories.DFcol1)
 
   if (NamedSlices) labs <- paste(df$names, "\n", labs)
-  if (custom.order != F) df$"names" <- factor(df$"names", levels = custom.order)
+  if (custom.order != FALSE) df$"names" <- factor(df$"names", levels = custom.order)
 
   p <- ggpubr::ggpie(
     data = df,
@@ -331,9 +331,9 @@ qpie <- function(
     title = plotname,
     palette = palette_use
     # , ...
-    ) +
+  ) +
     guides(fill = guide_legend(LegendTitle))
-    # theme(legend.title = LegendTitle)
+  # theme(legend.title = LegendTitle)
 
   if (LegendSide) p <- ggpubr::ggpar(p, legend = "right")
   if (custom.margin) p <- p + coord_polar(theta = "y", clip = "off")
@@ -375,8 +375,8 @@ qpie <- function(
 #' @param palette_use GGpubr Color palette to use.
 #' @param col Color of the plot.
 #' @param xlab.angle Rotate X-axis labels by N degree. Default: 90
-#' @param xlab X-axis label.
-#' @param ylab Y-axis label.
+#' @param xlab X-axis label. Default: "".
+#' @param ylab Y-axis label. Default: NULL.
 #' @param logY Make Y axis log10-scale.
 #' @param label label
 #' @param hide.legend Hide legend. Default: TRUE.
@@ -422,10 +422,9 @@ qbarplot <- function(
     ylab = NULL,
     w = qqqAxisLength(vec, factor = 0.25), h = 5,
     ...) {
-
   stopifnot(is.numeric(vec))
   if (isFALSE(xlab)) xlab <- plotname
-  df <- qqqNamed.Vec.2.Tbl(namedVec = vec, strip.too.many.names = F)
+  df <- qqqNamed.Vec.2.Tbl(namedVec = vec, strip.too.many.names = FALSE)
 
   if (length(unique(df$"names")) == 1) df$"names" <- as.character(1:length(vec))
 
@@ -460,7 +459,7 @@ qbarplot <- function(
 
   if (length(vec) > max.names) p <- p + ggplot2::guides(x = "none")
   if (hide.legend) p <- p + ggplot2::theme(legend.position = "none")
-  if(!is.null(legend.title)) p <- p + guides(fill = guide_legend(title = legend.title), color = "none")  # Hide the color legend
+  if (!is.null(legend.title)) p <- p + guides(fill = guide_legend(title = legend.title), color = "none") # Hide the color legend
 
   if (hline) p <- p + ggplot2::geom_hline(yintercept = hline)
   if (logY) p <- p + ggplot2::scale_y_log10()
@@ -475,7 +474,8 @@ qbarplot <- function(
   if (save) {
     qqSave(
       ggobj = p, title = plotname, fname = file_name, ext = ext,
-      w = w, h = h, limitsize = limitsize, also.pdf = also.pdf, save.obj = save.obj)
+      w = w, h = h, limitsize = limitsize, also.pdf = also.pdf, save.obj = save.obj
+    )
   }
   if (mdlink & save) qMarkdownImageLink(file_name)
   if (plot) p
@@ -487,10 +487,11 @@ qbarplot <- function(
 #'
 #' @description Draw and save a stacked barplot for each row of a dataframe.
 #' @param df The variable to plot.
-#' @param x Colname to split along X axis. Def colnames(df)[1]
-#' @param y Colname to count along y axis. Def colnames(df)[3]
-#' @param fill Color (split) by along Y.
+#' @param x Colname to split along X axis. Default: "Samples".
+#' @param y Colname to count along y axis. Default: "Fraction".
+#' @param z Colname to split along Y axis. Default: "Category.
 #' @param color Color (split) by along Y.
+# #' @param fill Color (split) by along Y.
 #' @param ext File extension (.pdf / .png).
 #' @param also.pdf Save plot in both png and pdf formats.
 #' @param save.obj Save the ggplot object to a file. Default: FALSE.
@@ -499,6 +500,7 @@ qbarplot <- function(
 #' @param suffix Optional suffix added to the filename. Default is NULL.
 #' @param caption Optional text added to bottom right corner of the plot. Default = suffix
 #' @param filename Manually provided filename (optional). Default: parse from `plotname`,
+#' @param scale Scale the y axis. Default: TRUE.
 #' @param plot Display the plot.
 #' @param save Save the plot into a file.
 #' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "path_of_report".
@@ -506,7 +508,7 @@ qbarplot <- function(
 #' @param filtercol Color bars below / above the threshold with red / green. Define the direction by -1 or 1. Takes effect if "*line" is defined.
 #' @param palette_use GGpubr Color palette to use.
 #' @param xlab.angle Rotate X-axis labels by N degree. Default: 90
-#' @param xlab X-axis label.
+#' @param xlab X-axis label. Default: `x`.
 #' @param logY Make Y axis log10-scale.
 #' @param label label
 #' @param hide.legend hide legend
@@ -515,6 +517,7 @@ qbarplot <- function(
 #' @param annotation_logticks_Y Logical indicating whether to add annotation logticks on Y-axis. Default follows the value of `logY`.
 #' @param grid Character indicating the axis to add gridlines. Options are 'x', 'y', or 'xy'. Default is 'y'.
 #' @param max.categ The maximum allowed number of unique categories.
+# #' @param top The number of top categories to keep. Default: NULL.
 #' @param w Width of the plot.
 #' @param h Height of the plot.
 #' @param ... Pass any other parameter of the corresponding plotting function(most of them should work).
@@ -560,13 +563,14 @@ qbarplot.stacked.from.wide.df <- function(
     limitsize = FALSE,
     grid = "y",
     max.categ = 10,
-    top = NULL,
+    # top = NULL,
     w = qqqAxisLength(df, factor = .7), h = 5,
     ...) {
-
   message(plotname)
-  stopifnot(is.data.frame(df),
-            ncol(df) > 2)
+  stopifnot(
+    is.data.frame(df),
+    ncol(df) > 2
+  )
 
   # if (is.null(xlab)) xlab <- if (scale) paste("%", x ) else x
   if (is.null(subtitle)) subtitle <- paste("Median:", iround(median(df[[2]])))
@@ -576,22 +580,23 @@ qbarplot.stacked.from.wide.df <- function(
   # }
 
   df_long <- df |>
-    tibble::rownames_to_column(var = x) |>  # Convert row names to a column
-    tidyr::pivot_longer(cols = -!!sym(x),      # Convert wide to long format
-                        names_to = z, #"category"
-                        values_to = y # "Fraction"
+    tibble::rownames_to_column(var = x) |> # Convert row names to a column
+    tidyr::pivot_longer(
+      cols = -!!sym(x), # Convert wide to long format
+      names_to = z, # "category"
+      values_to = y # "Fraction"
     )
 
   p <- ggpubr::ggbarplot(
     data = df_long, x = x, y = y,
     color = color,
-    fill = z,   # Use the 'category' column created in long format
+    fill = z, # Use the 'category' column created in long format
     subtitle = subtitle,
     title = plotname, xlab = xlab,
     caption = caption,
     label = label,
     palette = palette_use,
-    position = if(scale) position_fill() else position_stack(),
+    position = if (scale) position_fill() else position_stack(),
     ...
   ) +
     ggpubr::grids(axis = "y") +
@@ -626,9 +631,9 @@ qbarplot.stacked.from.wide.df <- function(
 #'
 #' @description Draw and save a barplot for tibbles or dataframes
 #' @param df The variable to plot.
-#' @param x Colname to split along X axis. Def colnames(df)[1]
-#' @param y Colname to count along y axis. Def colnames(df)[3]
-#' @param fill Color (split) by along Y.
+#' @param x Colname to split along X axis. Default: `colnames(df)[1]`.
+#' @param y Colname to count along y axis. Default: `colnames(df)[2]`.
+#' @param fill Color (split) by along Y. Default: `colnames(df)[3]`.
 #' @param color Color (split) by along Y.
 #' @param ext File extension (.pdf / .png).
 #' @param also.pdf Save plot in both png and pdf formats.
@@ -646,7 +651,7 @@ qbarplot.stacked.from.wide.df <- function(
 #' @param filtercol Color bars below / above the threshold with red / green. Define the direction by -1 or 1. Takes effect if "*line" is defined.
 #' @param palette_use GGpubr Color palette to use.
 #' @param xlab.angle Rotate X-axis labels by N degree. Default: 90
-#' @param xlab X-axis label.
+#' @param xlab X-axis label. Default: NULL.
 #' @param logY Make Y axis log10-scale.
 #' @param annotation_logticks_Y Logical indicating whether to add annotation logticks on Y-axis. Default follows the value of `logY`.
 #' @param label label
@@ -696,13 +701,12 @@ qbarplot.df <- function(
     max.categ = 10,
     w = qqqAxisLength(df), h = 5,
     ...) {
-
   message(plotname)
   stopifnot(is.data.frame(df), ncol(df) > 2,
-            "Y axis must be numeric" = is.numeric(y)
-            )
+    "Y axis must be numeric" = is.numeric(y)
+  )
 
-  if (is.null(xlab)) xlab <- if (scale) paste("%", x ) else x
+  if (is.null(xlab)) xlab <- if (scale) paste("%", x) else x
   if (is.null(subtitle)) subtitle <- paste("Median:", iround(median(df[[2]])))
 
   if (is.numeric(df[[fill]])) {
@@ -720,7 +724,7 @@ qbarplot.df <- function(
     caption = caption,
     label = label,
     palette = palette_use,
-    position = if(scale) position_fill() else position_stack(),
+    position = if (scale) position_fill() else position_stack(),
     ...
   ) +
     ggpubr::grids(axis = "y") +
@@ -754,13 +758,17 @@ qbarplot.df <- function(
 #' @title qscatter
 #'
 #' @description Draw and save a 2D-scatter plot.
+#'
 #' @param df_XYcol Data, as 2 column data frame, where col.1 is X axis.
+#' @param x The index or name of the column to be plotted on the X axis. Default: `1`.
+#' @param y The index or name of the column to be plotted on the Y axis. Default: `2`.
 #' @param plotname The name of the file and title of the plot.
 #' @param subtitle Optional subtitle text added below the title. Default is NULL.
 #' @param suffix Optional suffix added to the filename. Default is NULL.
 #' @param caption Optional text added to bottom right corner of the plot. Default = suffix
 #' @param filename Manually provided filename (optional). Default: parse from `plotname`,
-#' @param label Point labels
+#' @param label Point labels. Default: NULL.
+#' @param repel Repel labels from each other. Default: TRUE.
 #' @param col Color of the plot.
 #' @param ext File extension (.pdf / .png).
 #' @param also.pdf Save plot in both png and pdf formats.
@@ -769,13 +777,15 @@ qbarplot.df <- function(
 #' @param logY Make Y axis log10-scale.
 #' @param hline Draw a horizontal line on the plot, yintercept or FALSE
 #' @param vline Draw a vertical line on the plot, xintercept or FALSE.
-#' @param abline Draw a sloped line on the plot. Set to FALSE, or intercept = abline[1], slope = abline[2].
+#' @param abline Draw a sloped line on the plot. Set to FALSE, or `intercept = abline[1], slope = abline[2]`.
 #' @param line.col Color of the lines (vline, hline, abline). Default: "darkgrey".
 #' @param line.width Width of the line (vline, hline, abline). Default: 0.5.
 #' @param line.type Type of the line (vline, hline, abline). Default: "dashed".
 #' @param add_contour_plot Add 2D contour plot. See: http://www.sthda.com/english/articles/32-r-graphics-essentials/131-plot-two-continuous-variables-scatter-graph-and-alternatives/#continuous-bivariate-distribution
 #' @param correlation_r2 Add a correlation value to the plot
 #' @param plot Display the plot.
+#' @param xlab X-axis label. Default: NULL.
+#' @param ylab Y-axis label. Default: NULL.
 #' @param xlab.angle Rotate X-axis labels by N degree. Default: 90
 #' @param palette_use GGpubr Color palette to use.
 #' @param hide.legend hide legend
@@ -787,6 +797,7 @@ qbarplot.df <- function(
 #' @param annotation_logticks_X Logical indicating whether to add annotation logticks on X-axis. Default follows the value of `logX`.
 #' @param grid Character indicating the axis to add gridlines. Options are 'x', 'y', or 'xy'. Default is 'y'.
 #' @param ... Pass any other parameter of the corresponding plotting function(most of them should work).
+#'
 #' @examples dfx <- as.data.frame(cbind("AA" = rnorm(500), "BB" = rnorm(500)))
 #' qscatter(dfx, suffix = "2D.gaussian")
 #'
@@ -823,24 +834,26 @@ qscatter <- function(
     ...) {
   #
   print(plotname)
-  stopifnot(ncol(df_XYcol) >= 2
-            , is.numeric(x) | is.character(x)
-            , is.numeric(y) | is.character(y)
-            )
+  stopifnot(
+    ncol(df_XYcol) >= 2,
+    is.numeric(x) | is.character(x),
+    is.numeric(y) | is.character(y)
+  )
 
   if (is.matrix(df_XYcol)) df_XYcol <- as.data.frame(df_XYcol)
 
-  if(!is.numeric(x)) {
-    stopifnot(x %in% colnames(df_XYcol) )
+  if (!is.numeric(x)) {
+    stopifnot(x %in% colnames(df_XYcol))
     x <- which(colnames(df_XYcol) == x)
   }
 
-  if(!is.numeric(y)) {
-    stopifnot(y %in% colnames(df_XYcol) )
+  if (!is.numeric(y)) {
+    stopifnot(y %in% colnames(df_XYcol))
     y <- which(colnames(df_XYcol) == y)
   }
 
-  vars <- colnames(df_XYcol); names(vars) <- vars
+  vars <- colnames(df_XYcol)
+  names(vars) <- vars
   cat("Variable (column) names 1-5:", head(vars), "...\n")
   # browser()
 
@@ -898,13 +911,19 @@ qscatter <- function(
 #'
 #' @description Draw and save a boxplot
 #' @param df_XYcol_or_list Data, as 2 column data frame, where col.1 is X axis, alternatively a uniquely named list ov values.
+#' @param x The index or name of the column to be plotted on the X axis. Default: `1`.
+#' @param y The index or name of the column to be plotted on the Y axis. Default: `2`.
+#' @param col The index or name of the column to be used for coloring the plot. Default: `NULL`.
+#' @param fill Fill color of the plot. Default: `gold`.
 #' @param plotname The title of the plot and the name of the file (unless specified in `filename`).
 #' @param subtitle Optional subtitle text added below the title. Default is NULL.
+#' @param suffix Optional suffix added to the plotname. Default is NULL.
 #' @param caption Optional text added to bottom right corner of the plot. Default = suffix
 #' @param filename Manually provided filename (optional). Default: parse from `plotname`,
 #' @param ext File extension (.pdf / .png).
 #' @param also.pdf Save plot in both png and pdf formats.
 #' @param save.obj Save the ggplot object to a file. Default: FALSE.
+#' @param ylab Y-axis label. Default: `NULL`.
 #' @param logY Make Y axis log10-scale.
 #' @param hline Draw a horizontal line on the plot.
 #' @param vline Draw a vertical line on the plot.
@@ -922,6 +941,7 @@ qscatter <- function(
 #' @param annotation_logticks_Y Logical indicating whether to add annotation logticks on Y-axis. Default follows the value of `logY`.
 #' @param grid Character indicating the axis to add gridlines. Options are 'x', 'y', or 'xy'. Default is 'y'.
 #' @param max.categ The maximum allowed number of unique categories.
+#' @param add Add additional graphical elements to the plot. Default: NULL.
 #' @param w Width of the plot.
 #' @param h Height of the plot.
 #' @param ... Pass any other parameter of the corresponding plotting function(most of them should work).
@@ -945,7 +965,6 @@ qboxplot <- function(
     stat.test = TRUE,
     # , stat.method = "wilcox.test", stat.label.y.npc = 0, stat.label.x = .5
     stat.method = NULL, stat.label.y.npc = "top", stat.label.x = NULL,
-
     palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4],
     hide.legend = FALSE,
     also.pdf = TRUE, save.obj = FALSE,
@@ -988,36 +1007,39 @@ qboxplot <- function(
   if (CodeAndRoll2::is.list2(df_XYcol_or_list)) {
     lsX <- df_XYcol_or_list
     df_XYcol <- qqqList.2.DF.ggplot(lsX)
-    if (length(fill)  == length(lsX)) {
+    if (length(fill) == length(lsX)) {
       fill <- rep(fill, sapply(lsX, length))
     }
   } else {
     df_XYcol <- df_XYcol_or_list
     stopifnot(fill %in% colnames(df_XYcol) | length(fill) == nrow(df_XYcol) |
-                is.character(fill) | is.null(fill))
+      is.character(fill) | is.null(fill))
   }
 
   .assertMaxCategories(df_XYcol, col = x, max.categ)
-  vars <- colnames(df_XYcol); names(vars) <- vars
+  vars <- colnames(df_XYcol)
+  names(vars) <- vars
 
 
   palette_use_bac <- palette_use
-  if(length(fill) > 1) {
+  if (length(fill) > 1) {
     stopifnot(length(fill) == nrow(df_XYcol) | length(fill) == 1)
-    if( length(fill) != nrow(df_XYcol)) stop("Length of fill must be 1 or equal to the number of rows in the data frame.")
-  } else if(length(fill) == 1) {
+    if (length(fill) != nrow(df_XYcol)) stop("Length of fill must be 1 or equal to the number of rows in the data frame.")
+  } else if (length(fill) == 1) {
     fill <- rep(fill, nrow(df_XYcol))
     palette_use <- fill
-  } else message("fill is NULL. Using default fill color.")
+  } else {
+    message("fill is NULL. Using default fill color.")
+  }
 
-  df_XYcol$'condition' <- fill
-  fill = "condition"
+  df_XYcol$"condition" <- fill
+  fill <- "condition"
 
 
-  if( !is.null(col)) {
+  if (!is.null(col)) {
     # browser()
-    if( is.numeric(col) & col < length(vars) ) col <- col
-    if( col %in% vars ) col <- vars[col]
+    if (is.numeric(col) & col < length(vars)) col <- col
+    if (col %in% vars) col <- vars[col]
     fill <- col # if col (color as a column name) is provided, fill is set to col
     palette_use <- palette_use_bac
   }
@@ -1035,7 +1057,7 @@ qboxplot <- function(
     add = add,
     ...
   ) +
-    ggplot2::labs(y = ylab)  +
+    ggplot2::labs(y = ylab) +
     ggpubr::grids(axis = "y") +
     ggplot2::theme(axis.text.x = ggplot2::element_text(angle = xlab.angle, hjust = 1))
 
@@ -1065,6 +1087,10 @@ qboxplot <- function(
 #'
 #' @description Draw and save a violin plot
 #' @param df_XYcol_or_list Data, as 2 column data frame, where col.1 is X axis, alternatively a uniquely named list ov values.
+#' @param x The index or name of the column to be plotted on the X axis. Default: `1`.
+#' @param y The index or name of the column to be plotted on the Y axis. Default: `2`.
+#' @param col The index or name of the column to be used for coloring the plot. Default: `NULL`.
+#' @param fill Fill color of the plot. Default: `gold`.
 #' @param plotname Name of the plot
 #' @param subtitle Optional subtitle text added below the title. Default is NULL.
 #' @param suffix Optional suffix added to the filename. Default is NULL.
@@ -1125,16 +1151,16 @@ qviolin <- function(
     max.categ = 100,
     w = qqqAxisLength(df_XYcol_or_list), h = 6,
     ...) {
-
   df_XYcol <- if (CodeAndRoll2::is.list2(df_XYcol_or_list)) qqqList.2.DF.ggplot(df_XYcol_or_list) else df_XYcol_or_list
   message("nrow(df_XYcol): ", nrow(df_XYcol))
   .assertMaxCategories(df_XYcol, col = x, max.categ)
 
   # Define fill color
-  vars <- colnames(df_XYcol); names(vars) <- vars
-  if( !is.null(col)) {
-    if( is.numeric(col) & col < length(vars) ) col <- col
-    if( col %in% vars ) col <- vars[col]
+  vars <- colnames(df_XYcol)
+  names(vars) <- vars
+  if (!is.null(col)) {
+    if (is.numeric(col) & col < length(vars)) col <- col
+    if (col %in% vars) col <- vars[col]
     fill <- col # if col (color as a column name) is provided, fill is set to col
   }
 
@@ -1177,11 +1203,16 @@ qviolin <- function(
 #'
 #' @description Generates a stripchart and saves the plot for a given 2-column dataframe and offers several customizations.
 #' @param df_XYcol_or_list Data, as 2 column data frame, where col.1 is X axis, alternatively a uniquely named list ov values.
+#' @param x The index or name of the column to be plotted on the X axis. Default: `1`.
+#' @param y The index or name of the column to be plotted on the Y axis. Default: `2`.
+#' @param col The index or name of the column to be used for coloring the plot. Default: `NULL`.
+#' @param fill Fill color of the plot. Default: `gold`.
 #' @param plotname Name of the plot
 #' @param subtitle Optional subtitle text added below the title. Default is NULL.
 #' @param suffix Optional suffix added to the filename. Default is NULL.
 #' @param caption Optional text added to bottom right corner of the plot. Default = suffix
 #' @param filename Manually provided filename (optional). Default: parse from `plotname`,
+#' @param ylab Y-axis label. Default: NULL.z
 #' @param plot Display the plot.
 #' @param add Add boxplot or violin chart? Default  add = c("violin", "mean_sd"), it can be "boxplot" or only "mean_sd".
 #' @param ext File extension (.pdf / .png).
@@ -1241,27 +1272,26 @@ qstripchart <- function(
     max.categ = 100,
     w = qqqAxisLength(df_XYcol_or_list), h = 6,
     ...) {
-
   message("Column 1 should be the X-, Column 2 the Y-axis.")
   stopifnot(
     CodeAndRoll2::is.list2(df_XYcol_or_list) | is.data.frame(df_XYcol_or_list)
     # , length(df_XYcol_or_list) > 2
-    , length(x) == 1, length(y) == 1
-    , is.numeric(x) | is.character(x)
-    , is.numeric(y) | is.character(y)
-    , is.null(col) | is.numeric(col) | is.character(col)
-    , is.null(fill) | is.numeric(fill) | is.character(fill)
-
+    , length(x) == 1, length(y) == 1,
+    is.numeric(x) | is.character(x),
+    is.numeric(y) | is.character(y),
+    is.null(col) | is.numeric(col) | is.character(col),
+    is.null(fill) | is.numeric(fill) | is.character(fill)
   )
 
   df_XYcol <- if (CodeAndRoll2::is.list2(df_XYcol_or_list)) qqqList.2.DF.ggplot(df_XYcol_or_list) else df_XYcol_or_list
   .assertMaxCategories(df_XYcol, col = x, max.categ)
 
   # Define fill color
-  vars <- colnames(df_XYcol); names(vars) <- vars
-  if( !is.null(col)) {
-    if( is.numeric(col) & col < length(vars) ) col <- col
-    if( col %in% vars ) col <- vars[col]
+  vars <- colnames(df_XYcol)
+  names(vars) <- vars
+  if (!is.null(col)) {
+    if (is.numeric(col) & col < length(vars)) col <- col
+    if (col %in% vars) col <- vars[col]
     fill <- col # if col (color as a column name) is provided, fill is set to col
   }
   # browser()
@@ -1354,7 +1384,7 @@ qvenn <- function(
     w = 8, h = 0.75 * w,
     ...) {
   #
-  if(!is.null(caption2)) caption <- paste0(caption2, "\n", caption, "\n")
+  if (!is.null(caption2)) caption <- paste0(caption2, "\n", caption, "\n")
 
   p <- ggVennDiagram::ggVennDiagram(list, ..., ) +
     scale_fill_gradient(low = col.min, high = col.max) +
@@ -1377,8 +1407,12 @@ qvenn <- function(
     sppp(plotname, suffix, s2, "venn", ext)
   }
 
-  if (save) qqSave(ggobj = p, title = plotname, fname = file_name,
-                   ext = ext, w = w, h = h, also.pdf = also.pdf, save.obj = save.obj)
+  if (save) {
+    qqSave(
+      ggobj = p, title = plotname, fname = file_name,
+      ext = ext, w = w, h = h, also.pdf = also.pdf, save.obj = save.obj
+    )
+  }
   if (mdlink & save) qMarkdownImageLink(file_name)
   if (plot) p
 }
@@ -1455,8 +1489,8 @@ qvenn <- function(
 #     color = colorRampPalette(c( "#0073c2","white","#efc000"))(100),
 #     legendName = "Intensity",
 #     scale = "row",
-#     cluster_rows = F,
-#     cluster_cols = F,
+#     cluster_rows = FALSE,
+#     cluster_cols = FALSE,
 #     annotation_rows = NULL,
 #     annotation_cols = NULL,
 #     annotation_color = NULL,
@@ -1583,7 +1617,8 @@ qqSave <- function(
       h <- wA4 / 2
     }
   }
-  fnp <- paste0(getwd(), "/", fname); print(fnp)
+  fnp <- paste0(getwd(), "/", fname)
+  print(fnp)
 
   # Set the plot background to white
   ggobj <- ggobj + theme(plot.background = element_rect(fill = bgcol, color = bgcol))
@@ -1593,15 +1628,17 @@ qqSave <- function(
     cowplot::save_plot(
       plot = ggobj, filename = fname2, base_width = w, base_height = h,
       title = ww.ttl_field(title, creator = "ggExpress"),
-      ... )
+      ...
+    )
   }
 
   cowplot::save_plot(
     plot = ggobj, filename = fname,
-    base_width = w, base_height = h, ...)
+    base_width = w, base_height = h, ...
+  )
 
-  if(save.obj) {
-    fnp.qs <- sppp(fnp, 'qs')
+  if (save.obj) {
+    fnp.qs <- sppp(fnp, "qs")
     qs::qsave(ggobj, file = fnp.qs)
     CMND <- paste0("ggplot_obj <- xread('", fnp.qs, "')")
     message(CMND)
@@ -1634,7 +1671,7 @@ q32vA4_grid_plot <- function(
     plot_list,
     suffix = NULL,
     plotname = FixPlotName(substitute(plot_list), suffix),
-    plot = F,
+    plot = FALSE,
     nrow = 3, ncol = 2, extension = c("pdf", "png")[2],
     scale = 1,
     h = hA4 * scale, w = wA4 * scale,
@@ -1724,6 +1761,7 @@ qMarkdownImageLink <- function(file_name = "myplot.pdf") {
 #' @description Define Axis Length
 #' @param vec The variable to plot.
 #' @param minLength minLength
+#' @param factor Length adjustment factor.
 #'
 #' @examples qqqAxisLength()
 qqqAxisLength <- function(vec = 1:20, minLength = 6, factor = 0.4) {
diff --git a/man/q32vA4_grid_plot.Rd b/man/q32vA4_grid_plot.Rd
index ecced4d..cfed473 100644
--- a/man/q32vA4_grid_plot.Rd
+++ b/man/q32vA4_grid_plot.Rd
@@ -8,7 +8,7 @@ q32vA4_grid_plot(
   plot_list,
   suffix = NULL,
   plotname = FixPlotName(substitute(plot_list), suffix),
-  plot = F,
+  plot = FALSE,
   nrow = 3,
   ncol = 2,
   extension = c("pdf", "png")[2],
diff --git a/man/qbarplot.Rd b/man/qbarplot.Rd
index 743d62b..93fd58b 100644
--- a/man/qbarplot.Rd
+++ b/man/qbarplot.Rd
@@ -72,7 +72,7 @@ qbarplot(
 
 \item{col}{Color of the plot.}
 
-\item{xlab}{X-axis label.}
+\item{xlab}{X-axis label. Default: "".}
 
 \item{xlab.angle}{Rotate X-axis labels by N degree. Default: 90}
 
@@ -94,6 +94,8 @@ qbarplot(
 
 \item{grid}{Character indicating the axis to add gridlines. Options are 'x', 'y', or 'xy'. Default is 'y'.}
 
+\item{ylab}{Y-axis label. Default: NULL.}
+
 \item{w}{Width of the plot.}
 
 \item{h}{Height of the plot.}
diff --git a/man/qbarplot.df.Rd b/man/qbarplot.df.Rd
index 2c663ae..3b9a0a2 100644
--- a/man/qbarplot.df.Rd
+++ b/man/qbarplot.df.Rd
@@ -36,7 +36,6 @@ qbarplot.df(
   limitsize = FALSE,
   grid = "y",
   max.categ = 10,
-  top = NULL,
   w = qqqAxisLength(df),
   h = 5,
   ...
@@ -45,11 +44,11 @@ qbarplot.df(
 \arguments{
 \item{df}{The variable to plot.}
 
-\item{x}{Colname to split along X axis. Def colnames(df)\link{1}}
+\item{x}{Colname to split along X axis. Default: \code{colnames(df)[1]}.}
 
-\item{y}{Colname to count along y axis. Def colnames(df)\link{3}}
+\item{y}{Colname to count along y axis. Default: \code{colnames(df)[2]}.}
 
-\item{fill}{Color (split) by along Y.}
+\item{fill}{Color (split) by along Y. Default: \code{colnames(df)[3]}.}
 
 \item{color}{Color (split) by along Y.}
 
@@ -71,6 +70,8 @@ qbarplot.df(
 
 \item{filename}{Manually provided filename (optional). Default: parse from \code{plotname},}
 
+\item{scale}{Scale the Y axis to 100\%.}
+
 \item{plot}{Display the plot.}
 
 \item{save}{Save the plot into a file.}
@@ -85,7 +86,7 @@ qbarplot.df(
 
 \item{xlab.angle}{Rotate X-axis labels by N degree. Default: 90}
 
-\item{xlab}{X-axis label.}
+\item{xlab}{X-axis label. Default: NULL.}
 
 \item{logY}{Make Y axis log10-scale.}
 
@@ -99,6 +100,8 @@ qbarplot.df(
 
 \item{grid}{Character indicating the axis to add gridlines. Options are 'x', 'y', or 'xy'. Default is 'y'.}
 
+\item{max.categ}{Maximum number of categories to show on the plot. Default is 10.}
+
 \item{w}{Width of the plot.}
 
 \item{h}{Height of the plot.}
diff --git a/man/qbarplot.stacked.from.wide.df.Rd b/man/qbarplot.stacked.from.wide.df.Rd
index ff8d347..acea4cd 100644
--- a/man/qbarplot.stacked.from.wide.df.Rd
+++ b/man/qbarplot.stacked.from.wide.df.Rd
@@ -36,7 +36,6 @@ qbarplot.stacked.from.wide.df(
   limitsize = FALSE,
   grid = "y",
   max.categ = 10,
-  top = NULL,
   w = qqqAxisLength(df, factor = 0.7),
   h = 5,
   ...
@@ -45,9 +44,11 @@ qbarplot.stacked.from.wide.df(
 \arguments{
 \item{df}{The variable to plot.}
 
-\item{x}{Colname to split along X axis. Def colnames(df)\link{1}}
+\item{x}{Colname to split along X axis. Default: "Samples".}
 
-\item{y}{Colname to count along y axis. Def colnames(df)\link{3}}
+\item{y}{Colname to count along y axis. Default: "Fraction".}
+
+\item{z}{Colname to split along Y axis. Default: "Category.}
 
 \item{color}{Color (split) by along Y.}
 
@@ -69,6 +70,8 @@ qbarplot.stacked.from.wide.df(
 
 \item{filename}{Manually provided filename (optional). Default: parse from \code{plotname},}
 
+\item{scale}{Scale the y axis. Default: TRUE.}
+
 \item{plot}{Display the plot.}
 
 \item{save}{Save the plot into a file.}
@@ -83,7 +86,7 @@ qbarplot.stacked.from.wide.df(
 
 \item{xlab.angle}{Rotate X-axis labels by N degree. Default: 90}
 
-\item{xlab}{X-axis label.}
+\item{xlab}{X-axis label. Default: \code{x}.}
 
 \item{logY}{Make Y axis log10-scale.}
 
@@ -104,8 +107,6 @@ qbarplot.stacked.from.wide.df(
 \item{h}{Height of the plot.}
 
 \item{...}{Pass any other parameter of the corresponding plotting function(most of them should work).}
-
-\item{fill}{Color (split) by along Y.}
 }
 \description{
 Draw and save a stacked barplot for each row of a dataframe.
diff --git a/man/qboxplot.Rd b/man/qboxplot.Rd
index b398fc7..f6af4ef 100644
--- a/man/qboxplot.Rd
+++ b/man/qboxplot.Rd
@@ -46,10 +46,20 @@ qboxplot(
 \arguments{
 \item{df_XYcol_or_list}{Data, as 2 column data frame, where col.1 is X axis, alternatively a uniquely named list ov values.}
 
+\item{x}{The index or name of the column to be plotted on the X axis. Default: \code{1}.}
+
+\item{y}{The index or name of the column to be plotted on the Y axis. Default: \code{2}.}
+
+\item{col}{The index or name of the column to be used for coloring the plot. Default: \code{NULL}.}
+
+\item{fill}{Fill color of the plot. Default: \code{gold}.}
+
 \item{plotname}{The title of the plot and the name of the file (unless specified in \code{filename}).}
 
 \item{subtitle}{Optional subtitle text added below the title. Default is NULL.}
 
+\item{suffix}{Optional suffix added to the plotname. Default is NULL.}
+
 \item{caption}{Optional text added to bottom right corner of the plot. Default = suffix}
 
 \item{filename}{Manually provided filename (optional). Default: parse from \code{plotname},}
@@ -74,6 +84,8 @@ qboxplot(
 
 \item{ext}{File extension (.pdf / .png).}
 
+\item{ylab}{Y-axis label. Default: \code{NULL}.}
+
 \item{logY}{Make Y axis log10-scale.}
 
 \item{annotation_logticks_Y}{Logical indicating whether to add annotation logticks on Y-axis. Default follows the value of \code{logY}.}
@@ -94,6 +106,8 @@ qboxplot(
 
 \item{max.categ}{The maximum allowed number of unique categories.}
 
+\item{add}{Add additional graphical elements to the plot. Default: NULL.}
+
 \item{w}{Width of the plot.}
 
 \item{h}{Height of the plot.}
diff --git a/man/qdensity.Rd b/man/qdensity.Rd
index 36421dc..0a4e153 100644
--- a/man/qdensity.Rd
+++ b/man/qdensity.Rd
@@ -11,6 +11,7 @@ qdensity(
   ext = MarkdownHelpers::ww.set.file.extension(default = "png", also_pdf = also.pdf),
   xlab = FALSE,
   plot = TRUE,
+  xlab.angle = 90,
   plotname = FixPlotName(substitute(vec)),
   subtitle = NULL,
   suffix = NULL,
@@ -22,10 +23,9 @@ qdensity(
   logY = FALSE,
   palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb",
     "uchicago")[4],
-  xlab.angle = 90,
   hide.legend = TRUE,
   max.names = 50,
-  grid = F,
+  grid = FALSE,
   w = 5,
   h = w,
   ...
@@ -40,10 +40,12 @@ qdensity(
 
 \item{ext}{File extension (.pdf / .png).}
 
-\item{xlab}{X-axis label.}
+\item{xlab}{X-axis label. Default: FALSE.}
 
 \item{plot}{Display the plot.}
 
+\item{xlab.angle}{Rotate X-axis labels by N degree. Default: 90}
+
 \item{plotname}{The title of the plot and the name of the file (unless specified in \code{filename}).}
 
 \item{subtitle}{Optional subtitle text added below the title. Default is NULL.}
@@ -64,8 +66,6 @@ qdensity(
 
 \item{palette_use}{GGpubr Color palette to use.}
 
-\item{xlab.angle}{Rotate X-axis labels by N degree. Default: 90}
-
 \item{hide.legend}{hide legend}
 
 \item{max.names}{The maximum number of names still to be shown on the axis.}
diff --git a/man/qpie.Rd b/man/qpie.Rd
index 43425a5..2dcb451 100644
--- a/man/qpie.Rd
+++ b/man/qpie.Rd
@@ -88,13 +88,13 @@ qpie(
 
 \item{both_pc_and_value}{Report both percentage AND number.}
 
+\item{labels}{Slice labels. Set to NULL to remove slice names.}
+
 \item{w}{Width of the plot.}
 
 \item{h}{Height of the plot.}
 
 \item{...}{Pass any other parameter of the corresponding plotting function(most of them should work).}
-
-\item{label}{Slice labels. Set to NULL to remove slice names.}
 }
 \description{
 Draw and save a pie chart
diff --git a/man/qqqAxisLength.Rd b/man/qqqAxisLength.Rd
index c2edca0..5b6e0a2 100644
--- a/man/qqqAxisLength.Rd
+++ b/man/qqqAxisLength.Rd
@@ -10,6 +10,8 @@ qqqAxisLength(vec = 1:20, minLength = 6, factor = 0.4)
 \item{vec}{The variable to plot.}
 
 \item{minLength}{minLength}
+
+\item{factor}{Length adjustment factor.}
 }
 \description{
 Define Axis Length
diff --git a/man/qscatter.Rd b/man/qscatter.Rd
index ae17d39..8bc030d 100644
--- a/man/qscatter.Rd
+++ b/man/qscatter.Rd
@@ -49,6 +49,10 @@ qscatter(
 \arguments{
 \item{df_XYcol}{Data, as 2 column data frame, where col.1 is X axis.}
 
+\item{x}{The index or name of the column to be plotted on the X axis. Default: \code{1}.}
+
+\item{y}{The index or name of the column to be plotted on the Y axis. Default: \code{2}.}
+
 \item{plotname}{The name of the file and title of the plot.}
 
 \item{subtitle}{Optional subtitle text added below the title. Default is NULL.}
@@ -65,7 +69,9 @@ qscatter(
 
 \item{col}{Color of the plot.}
 
-\item{label}{Point labels}
+\item{label}{Point labels. Default: NULL.}
+
+\item{repel}{Repel labels from each other. Default: TRUE.}
 
 \item{palette_use}{GGpubr Color palette to use.}
 
@@ -81,13 +87,17 @@ qscatter(
 
 \item{annotation_logticks_X}{Logical indicating whether to add annotation logticks on X-axis. Default follows the value of \code{logX}.}
 
+\item{xlab}{X-axis label. Default: NULL.}
+
+\item{ylab}{Y-axis label. Default: NULL.}
+
 \item{xlab.angle}{Rotate X-axis labels by N degree. Default: 90}
 
 \item{hline}{Draw a horizontal line on the plot, yintercept or FALSE}
 
 \item{vline}{Draw a vertical line on the plot, xintercept or FALSE.}
 
-\item{abline}{Draw a sloped line on the plot. Set to FALSE, or intercept = abline\link{1}, slope = abline\link{2}.}
+\item{abline}{Draw a sloped line on the plot. Set to FALSE, or \verb{intercept = abline[1], slope = abline[2]}.}
 
 \item{line.col}{Color of the lines (vline, hline, abline). Default: "darkgrey".}
 
diff --git a/man/qstripchart.Rd b/man/qstripchart.Rd
index 259dcbc..e415f34 100644
--- a/man/qstripchart.Rd
+++ b/man/qstripchart.Rd
@@ -46,6 +46,14 @@ qstripchart(
 \arguments{
 \item{df_XYcol_or_list}{Data, as 2 column data frame, where col.1 is X axis, alternatively a uniquely named list ov values.}
 
+\item{x}{The index or name of the column to be plotted on the X axis. Default: \code{1}.}
+
+\item{y}{The index or name of the column to be plotted on the Y axis. Default: \code{2}.}
+
+\item{col}{The index or name of the column to be used for coloring the plot. Default: \code{NULL}.}
+
+\item{fill}{Fill color of the plot. Default: \code{gold}.}
+
 \item{plotname}{Name of the plot}
 
 \item{subtitle}{Optional subtitle text added below the title. Default is NULL.}
@@ -56,6 +64,8 @@ qstripchart(
 
 \item{filename}{Manually provided filename (optional). Default: parse from \code{plotname},}
 
+\item{ylab}{Y-axis label. Default: NULL.z}
+
 \item{plot}{Display the plot.}
 
 \item{add}{Add boxplot or violin chart? Default  add = c("violin", "mean_sd"), it can be "boxplot" or only "mean_sd".}
diff --git a/man/qviolin.Rd b/man/qviolin.Rd
index 1bdfc96..451cc48 100644
--- a/man/qviolin.Rd
+++ b/man/qviolin.Rd
@@ -43,6 +43,14 @@ qviolin(
 \arguments{
 \item{df_XYcol_or_list}{Data, as 2 column data frame, where col.1 is X axis, alternatively a uniquely named list ov values.}
 
+\item{x}{The index or name of the column to be plotted on the X axis. Default: \code{1}.}
+
+\item{y}{The index or name of the column to be plotted on the Y axis. Default: \code{2}.}
+
+\item{col}{The index or name of the column to be used for coloring the plot. Default: \code{NULL}.}
+
+\item{fill}{Fill color of the plot. Default: \code{gold}.}
+
 \item{plotname}{Name of the plot}
 
 \item{subtitle}{Optional subtitle text added below the title. Default is NULL.}