diff --git a/.gitignore b/.gitignore
index 9cd12d8..5460e43 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,4 +47,5 @@ vignettes/*.pdf
 *.knit.md
 
 # R Environment Variables
-.Renviron
\ No newline at end of file
+.Renviron
+.Rproj.user
diff --git a/DESCRIPTION b/DESCRIPTION
index 4b4bcb6..bb986cd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MarkdownReports
 Title: Generate Scientific Figures and Reports Easily
-Version: 4.1.1.3
+Version: 4.1.0
 Authors@R: 
     person(given = "Abel",
            family = "Vertesy",
@@ -36,6 +36,7 @@ Imports:
     vioplot
 Encoding: UTF-8
 LazyData: true
-Packaged: 2019-11-27 16:25:54
+Packaged: 2020-12-16 11:20:44
 Repository: CRAN
-RoxygenNote: 7.0.0
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1
diff --git a/Development/Development.bac b/Development/Development.bac
index 66c77f2..6caad91 100644
--- a/Development/Development.bac
+++ b/Development/Development.bac
@@ -37,7 +37,7 @@ utils::globalVariables(c('OutDirOrig', 'OutDir', 'ParentDir', 'path_of_report',
 #' @param OutDir The output directory (absolute / full path).
 #' @param title Manually set the title of the report.
 #' @param append Set append to TRUE if you do not want to overwrite the previous report.
-#' @param backupfolder Create a time-stamped backup folder inside the working directory (OutDir).
+#' @param backupfolder Create a time-stamped backup folder inside the working directory (OutDir)?
 #' @param recursive.folder Create output folder recursively, if parent folders do not exist. Parameter for dir.create().
 #' Use continue_logging_markdown() if you return logging into an existing report.
 #' FALSE by default: rerunning the script overwrites the previous report. Archive reports manually
@@ -73,7 +73,7 @@ utils::globalVariables(c('OutDirOrig', 'OutDir', 'ParentDir', 'path_of_report',
 #' append = TRUE, b.png4Github = TRUE)
 
 setup_MarkdownReports <-
-  function(OutDir = getwd(),
+  function (OutDir = getwd(),
             scriptname = basename(OutDir),
             title = "",
             setDir = TRUE,
@@ -101,8 +101,8 @@ setup_MarkdownReports <-
     if (!exists(OutDir)) {
       dir.create(OutDir, showWarnings = FALSE, recursive = recursive.folder)
     }
-    OutDir = AddTrailingSlash(OutDir) # add '/' if necessary
-    OutDir = RemoveDoubleSlash(OutDir)
+    if (!substrRight(OutDir, 1) == "/")
+      OutDir = paste0(OutDir, "/") # add '/' if necessary
 
     ww.assign_to_global("OutDir", OutDir, 1)
     iprint("All files will be saved under 'OutDir': ", OutDir)
@@ -147,7 +147,7 @@ setup_MarkdownReports <-
         capture.output(
           sessioninfo::session_info()
         ),con = paste0(".sessionInfo.", format(Sys.time(), format ="%Y.%m.%d" ),".txt")
-        )
+      )
 
       options("width"= defWidth)
       rm(defWidth)
@@ -173,7 +173,7 @@ setup_MarkdownReports <-
     ww.assign_to_global("b.scriptname", scriptname, 1)
     ww.assign_to_global("b.def.color", b.def.color, 1)
     ww.assign_to_global("b.report.not.found",
-           "Path to the Markdown report file is not defined in path_of_report", 1)
+                        "Path to the Markdown report file is not defined in path_of_report", 1)
   }
 
 # create_set_SubDir
@@ -190,16 +190,18 @@ setup_MarkdownReports <-
 #' @examples create_set_SubDir (makeOutDirOrig = TRUE, setDir = TRUE, "MySubFolder")
 
 create_set_SubDir <-
-  function(..., define.ParentDir = TRUE,
+  function (..., define.ParentDir = TRUE,
             setDir = TRUE,
             verbose = TRUE) {
     b.Subdirname = kollapse(...)
     OutDir = ww.set.OutDir()
 
     NewOutDir = kollapse(OutDir, ..., print = FALSE)
-
-    NewOutDir = AddTrailingSlash(NewOutDir) # add '/' if necessary
-    NewOutDir = RemoveDoubleSlash(NewOutDir)
+    if (!substrRight(NewOutDir, 1) == "/")
+      NewOutDir = paste0(NewOutDir, "/") # add '/' if necessary
+    NewOutDir = gsub(x = NewOutDir,
+                     pattern = '//',
+                     replacement = '/') # replace //
     if (verbose) iprint("All files will be saved under 'NewOutDir': ", NewOutDir)
     if (!dir.exists(NewOutDir)) {
       dir.create(NewOutDir, showWarnings = FALSE)
@@ -233,7 +235,7 @@ create_set_SubDir <-
 #' @examples create_set_Original_OutDir (getwd(),"/")
 
 create_set_Original_OutDir <-
-  function(NewOutDir = OutDirOrig,
+  function (NewOutDir = OutDirOrig,
             b.Subdirname = FALSE,
             setDir = TRUE,
             verbose = TRUE) {
@@ -257,7 +259,7 @@ create_set_Original_OutDir <-
 #' @examples OutDir = paste0(getwd(),"/", collapse = "")
 #' continue_logging_markdown (b.scriptname = "Analysis")
 
-continue_logging_markdown <- function(b.scriptname) {
+continue_logging_markdown <- function (b.scriptname) {
   path = ww.set.OutDir()
   path_of_report <-
     kollapse(path, b.scriptname, ".log.md", print = FALSE)
@@ -287,10 +289,13 @@ continue_logging_markdown <- function(b.scriptname) {
 #' @export
 #' @examples create_set_OutDir (setDir = TRUE, getwd(),"/"   )
 
-create_set_OutDir <- function(..., setDir = TRUE, verbose = TRUE) {
+create_set_OutDir <- function (..., setDir = TRUE, verbose = TRUE) {
   OutDir = kollapse(..., print = FALSE)
-  OutDir = AddTrailingSlash(OutDir) # add '/' if necessary
-  OutDir = RemoveDoubleSlash(OutDir)
+  if (!substrRight(OutDir, 1) == "/")
+    OutDir = paste0(OutDir, "/") # add '/' if necessary
+  OutDir = gsub(x = OutDir,
+                pattern = '//',
+                replacement = '/')
   if (verbose) iprint("All files will be saved under 'OutDir': ", OutDir)
   if (!exists(OutDir)) {
     dir.create(OutDir, showWarnings = FALSE)
@@ -313,7 +318,7 @@ create_set_OutDir <- function(..., setDir = TRUE, verbose = TRUE) {
 #' @param plotname Title of the plot (main parameter) and also the name of the file.
 #' @param OverwritePrevPDF Overwrite previous PDF image (as name stored in plotnameLastPlot).
 #' If FALSE, it creates a name from the date.
-#' @param ... Pass any other parameter of the corresponding plotting function(most of them should
+#' @param ... Pass any other parameter of the corresponding plotting function (most of them should
 #'   work).
 #' @param w Width of the saved pdf image, in inches.
 #' @param h Height of the saved pdf image, in inches.
@@ -325,7 +330,7 @@ create_set_OutDir <- function(..., setDir = TRUE, verbose = TRUE) {
 #' , mdlink = FALSE, ManualName = FALSE)
 
 wplot_save_this <-
-  function(plotname = ww.autoPlotName(),
+  function (plotname = ww.autoPlotName(),
             ...,
             OverwritePrevPDF = TRUE,
             w = unless.specified("b.defSize", 7),
@@ -347,39 +352,6 @@ wplot_save_this <-
   }
 
 
-#' wplot_save_pheatmap
-#'
-#' Save pheatmap object. Modified from:
-#' https://stackoverflow.com/questions/43051525/how-to-draw-pheatmap-plot-to-screen-and-also-save-to-file
-#' @param x The pheatmap object to save.
-#' @param filename File name (saved as .pdf, inside working directory).
-#' @param width width of the plot in inches.
-#' @param height height of the plot in inches.
-#' @export
-#'
-#' @examples test = matrix(rnorm(200), 20, 10);
-#' colnames(test) = paste("Test", 1:10, sep = "");
-#' rownames(test) = paste("Gene", 1:20, sep = "");
-#' ph.test <- pheatmap::pheatmap(test);
-#' wplot_save_pheatmap(ph.test)
-
-wplot_save_pheatmap <-
-  function(x,
-           filename = substitute(x),
-           width = 15,
-           height = width) {
-    stopifnot(!missing(x))
-    filename <- ppp(filename, ".heatmap.pdf")
-    pdf(file = filename,
-        width = width,
-        height = height)
-    grid::grid.newpage()
-    grid::grid.draw(x$gtable)
-    dev.off()
-    print(kpps(getwd(), filename))
-  }
-
-
 #' wplot
 #'
 #' Create and save scatter plots as .pdf, in "OutDir". If mdlink = TRUE, it inserts a .pdf and a .png
@@ -393,7 +365,7 @@ wplot_save_pheatmap <-
 #' @param df2col Input data frame to be plotted_2columns
 #' @param col Color of the plot.
 #' @param pch Define the symbol for each data point. A number [0-25] or any string between ""-s.
-#' @param ... Pass any other parameter of the corresponding plotting function(most of them should
+#' @param ... Pass any other parameter of the corresponding plotting function (most of them should
 #'   work).
 #' @param plotname Title of the plot (main parameter) and also the name of the file.
 #' @param ylim manual Y-limits error bar
@@ -433,7 +405,7 @@ wplot_save_pheatmap <-
 #' a = FALSE, b = FALSE, lty = 1, lwd = 1, col_abline = 1)
 
 wplot <-
-  function(df2col,
+  function (df2col,
             col = 1,
             pch = 18,
             ...,
@@ -561,7 +533,7 @@ wplot <-
 #' A scatterplot with color gradient and color legend. Modified from:
 #' http://stackoverflow.com/questions/20127282/r-color-scatterplot-points-by-col-value-with-legend
 #'
-#' @param ... Pass any other parameter of the corresponding plotting function(most of them should
+#' @param ... Pass any other parameter of the corresponding plotting function (most of them should
 #'   work).
 #' @param xlab X axis label
 #' @param ylab Y axis label
@@ -602,7 +574,7 @@ wplot <-
 
 
 wscatter.fill <-
-  function(df2col = cbind("A" = rnorm(100), "B" = rnorm(100)),
+  function (df2col = cbind("A" = rnorm(100), "B" = rnorm(100)),
             ...,
             color,
             xlim = range(df2col[, 1]),
@@ -750,7 +722,7 @@ wscatter.fill <-
 #' link in the markdown report, set by "path_of_report". The .png version is not created, only the
 #' link is put in place, not to overwrite previous versions.
 #' @param variable The variable to plot.
-#' @param ... Pass any other parameter of the corresponding plotting function(most of them should
+#' @param ... Pass any other parameter of the corresponding plotting function (most of them should
 #'   work).
 #' @param col Color of the plot.
 #' @param sub Subtitle below the plot.
@@ -788,7 +760,7 @@ wscatter.fill <-
 #' arrow_width = 0.1, arrow_lwd = 1)
 
 wbarplot <-
-  function(variable,
+  function (variable,
             ...,
             col = unless.specified("b.def.colors", "gold1"),
             sub = FALSE,
@@ -955,7 +927,7 @@ wbarplot <-
 #' @param lcol Color of the line.
 #' @param filtercol Color bars below / above the threshold with red / green. Define the direction by
 #'   -1 or 1. Takes effect if "vline" is defined.
-#' @param ... Pass any other parameter of the corresponding plotting function(most of them should
+#' @param ... Pass any other parameter of the corresponding plotting function (most of them should
 #'   work).
 #' @param filter filtervalues
 #' @param passequal Pass equal values
@@ -971,7 +943,7 @@ wbarplot <-
 #' lcol = 2, filtercol = 0)
 
 whist <-
-  function(variable,
+  function (variable,
             ...,
             breaks = 20,
             col = unless.specified("b.def.color", "gold1"),
@@ -1110,7 +1082,7 @@ whist <-
 #' link in the markdown report, set by "path_of_report". The .png version is not created, only the
 #' link is put in place, not to overwrite previous versions.
 #' @param yourlist The variable to plot.
-#' @param ... Pass any other parameter of the corresponding plotting function(most of them should
+#' @param ... Pass any other parameter of the corresponding plotting function (most of them should
 #'   work).
 #' @param main Title of the plot and also the name of the file.
 #' @param sub Subtitle below the plot.
@@ -1131,7 +1103,7 @@ whist <-
 #'  tilted_text = FALSE, w = 7, mdlink = FALSE)
 
 wboxplot <-
-  function(yourlist,
+  function (yourlist,
             main = as.character(substitute(yourlist)),
             sub = FALSE,
             ylab = "",
@@ -1202,7 +1174,7 @@ wboxplot <-
 #' link is put in place, not to overwrite previous versions.
 #' @param NamedVector The variable to plot.
 #' @param plotname Title of the plot (main parameter) and also the name of the file.
-#' @param ... Pass any other parameter of the corresponding plotting function(most of them should
+#' @param ... Pass any other parameter of the corresponding plotting function (most of them should
 #'   work).
 #' @param percentage Display percentage instead of counts. TRUE by default.
 #' @param both_pc_and_value Report both percentage AND number.
@@ -1218,7 +1190,7 @@ wboxplot <-
 #' w = 7, mdlink = FALSE)
 
 wpie <-
-  function(NamedVector,
+  function (NamedVector,
             percentage = TRUE,
             both_pc_and_value = FALSE,
             plotname = substitute(NamedVector),
@@ -1289,7 +1261,7 @@ wpie <-
 #' link is put in place, not to overwrite previous versions.
 #'
 #' @param yourlist Input list to be plotted.
-#' @param ... Pass any other parameter of the corresponding plotting function(most of them should
+#' @param ... Pass any other parameter of the corresponding plotting function (most of them should
 #'   work).
 #' @param main Title of the plot (main parameter) and also the name of the file.
 #' @param sub Subtitle below the plot.
@@ -1324,7 +1296,7 @@ wpie <-
 #' wstripchart (yourlist = my.ls)
 
 wstripchart <-
-  function(yourlist,
+  function (yourlist,
             main = as.character(substitute(yourlist)),
             sub = NULL,
             ylab = "",
@@ -1442,7 +1414,7 @@ wstripchart <-
 #' .pdf and a .png link in the markdown report, set by "path_of_report". The .png version is not
 #' created, only the link is put in place, not to overwrite previous versions.
 #' @param yourlist Input list to be plotted.
-#' @param ... Pass any other parameter of the corresponding plotting function(most of them should
+#' @param ... Pass any other parameter of the corresponding plotting function (most of them should
 #'   work).
 #' @param main Title of the plot (main parameter) and also the name of the file.
 #' @param sub Subtitle below the plot.
@@ -1476,110 +1448,110 @@ wstripchart <-
 #' metod = jitter, jitter = 0.2, w = 7, incrBottMarginBy = 0, tilted_text = FALSE, mdlink = FALSE)
 
 
-wstripchart_list <- function(yourlist,
-            ...,
-            main = as.character(substitute(yourlist)),
-            sub = NULL,
-            ylab = "",
-            xlab = "",
-            border = 1,
-            bxpcol = 0,
-            pch = 18,
-            pchlwd = 1,
-            pchcex = 1.5,
-            incrBottMarginBy = 0,
-            tilted_text = FALSE,
-            bg = "chartreuse2",
-            col = "black",
-            metod = "jitter",
-            jitter = 0.2,
-            savefile = unless.specified("b.save.wplots"),
-            w = unless.specified("b.defSize"),
-            h = w,
-            mdlink = ww.set.mdlink(),
-            PNG = unless.specified("b.usepng", F)) {
-    fname = kollapse(main, ".stripchart")
-    if (incrBottMarginBy) {
-      .ParMarDefault <- par("mar")
-      par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4]))
-    } 	# Tune the margin
-    cexNsize = 1 / abs(log10(length(list)))
-    cexNsize = min(cexNsize, 1)
-    if (tilted_text) {
-      xlab = FALSE
-    } else {
-      xlab = TRUE
-    }
-    plotname <-
-      main # to avoid circular reference in the inside function argument
-    boxplot(
-      yourlist,
-      ...,
-      show.names = xlab,
-      main = plotname,
-      sub = sub,
-      border = border,
-      outpch = NA,
-      las = 2,
-      ylab = NA,
-      col = bxpcol,
-      cex.axis = cexNsize
-    )
-    mtext(ylab, side = 2, line = 2)
-    for (i in 1:length(yourlist)) {
-      if (length(na.omit.strip(yourlist[[i]]))) {
-        j = k = i
-        if (length(1) < length(yourlist)) {
-          j = 1
-        }
-        if (length(bg) < length(yourlist)) {
-          k = 1
-        }
-        stripchart(
-          na.omit.strip(yourlist[[i]]),
-          at = i,
-          add = TRUE
-          ,
-          vertical = TRUE,
-          method = "jitter",
-          jitter = jitter
-          ,
-          pch = pch,
-          bg = bg[[k]],
-          col = col[[j]],
-          lwd = pchlwd,
-          cex = pchcex
-        )
+wstripchart_list <- function (yourlist,
+                              ...,
+                              main = as.character(substitute(yourlist)),
+                              sub = NULL,
+                              ylab = "",
+                              xlab = "",
+                              border = 1,
+                              bxpcol = 0,
+                              pch = 18,
+                              pchlwd = 1,
+                              pchcex = 1.5,
+                              incrBottMarginBy = 0,
+                              tilted_text = FALSE,
+                              bg = "chartreuse2",
+                              col = "black",
+                              metod = "jitter",
+                              jitter = 0.2,
+                              savefile = unless.specified("b.save.wplots"),
+                              w = unless.specified("b.defSize"),
+                              h = w,
+                              mdlink = ww.set.mdlink(),
+                              PNG = unless.specified("b.usepng", F)) {
+  fname = kollapse(main, ".stripchart")
+  if (incrBottMarginBy) {
+    .ParMarDefault <- par("mar")
+    par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4]))
+  } 	# Tune the margin
+  cexNsize = 1 / abs(log10(length(list)))
+  cexNsize = min(cexNsize, 1)
+  if (tilted_text) {
+    xlab = FALSE
+  } else {
+    xlab = TRUE
+  }
+  plotname <-
+    main # to avoid circular reference in the inside function argument
+  boxplot(
+    yourlist,
+    ...,
+    show.names = xlab,
+    main = plotname,
+    sub = sub,
+    border = border,
+    outpch = NA,
+    las = 2,
+    ylab = NA,
+    col = bxpcol,
+    cex.axis = cexNsize
+  )
+  mtext(ylab, side = 2, line = 2)
+  for (i in 1:length(yourlist)) {
+    if (length(na.omit.strip(yourlist[[i]]))) {
+      j = k = i
+      if (length(1) < length(yourlist)) {
+        j = 1
       }
-    } # for
-    if (tilted_text) {
-      xx = min(unlist(yourlist), na.rm = TRUE)
-      text(
-        x = 1:length(yourlist),
-        y = xx,
-        labels = names(yourlist)
+      if (length(bg) < length(yourlist)) {
+        k = 1
+      }
+      stripchart(
+        na.omit.strip(yourlist[[i]]),
+        at = i,
+        add = TRUE
         ,
-        xpd = TRUE,
-        srt = 45,
-        adj = c(1, 3)
-      )
-    }
-    if (savefile) {
-      ww.dev.copy(
-        PNG_ = PNG,
-        fname_ = fname,
-        w_ = w,
-        h_ = h
+        vertical = TRUE,
+        method = "jitter",
+        jitter = jitter
+        ,
+        pch = pch,
+        bg = bg[[k]],
+        col = col[[j]],
+        lwd = pchlwd,
+        cex = pchcex
       )
     }
-    if (incrBottMarginBy) {
-      par("mar" = .ParMarDefault)
-    }
-    ww.assign_to_global("plotnameLastPlot", fname, 1)
-    if (mdlink & savefile) {
-      md.image.linker(fname_wo_ext = fname)
-    }
+  } # for
+  if (tilted_text) {
+    xx = min(unlist(yourlist), na.rm = TRUE)
+    text(
+      x = 1:length(yourlist),
+      y = xx,
+      labels = names(yourlist)
+      ,
+      xpd = TRUE,
+      srt = 45,
+      adj = c(1, 3)
+    )
   }
+  if (savefile) {
+    ww.dev.copy(
+      PNG_ = PNG,
+      fname_ = fname,
+      w_ = w,
+      h_ = h
+    )
+  }
+  if (incrBottMarginBy) {
+    par("mar" = .ParMarDefault)
+  }
+  ww.assign_to_global("plotnameLastPlot", fname, 1)
+  if (mdlink & savefile) {
+    md.image.linker(fname_wo_ext = fname)
+  }
+}
 
 
 
@@ -1593,7 +1565,7 @@ wstripchart_list <- function(yourlist,
 #'
 #' @param yourlist Input list to be plotted.
 #' @param ... Pass any other parameter of the corresponding
-#' plotting function(most of them should work).
+#' plotting function (most of them should work).
 #' @param main Title of the plot (main parameter) and also the name of the file.
 #' @param sub Subtitle below the plot.
 #' @param xlab X-axis label.
@@ -1620,7 +1592,7 @@ wstripchart_list <- function(yourlist,
 
 
 wvioplot_list <-
-  function(yourlist,
+  function (yourlist,
             ...,
             main = as.character(substitute(yourlist)),
             sub = NULL,
@@ -1728,7 +1700,7 @@ wvioplot_list <-
 #' not to overwrite previous versions.
 #' @param yourlist Input list to be plotted.
 #' @param ... Pass any other parameter of the corresponding plotting
-#' function(most of them should work).
+#' function (most of them should work).
 #' @param main Title of the plot (main parameter) and also the name of the file.
 #' @param sub Subtitle below the plot.
 #' @param xlab X-axis label.
@@ -1759,7 +1731,7 @@ wvioplot_list <-
 #' # bg = 0, col = "black", metod = "jitter", jitter = 0.1, w = 7, mdlink = FALSE)
 
 wviostripchart_list <-
-  function(yourlist,
+  function (yourlist,
             ...,
             pch = 20,
             viocoll = c(2:(length(yourlist) + 1)),
@@ -1874,7 +1846,7 @@ wviostripchart_list <-
 #' @param fill Background color vec
 #' @param subt Subtitle
 #' @param ... Pass any other parameter of the corresponding venn.diagram()
-#' function(most of them should work).
+#' function (most of them should work).
 #' @param w Width of the saved pdf image, in inches.
 #' @param h Height of the saved pdf image, in inches.
 #' @param mdlink Insert a .pdf and a .png image link in the markdown report,
@@ -1888,7 +1860,7 @@ wviostripchart_list <-
 
 # @importFrom VennDiagram venn.diagram
 wvenn <-
-  function(yourlist,
+  function (yourlist,
             imagetype = "png",
             alpha = .5,
             fill = 1:length(yourlist),
@@ -1955,7 +1927,7 @@ wvenn <-
 #'
 #' @param df Input data frame to be plotted
 #' @param ... Pass any other parameter of the corresponding
-#' plotting function(most of them should work).
+#' plotting function (most of them should work).
 #' @param col Color of the plot.
 #' @param savefile Save plot as pdf in OutDir, TRUE by default.
 #' @param w Width of the saved pdf image, in inches.
@@ -1970,7 +1942,7 @@ wvenn <-
 
 
 wbarplot_dfCol <-
-  function(df,
+  function (df,
             ...,
             colName,
             col = unless.specified("b.def.colors", "gold1"),
@@ -2009,12 +1981,12 @@ wbarplot_dfCol <-
 #'
 #' Use this version of whist() if you iterate over columns  or rows of a data frame.
 #' You can name the file by naming the variable.
-#' Cannot be used with dynamically called variables (e.g. call vectors within a loop).
+#' Cannot be used with dynamically called variables [e.g. call vectors within a loop]
 #'
 #' @param df Input data frame to be plotted
 #' @param col Color of the plot.
 #' @param ... Pass any other parameter of the corresponding
-#' plotting function(most of them should work).
+#' plotting function (most of them should work).
 #' @param savefile Save plot as pdf in OutDir, TRUE by default.
 #' @param w Width of the saved pdf image, in inches.
 #' @param h Height of the saved pdf image, in inches.
@@ -2028,7 +2000,7 @@ wbarplot_dfCol <-
 #' whist_dfCol (df, colName="a", col = "gold", w = 7)
 
 whist_dfCol <-
-  function(df,
+  function (df,
             colName,
             col = unless.specified("b.def.colors", "gold1"),
             ...,
@@ -2088,7 +2060,7 @@ whist_dfCol <-
 #' Create A4 PDFs to plot multiple subplots in one file
 #' @param pname Title of the plot (main parameter) and also the name of the file.
 #' @param ... Pass any other parameter of the corresponding
-#' plotting function(most of them should work).
+#' plotting function (most of them should work).
 #' @param w Width of the saved pdf image, in inches. c("A4" = 8.27, "1col.nature" = 3.50,
 #' "2col.nature" = 7.20, "1col.cell" = 3.35, "1.5col.cell" = 4.49, "2col.cell" = 6.85).
 #' @param h Height of the saved pdf image, in inches.
@@ -2106,7 +2078,7 @@ whist_dfCol <-
 
 
 pdfA4plot_on <-
-  function(pname = date(),
+  function (pname = date(),
             ...,
             w = unless.specified("b.defSize.fullpage", 8.27),
             h = 11.69,
@@ -2160,7 +2132,7 @@ pdfA4plot_on <-
 
 
 pdfA4plot_on.layout <-
-  function(pname = date(),
+  function (pname = date(),
             ...,
             layout_mat = rbind(1, c(2, 3), 4:5),
             w = unless.specified("b.defSize.fullpage", 8.27),
@@ -2201,7 +2173,7 @@ pdfA4plot_on.layout <-
 #' @examples pdfA4plot_on.layout(pname = "MyA4_w_layout");  hist(rnorm(100)); hist(-rnorm(100))
 #' hist(10+rnorm(100)); pdfA4plot_off()
 
-pdfA4plot_off <- function() {
+pdfA4plot_off <- function () {
   x = if (exists("b.mfrow_def"))
     b.mfrow_def
   else
@@ -2233,12 +2205,12 @@ pdfA4plot_off <- function() {
 #' @param lower Size of the lower error bar. By default, it equals the upper error bar.
 #' @param width.whisker Width of the error bar whisker.
 #' @param ... Pass any other argument to the arrows function.
-#' arrows function(most of them should work).
+#' arrows function (most of them should work).
 #' @export
 #' @examples plot (1); error_bar (x = 1, y = 1, upper = .1, width.whisker = 0.1)
 
 error_bar <-
-  function(x,
+  function (x,
             y,
             upper,
             lower = upper,
@@ -2433,17 +2405,18 @@ wlegend.label <-
 #' @param w Width of the saved pdf image, in inches.
 #' @param h Height of the saved pdf image, in inches.
 #' @param ... Pass any other parameter of the corresponding
-#' text function(most of them should work).
+#' text function (most of them should work).
 #' @import graphics
 #' @export
 #'
 #' @examples barplot (1:10);
-#' barplot_label(barplotted_variable = 1:10, labels = 11:2, filename = "myBarplot.pdf")
+#' barplot_label (barplotted_variable = 1:10, labels = 11:2, filename = "myBarplot.pdf")
+
 
 
 
 barplot_label <-
-  function(barplotted_variable,
+  function (barplotted_variable,
             labels = iround(barplotted_variable),
             bottom = FALSE,
             TopOffset = .5,
@@ -2552,7 +2525,7 @@ wLinRegression <-
 #' @export
 #' @examples try.dev.off ()
 
-try.dev.off <- function() {
+try.dev.off <- function () {
   try(dev.off(), silent = TRUE)
 }
 
@@ -2700,7 +2673,7 @@ color_check <- function(..., incrBottMarginBy = 0, savefile = FALSE ) {
 #' @export
 #' @examples iprint ("Hello ", "you ", 3, ", ", 11, " year old kids.")
 
-iprint <- function(...) {
+iprint <- function (...) {
   argument_list <- c(...)
   print(paste(argument_list, collapse = " "))
 }
@@ -2716,11 +2689,11 @@ any_print = iprint # for compatibility
 #' @export
 #' @examples MyFriends = c("Peter", "Bence"); llprint ("My friends are: ", MyFriends )
 
-llprint <- function(...) {
+llprint <- function (...) {
   argument_list <- c(...)
   LogEntry = print(paste(argument_list, collapse = " "))
   if (ww.variable.and.path.exists(path_of_report,
-      alt.message = "NOT LOGGED: Log path and filename is not defined in path_of_report") ) {
+                                  alt.message = "NOT LOGGED: Log path and filename is not defined in path_of_report") ) {
     write(kollapse("\n", LogEntry, print = FALSE),
           path_of_report,
           append = TRUE)
@@ -2737,12 +2710,12 @@ llprint <- function(...) {
 #' @export
 #' @examples MyFriends = c("Peter", "Bence"); llogit ("My friends are: ", MyFriends )
 
-llogit <- function(...) {
+llogit <- function (...) {
   argument_list <- c(...)
   LogEntry = paste(argument_list, collapse = " ")
   LogEntry = gsub("^ +| +$", "", LogEntry)
   if (ww.variable.and.path.exists(path_of_report,
-      alt.message = "NOT LOGGED: Log path and filename is not defined in path_of_report")) {
+                                  alt.message = "NOT LOGGED: Log path and filename is not defined in path_of_report")) {
     write(kollapse("\n", LogEntry, print = FALSE),
           path_of_report,
           append = TRUE)
@@ -2761,7 +2734,7 @@ llogit <- function(...) {
 #' @examples md.write.as.list()
 
 md.write.as.list <-
-  function(vector = 1:3,
+  function (vector = 1:3,
             h = 4,
             numbered = FALSE,
             ...) {
@@ -2796,7 +2769,7 @@ md.write.as.list <-
 #' @examples md.image.linker (fname_wo_ext = "MyPlot"  )
 
 md.image.linker <-
-  function(fname_wo_ext, OutDir_ = ww.set.OutDir()) {
+  function (fname_wo_ext, OutDir_ = ww.set.OutDir()) {
     splt = strsplit(fname_wo_ext, "/")
     fn = splt[[1]][length(splt[[1]])]
     if (unless.specified("b.usepng")) {
@@ -2857,23 +2830,20 @@ llwrite_list <- function(yourlist, printName = "self") {
 #' @param ManualName Specify full filename if you do not want to name it by the variable name.
 #' @param o Open the file after saving? FALSE by default
 #' @param gzip Compress the file after saving? FALSE by default
-#' @param separator Field separator, such as "," for csv
 #' @param ... Pass any other argument to the kollapse() function used for file name.
 #' @export
 #' @examples YourDataFrameWithRowAndColumnNames = cbind("A" = rnorm(100), "B" = rpois(100, 8))
 #' rownames(YourDataFrameWithRowAndColumnNames) = letters[1:NROW(YourDataFrameWithRowAndColumnNames)]
 #' write.simple.tsv(YourDataFrameWithRowAndColumnNames)
 
-write.simple.tsv <- function(input_df, separator = "\t", extension = 'tsv', ManualName = "", o = FALSE,
-                             gzip = FALSE, ...  ) {
-  if (separator %in% c(',', ';')) extension <- 'csv'
+write.simple.tsv <- function(input_df, extension = 'tsv', ManualName = "", o = FALSE,
+                             gzip = FALSE , ...  ) {
   fname = kollapse (..., print = FALSE); if (nchar (fname) < 2 ) { fname = substitute(input_df) }
-
   if (nchar(ManualName)) {FnP = kollapse(ManualName)
   } else { FnP = ww.FnP_parser (fname, extension) }
-  utils::write.table (input_df, file = FnP, sep = separator, row.names = TRUE,
+  utils::write.table (input_df, file = FnP, sep = "\t", row.names = TRUE,
                       col.names = NA, quote = FALSE  )
-  printme = if (length(dim(input_df))) {
+  printme = if(length(dim(input_df))) {
     paste0("Dim: ", dim(input_df) )
   }else {
     paste0("Length (of your vector): ", length(input_df) )
@@ -2899,7 +2869,7 @@ write.simple.tsv <- function(input_df, separator = "\t", extension = 'tsv', Manu
 md.import <- function(from.file, to.file = path_of_report) {
   linez = readLines(from.file)
   if (ww.variable.and.path.exists(path_of_report,
-                               alt.message = "Log path and filename is not defined in path_of_report")) {
+                                  alt.message = "Log path and filename is not defined in path_of_report")) {
     iprint(length(linez),"lines from",basename(from.file) ,
            "are concatenated to:",basename(path_of_report))
   }
@@ -2920,7 +2890,7 @@ md.import <- function(from.file, to.file = path_of_report) {
 #' @export
 #' @examples md.LogSettingsFromList(parameterlist = list("min" = 4, "method" = "pearson", "max" = 10))
 
-md.LogSettingsFromList <- function(parameterlist,
+md.LogSettingsFromList <- function (parameterlist,
                                     maxlen = 20) {
   LZ = unlist(lapply(parameterlist, length)) # collapse paramters with multiple entires
   LNG = names(which(LZ > 1))
@@ -2935,44 +2905,13 @@ md.LogSettingsFromList <- function(parameterlist,
 }
 
 
-# Writing markdown tables --------------------------------------------------------------------------
-
-#' md.List2Table
-#'
-#' Broader variant of md.LogSettingsFromList(). Log the values (col2) from a named (col1) list, in a table format
-#'  in the report.
-#' @param title Title of the table.
-#' @param colname2 Name of the 2nd column.
-#' @param parameterlist List of Paramters.
-#' @param maxlen Maximum length of entries in a parameter list element,.
-#' @export
-#' @examples md.LogSettingsFromList(parameterlist = list("min" = 4, "method" = "pearson", "max" = 10))
-
-md.List2Table <- function(parameterlist,
-                           title="List elements",
-                           colname2="Value",
-                                    maxlen = 20) {
-  LZ = unlist(lapply(parameterlist, length)) # collapse paramters with multiple entires
-  LNG = names(which(LZ > 1))
-  for (i in LNG) {
-    if (length(parameterlist[[i]]) > maxlen)
-      parameterlist[[i]] = parameterlist[[i]][1:maxlen]
-    parameterlist[[i]] = paste(parameterlist[[i]], collapse = ", ")
-  } #for
-  DF = t(as.data.frame(parameterlist))
-  colnames(DF) = colname2
-  md.tableWriter.DF.w.dimnames(DF, title_of_table = title)
-}
-
-
-
 #' md.tableWriter.DF.w.dimnames
 #'
 #' Take an R data frame with row- and column- names, parse a markdown table from it,
 #' and write it to the markdown report, set by "path_of_report".
 #' @param df Input data frame to be plotted
 #' @param FullPath Full path to the file.
-#' @param percentify Format numbers between 0-1 to percentages 0-100.
+#' @param percentify Format numbers [0, 1] to percentages 0-100.
 #' @param title_of_table Title above the table (in the markdown report).
 #' @param print2screen Print the markdown formatted table to the sceen.
 #' @param WriteOut Write the table into a TSV file.
@@ -2982,7 +2921,7 @@ md.List2Table <- function(parameterlist,
 
 
 md.tableWriter.DF.w.dimnames <-
-  function(df,
+  function (df,
             FullPath = ww.set.path_of_report(),
             percentify = FALSE,
             title_of_table = NA,
@@ -3058,7 +2997,7 @@ md.tableWriter.DF.w.dimnames <-
 #' md.tableWriter.VEC.w.names (NamedVector = x, percentify = FALSE, title_of_table = NA)
 
 md.tableWriter.VEC.w.names <-
-  function(NamedVector,
+  function (NamedVector,
             FullPath = ww.set.path_of_report(),
             percentify = FALSE,
             title_of_table = NA,
@@ -3112,28 +3051,6 @@ md.tableWriter.VEC.w.names <-
 
 
 
-
-#' md.LinkTable
-#'
-#' Take a dataframe where every entry is a string containing an html link, parse and write out.
-#'  a properly formatted markdown table.
-#' @param tableOfLinkswRownames A dataframe where every entry is a string containing an html link.
-#' @export
-#'
-#' @examples tableOfLinkswRownames(tableOfLinkswRownames = df_of_LinksParsedByDatabaseLinkeR)
-
-md.LinkTable <- function(tableOfLinkswRownames) {
-  TBL = tableOfLinkswRownames
-  RN = rownames(tableOfLinkswRownames)
-  for (i in 1:ncol(tableOfLinkswRownames)) {
-    x = tableOfLinkswRownames[, i]
-    TBL[, i] = paste0("[", RN, "]", "(", x, ")")
-  } #for
-  md.tableWriter.DF.w.dimnames(TBL,
-                               FullPath = paste0(OutDir, substitute(tableOfLinkswRownames), ".tsv.md"))
-}
-
-
 #' md.import.table
 #'
 #' Import a table (.csv, or tab seprated values, .tsv file) and write it
@@ -3160,7 +3077,7 @@ md.import.table <-
            field.sep = "\t",
            to.file = path_of_report) {
     TTL = if (missing(title_of_table)){
-            basename(from.file.table)
+      basename(from.file.table)
     } else { title_of_table}
     importedtable = if (has.rownames) {
       utils::read.table(
@@ -3413,9 +3330,9 @@ stopif <-
 #' @param x Unrounded number.
 #' @param digitz Number of digits to keep. 3 by default.
 #' @export
-#' @examples iround(x = 2.3232, digitz = 3)
+#' @examples iround (x = 2.3232, digitz = 3)
 
-iround <- function(x, digitz = 3) {
+iround <- function (x, digitz = 3) {
   signif(x, digits = digitz)
 }
 
@@ -3461,7 +3378,7 @@ modus <- function(x) {
 #'
 #' @examples as.factor.numeric(LETTERS[1:4])
 
-as.factor.numeric <- function(vec, rename = FALSE, ...) {
+as.factor.numeric <- function (vec, rename = FALSE, ...) {
   vec2 = as.numeric(as.factor(vec, ...)) ;
   names (vec2) <- if ( !rename & !is.null(names(vec) ) ) { names (vec)
   } else { vec }
@@ -3508,7 +3425,7 @@ na.omit.strip <- function(object, silent = FALSE, ...) {
 #' @examples kollapse("Hello ", LETTERS[24],
 #' ", the winning numbers are ", c(1, 3, 5, 65, 11), " . Yay!")
 
-kollapse <- function(...,
+kollapse <- function (...,
                       collapseby = "",
                       print = TRUE) {
   if (print == TRUE) {
@@ -3525,20 +3442,20 @@ kollapse <- function(...,
 #' @export
 #' @examples substrRight  ("Not cool", n = 4)
 
-substrRight <- function(x, n) {
+substrRight <- function (x, n) {
   substr(x, nchar(x) - n + 1, nchar(x))
 }
 
 #' percentage_formatter
 #'
 #' Parse a string of 0-100% from a number between 0 and 1.
-#' @param x A vector of numbers between 0-1.
+#' @param x A vector of numbers between [0, 1]/
 #' @param digitz Number of digits to keep. 3 by default.
 #' @export
 #' @examples percentage_formatter (x = 4.2822212, digitz = 3)
 
-percentage_formatter <- function(x, digitz = 3) {
-  a = paste(100 * signif(x, digitz), "%", sep = " ")
+percentage_formatter <- function (x, digitz = 3) {
+  a = paste(100 * iround(x, digitz), "%", sep = " ")
   a[a == "NaN %"] = NaN
   a[a == "NA %"] = NA
   return(a)
@@ -3749,8 +3666,10 @@ ww.set.OutDir <- function() {
       iprint("OutDir not defined !!! Saving in working directory.")
       paste0(getwd(),"/", collapse = "")
     }
-  NewOutDir = AddTrailingSlash(NewOutDir) # add '/' if necessary
-  RemoveDoubleSlash(NewOutDir)
+  if (!substrRight(NewOutDir, 1) == "/"){
+    NewOutDir = paste0(NewOutDir, "/") # add '/' if necessary
+  }
+  gsub(x = NewOutDir, pattern = '//', replacement = '/')
 }
 
 
@@ -3839,7 +3758,7 @@ ww.set.mdlink <- function(NameOfaVariable = "b.mdlink",
 #' @examples ww.md.image.link.parser ("/MyPlot.jpg"  )
 #' ww.md.image.link.parser (getwd(),"/MyPlot.jpg"  )
 
-ww.md.image.link.parser <- function(...) {
+ww.md.image.link.parser <- function (...) {
   FullPath = kollapse(..., print = FALSE)
   splt = strsplit(FullPath, "/")
   fn = splt[[1]][length(splt[[1]])]
@@ -3853,7 +3772,7 @@ ww.md.image.link.parser <- function(...) {
 #' @export
 #' @examples ww.ttl_field("/Users/myplot.jpg")
 
-ww.ttl_field <- function(flname) {
+ww.ttl_field <- function (flname) {
   paste0(basename(flname), " by ", if (exists("b.scriptname"))
     b.scriptname
     else
@@ -3868,7 +3787,7 @@ ww.ttl_field <- function(flname) {
 #' @export
 #' @examples ww.autoPlotName()
 
-ww.autoPlotName <- function(name = NULL) {
+ww.autoPlotName <- function (name = NULL) {
   if (is.null(name)) {
     filename = if (exists("plotnameLastPlot")) {
       plotnameLastPlot
@@ -3886,7 +3805,7 @@ ww.autoPlotName <- function(name = NULL) {
 #'
 #' Parser for dev.copy to save as PDF or PNG
 #' @param PNG_ Set to true if you want to save the plot as PNG instead of the default PDF.
-#' @param PNG_res deafult 450
+#' @param PNG_res default 100
 #' @param w_ Width of the saved pdf image, in inches.
 #' @param h_ Height of the saved pdf image, in inches.
 #' @param fname_ File name
@@ -3894,13 +3813,13 @@ ww.autoPlotName <- function(name = NULL) {
 #' @examples try.dev.off(); plot(1); # ww.dev.copy(PNG = FALSE, w_ = 7, h_ = 7, fname_ = "myNewplot")
 
 ww.dev.copy <- function(PNG_ = FALSE,
-                        PNG_res = 450,
+                        PNG_res = 100,
                         w_,
                         h_,
                         fname_) {
   if (PNG_) {
     dev.copy(
-      png,
+      device = png,
       filename = ww.FnP_parser(fname_, "png"),
       res = PNG_res,
       width = w_ * 100,
@@ -3953,7 +3872,7 @@ ww.assign_to_global <- function(name, value, pos=1){
 #' append = TRUE, b.png4Github = TRUE)
 
 setup_logging_markdown <-
-  function(fname,
+  function (fname,
             title = "",
             append = TRUE,
             b.png4Github = TRUE) {
@@ -3970,7 +3889,7 @@ setup_logging_markdown <-
           path_of_report,
           append = TRUE)
     BackupDir = kollapse( OutDir, "/", substr(fname, 1, nchar(fname)), "_",
-      format(Sys.time(), "%Y_%m_%d-%Hh"), print = FALSE
+                          format(Sys.time(), "%Y_%m_%d-%Hh"), print = FALSE
     )
     if (!exists(BackupDir)) {
       dir.create(BackupDir, showWarnings = FALSE)
@@ -3987,7 +3906,7 @@ setup_logging_markdown <-
 #' @export
 #' @examples a = 1; b = 2; log_settings_MarkDown (a,b)
 
-log_settings_MarkDown <- function(...) {
+log_settings_MarkDown <- function (...) {
   print("Use md.LogSettingsFromList() for a list of parameters")
   call <- match.call()
   namez = sapply(as.list(call[-1]), deparse)
@@ -3999,79 +3918,3 @@ log_settings_MarkDown <- function(...) {
 
 
 
-#' AddTrailingSlash
-#'
-#' Adds a final slash '/', if missing from a string (file path).
-#' @param string The file path potentially missing the trailing slash
-#' @export
-#'
-#' @examples AddTrailingSlash (string = "stairway/to/heaven")
-
-AddTrailingSlash <- function(string = "stairway/to/heaven") { #
-  LastChr <- substr(string, nchar(string), nchar(string))
-  if (!LastChr == "/")
-    string = paste0(string, "/")
-  return(string)
-}
-
-#' RemoveDoubleSlash
-#'
-#' RemoveDoubleSlash removes multiple consecutive slashes (e.g. '//') from a string (file path). Also works for 2,3 consecutive slashes
-#' @param string The file path potentially having Double Slash
-#' @export
-#'
-#' @examples RemoveDoubleSlash (string = "stairway//to///heaven")
-
-RemoveDoubleSlash <- function(string = "stairway//to/heaven") { #
-  gsub(x = string, pattern = '//|///|////', replacement = '/')
-}
-
-
-#' RemoveFinalSlash
-#'
-#' RemoveFinalSlash removes the final slash from a string
-#' @param string The file path potentially having Final Slash
-#' @export
-#'
-#' @examples RemoveDoubleSlash (string = "stairway//to///heaven")
-
-RemoveFinalSlash <- function(string = "stairway/to/heaven/") { #
-  gsub(x = string, pattern = '/$', replacement = '')
-}
-
-
-
-#' FixPath
-#'
-#' FixPath removes multiple consecutive slashes (e.g. '//') from a string and adds a final '/' if missing from a file path.
-#' @param string The file path potentially having Double Slash
-#' @export
-#'
-#' @examples FixPath(string = "stairway//to/heaven")
-
-FixPath <- function(string = "stairway//to/heaven") { #
-  string <- gsub(x = string, pattern = '//|///|////', replacement = '/')
-  LastChr <- substr(string, nchar(string), nchar(string))
-  if (!LastChr == "/")
-    string = paste0(string, "/")
-  return(string)
-}
-
-
-#' ParseFilePath
-#'
-#' ParseFilePath pastes elements by slash, then removes Double Slashes '//' from a string and adds a final '/' if missing from a file path.
-#' @param ...  The set of strings (character vectors) to be parsed into a file path, and potentially having Double Slashes, potentially missing a trailing slash.
-#' @export
-#'
-#' @examples ParseFilePath(string = "stairway///to/heaven")
-
-ParseFilePath <- function(...) { #
-  string <- paste(..., sep = '/', collapse = '/')  # kollapse by (forward) slash
-  string <- gsub(x = string, pattern = '//', replacement = '/') # RemoveDoubleSlash
-  LastChr <- substr(string, nchar(string), nchar(string)) # AddTrailingSlash
-  if (!LastChr == "/")
-    string = paste0(string, "/")
-  return(string)
-}
-
diff --git a/man/create_set_Original_OutDir.Rd b/man/create_set_Original_OutDir.Rd
index df4644c..52a2fd7 100644
--- a/man/create_set_Original_OutDir.Rd
+++ b/man/create_set_Original_OutDir.Rd
@@ -4,7 +4,7 @@
 \alias{create_set_Original_OutDir}
 \title{Closing pair of the create_set_SubDir function. Call when chaning back to the main dir.
 Set the output directory of the script, and set the "NewOutDir" variable that is
- used by all ~wplot functions.}
+used by all ~wplot functions.}
 \usage{
 create_set_Original_OutDir(
   NewOutDir = OutDirOrig,
@@ -25,7 +25,7 @@ create_set_Original_OutDir(
 \description{
 Closing pair of the create_set_SubDir function. Call when chaning back to the main dir.
 Set the output directory of the script, and set the "NewOutDir" variable that is
- used by all ~wplot functions.
+used by all ~wplot functions.
 }
 \examples{
 create_set_Original_OutDir (getwd(),"/")
diff --git a/man/md.LogSettingsFromList.Rd b/man/md.LogSettingsFromList.Rd
index dbe5c32..c299249 100644
--- a/man/md.LogSettingsFromList.Rd
+++ b/man/md.LogSettingsFromList.Rd
@@ -13,7 +13,7 @@ md.LogSettingsFromList(parameterlist, maxlen = 20)
 }
 \description{
 Log the parameters & settings used in the script and stored in a list, in a table format
- in the report.
+in the report.
 }
 \examples{
 md.LogSettingsFromList(parameterlist = list("min" = 4, "method" = "pearson", "max" = 10))
diff --git a/man/md.import.table.Rd b/man/md.import.table.Rd
index e1884aa..e7a70c9 100644
--- a/man/md.import.table.Rd
+++ b/man/md.import.table.Rd
@@ -33,6 +33,6 @@ Import a table (.csv, or tab seprated values, .tsv file) and write it
 in markdown format to the report.
 }
 \examples{
-x = matrix(1:9,3); utils::write.table(x, sep = "\\t", file = "~/x.tsv");
+x = matrix(1:9,3); utils::write.table(x, sep = "\t", file = "~/x.tsv");
 md.import.table("~/x.tsv")
 }
diff --git a/man/md.tableWriter.DF.w.dimnames.Rd b/man/md.tableWriter.DF.w.dimnames.Rd
index 776d987..bd279cc 100644
--- a/man/md.tableWriter.DF.w.dimnames.Rd
+++ b/man/md.tableWriter.DF.w.dimnames.Rd
@@ -18,7 +18,7 @@ md.tableWriter.DF.w.dimnames(
 
 \item{FullPath}{Full path to the file.}
 
-\item{percentify}{Format numbers [0, 1] to percentages 0-100.}
+\item{percentify}{Format numbers \link{0, 1} to percentages 0-100.}
 
 \item{title_of_table}{Title above the table (in the markdown report).}
 
diff --git a/man/md.tableWriter.VEC.w.names.Rd b/man/md.tableWriter.VEC.w.names.Rd
index 4f13d20..c39052f 100644
--- a/man/md.tableWriter.VEC.w.names.Rd
+++ b/man/md.tableWriter.VEC.w.names.Rd
@@ -18,7 +18,7 @@ md.tableWriter.VEC.w.names(
 
 \item{FullPath}{Full path to the file.}
 
-\item{percentify}{Format numbers [0, 1] to percentages 0-100.}
+\item{percentify}{Format numbers \link{0, 1} to percentages 0-100.}
 
 \item{title_of_table}{Title above the table (in the markdown report).}
 
@@ -28,7 +28,7 @@ md.tableWriter.VEC.w.names(
 }
 \description{
 Take an R vector with names, parse a markdown table from it, and write it to the markdown report,
- set by "path_of_report".
+set by "path_of_report".
 }
 \examples{
 x = -1:2; names(x) = LETTERS[1:4]
diff --git a/man/percentage_formatter.Rd b/man/percentage_formatter.Rd
index fa34452..7c8144a 100644
--- a/man/percentage_formatter.Rd
+++ b/man/percentage_formatter.Rd
@@ -7,12 +7,12 @@
 percentage_formatter(x, digitz = 3)
 }
 \arguments{
-\item{x}{A vector of numbers between [0, 1]/}
+\item{x}{A vector of numbers between \link{0, 1}/}
 
 \item{digitz}{Number of digits to keep. 3 by default.}
 }
 \description{
-Parse a string of 0-100% from a number between 0 and 1.
+Parse a string of 0-100\% from a number between 0 and 1.
 }
 \examples{
 percentage_formatter (x = 4.2822212, digitz = 3)
diff --git a/man/setup_MarkdownReports.Rd b/man/setup_MarkdownReports.Rd
index e8f0440..3fe531b 100644
--- a/man/setup_MarkdownReports.Rd
+++ b/man/setup_MarkdownReports.Rd
@@ -46,7 +46,7 @@ into the timestamped subfolder within the OutDir.}
 
 \item{append}{Set append to TRUE if you do not want to overwrite the previous report.}
 
-\item{addTableOfContents}{write '[TOC]' below the header of the file, This is compiled to a
+\item{addTableOfContents}{write '\link{TOC}' below the header of the file, This is compiled to a
 proper Table Of Contents by, e.g. Typora.}
 
 \item{saveSessionInfo}{save 'sessioninfo::session_info()' results to '.session_info.DATE.txt.gz'}
diff --git a/man/setup_logging_markdown.Rd b/man/setup_logging_markdown.Rd
index 38ea402..3daf5a2 100644
--- a/man/setup_logging_markdown.Rd
+++ b/man/setup_logging_markdown.Rd
@@ -17,7 +17,7 @@ Use continue_logging_markdown() if you return logging into an existing report.}
 \item{b.png4Github}{A global variable, defined by this and used by the other functions.
 If TRUE (default), any link to the .png versions of images will be created in a
 GitHub compatible format. That means, when you upload your markdown report and the .png images
- to your GitHub wiki under "Reports/" the links will correctly display the images online.}
+to your GitHub wiki under "Reports/" the links will correctly display the images online.}
 }
 \description{
 Setup the markdown report file, create a sub directory in "OutDir". Its name is stamped with
diff --git a/man/whist.Rd b/man/whist.Rd
index 32f33fd..07a70d9 100644
--- a/man/whist.Rd
+++ b/man/whist.Rd
@@ -73,7 +73,7 @@ Design the line by "lty", "lwd" & "lcol" parameters.}
 Create and save histograms as .pdf, in "OutDir". If mdlink = TRUE, it inserts a .pdf and a .png
 link in the markdown report, set by "path_of_report". The .png version is not created, only the
 link is put in place, not to overwrite previous versions. Name the file by naming the variable!
-Cannot be used with dynamically called variables [e.g. call vectors within a loop]. "filtercol"
+Cannot be used with dynamically called variables \link{e.g. call vectors within a loop}. "filtercol"
 assumes  >= coloring!
 }
 \examples{
diff --git a/man/whist_dfCol.Rd b/man/whist_dfCol.Rd
index a8a7873..c65ec8d 100644
--- a/man/whist_dfCol.Rd
+++ b/man/whist_dfCol.Rd
@@ -36,7 +36,7 @@ plotting function (most of them should work).}
 \description{
 Use this version of whist() if you iterate over columns  or rows of a data frame.
 You can name the file by naming the variable.
-Cannot be used with dynamically called variables [e.g. call vectors within a loop]
+Cannot be used with dynamically called variables \link{e.g. call vectors within a loop}
 }
 \examples{
 try.dev.off(); df = cbind(a = rnorm(1:10), b = rnorm(10))
diff --git a/man/wplot.Rd b/man/wplot.Rd
index cf83b0c..87711b5 100644
--- a/man/wplot.Rd
+++ b/man/wplot.Rd
@@ -40,7 +40,7 @@ wplot(
 
 \item{col}{Color of the plot.}
 
-\item{pch}{Define the symbol for each data point. A number [0-25] or any string between ""-s.}
+\item{pch}{Define the symbol for each data point. A number \link{0-25} or any string between ""-s.}
 
 \item{...}{Pass any other parameter of the corresponding plotting function (most of them should
 work).}
diff --git a/man/wscatter.fill.Rd b/man/wscatter.fill.Rd
index 4ba18fd..11b04bd 100644
--- a/man/wscatter.fill.Rd
+++ b/man/wscatter.fill.Rd
@@ -51,7 +51,7 @@ work).}
 
 \item{nlevels}{Number of steps in the color gradient}
 
-\item{pch}{Define the symbol for each data point. A number [0-25] or any string between ""-s.}
+\item{pch}{Define the symbol for each data point. A number \link{0-25} or any string between ""-s.}
 
 \item{cex}{Size of the symbols}
 
diff --git a/man/wstripchart.Rd b/man/wstripchart.Rd
index 234be8c..f014793 100644
--- a/man/wstripchart.Rd
+++ b/man/wstripchart.Rd
@@ -56,7 +56,7 @@ stripchart().}
 \item{jitter}{The amount of horizontal scatter added to the individual data points (to avoid
 overlaps).}
 
-\item{pch}{Define the symbol for each data point. A number [0-25] or any string between ""-s.}
+\item{pch}{Define the symbol for each data point. A number \link{0-25} or any string between ""-s.}
 
 \item{pchlwd}{Define the outline width of the symbol for each data point.}
 
diff --git a/man/wstripchart_list.Rd b/man/wstripchart_list.Rd
index 04bca58..91821f6 100644
--- a/man/wstripchart_list.Rd
+++ b/man/wstripchart_list.Rd
@@ -48,7 +48,7 @@ are recycled if the length of border is less than the number of plots.}
 
 \item{bxpcol}{Color of the boxplot outlines.}
 
-\item{pch}{Define the symbol for each data point. A number [0-25] or any string between ""-s.}
+\item{pch}{Define the symbol for each data point. A number \link{0-25} or any string between ""-s.}
 
 \item{pchlwd}{Define the outline width of the symbol for each data point.}
 
diff --git a/man/wviostripchart_list.Rd b/man/wviostripchart_list.Rd
index b8b1754..8e44650 100644
--- a/man/wviostripchart_list.Rd
+++ b/man/wviostripchart_list.Rd
@@ -32,7 +32,7 @@ wviostripchart_list(
 \item{...}{Pass any other parameter of the corresponding plotting
 function (most of them should work).}
 
-\item{pch}{Define the symbol for each data point. A number [0-25] or any string between ""-s.}
+\item{pch}{Define the symbol for each data point. A number \link{0-25} or any string between ""-s.}
 
 \item{viocoll}{Background color of each individual violing plot.}
 
diff --git a/man/ww.dev.copy.Rd b/man/ww.dev.copy.Rd
index 87b0b0c..7935e67 100644
--- a/man/ww.dev.copy.Rd
+++ b/man/ww.dev.copy.Rd
@@ -4,12 +4,12 @@
 \alias{ww.dev.copy}
 \title{ww.dev.copy}
 \usage{
-ww.dev.copy(PNG_ = FALSE, PNG_res = 450, w_, h_, fname_)
+ww.dev.copy(PNG_ = FALSE, PNG_res = 100, w_, h_, fname_)
 }
 \arguments{
 \item{PNG_}{Set to true if you want to save the plot as PNG instead of the default PDF.}
 
-\item{PNG_res}{deafult 450}
+\item{PNG_res}{default 100}
 
 \item{w_}{Width of the saved pdf image, in inches.}
 
diff --git a/man/ww.set.mdlink.Rd b/man/ww.set.mdlink.Rd
index 27f2289..ea0ea84 100644
--- a/man/ww.set.mdlink.Rd
+++ b/man/ww.set.mdlink.Rd
@@ -14,7 +14,7 @@ ww.set.mdlink(NameOfaVariable = "b.mdlink", def = FALSE)
 \description{
 Internal function. Sets inserting a markdown link to the image
 (created by the wplot* function that calls this function) only if 'path_of_report' is defined
- and 'b.mdlink' is defined as TRUE.
+and 'b.mdlink' is defined as TRUE.
 }
 \examples{
 ww.set.mdlink() # It is an internal function, not intended for manual use.
diff --git a/man/ww.variable.and.path.exists.Rd b/man/ww.variable.and.path.exists.Rd
index aa93b8d..2c7fc4c 100644
--- a/man/ww.variable.and.path.exists.Rd
+++ b/man/ww.variable.and.path.exists.Rd
@@ -13,7 +13,7 @@ ww.variable.and.path.exists(path = path_of_report, alt.message = NULL)
 }
 \description{
 Check if a variable name is defined, and if so, does the path (to a file) stored in that
- variable points to an existing directory?
+variable points to an existing directory?
 }
 \examples{
 ww.variable.and.path.exists(path = B, alt.message = "Hello, your path/var does not exist.")