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vertesy · Oct 12, 2023 · f05cc57 · f05cc57
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diff --git 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: v0.7.2
+version: v0.7.3
 message: >-
   If you use this software, please cite it using these metadata.
 type: software

diff --git 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: 0.7.2
+Version: 0.7.3
 Authors@R: 
     person("Abel", "Vertesy", , "[email protected]", role = c("aut", "cre"))
 Author: Abel Vertesy <[email protected]> [aut, cre]
@@ -38,6 +38,6 @@ Imports:
     stats,
     tidyverse
 Encoding: UTF-8
-Packaged: 2023-09-04 18:38:27.811761
+Packaged: 2023-10-12 13:21:20.976129
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
diff --git a/Development/Create_the_ggExpress_Package.v0.1.R b/Development/Create_the_ggExpress_Package.v0.1.R
@@ -18,7 +18,7 @@ require('Stringendo')
 
 # Setup ------------------------
 PackageName = "ggExpress"
-package.version = "0.7.2"
+package.version = "0.7.3"
 setwd("~/GitHub/Packages/")
 
 RepositoryDir = kollapse("~/GitHub/Packages/", PackageName, "/")

diff --git a/Development/Development.bac b/Development/Development.bac
@@ -10,13 +10,13 @@
 # ____________________________________________________________________
 
 
-
 # _________________________________________________________________________________________________
 #' @title Quick Histogram Plotting
 #'
 #' @description This function generates a histogram and saves the plot for a given vector and offers several customizations.
 #' @param vec A numeric vector for which the histogram is to be plotted.
 #' @param ext File extension for the saved plot. Either '.pdf' or '.png'. Default is '.pdf'.
+#' @param also.pdf Save plot in both png and pdf formats
 #' @param xlab Label for the X-axis. By default, it uses the plot name.
 #' @param plot Logical indicating whether to display the plot. Default is TRUE.
 #' @param add Character defining the type of plot annotations to add. Default is 'median'.
@@ -50,7 +50,8 @@
 #'
 #' @export
 qhistogram <- function(vec
-                       , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'pdf')
+                       , also.pdf = FALSE
+                       , ext = MarkdownHelpers::ww.set.file.extension(def = 'png')
                        , xlab = FALSE, plot = TRUE, save = TRUE, mdlink = MarkdownHelpers::unless.specified('b.mdlink', def = FALSE)
                        , suffix = NULL
                        , plotname = FixPlotName(substitute(vec), suffix)
@@ -102,7 +103,7 @@ qhistogram <- function(vec
   }
   file_name <- FixPlotName(file_name)
 
-  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h)
+  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h, also.pdf = also.pdf)
   if (mdlink & save) qMarkdownImageLink(file_name)
   if (plot) p
 }
@@ -116,6 +117,7 @@ qhistogram <- function(vec
 #' @description Draw and save a density plot.
 #' @param vec The variable to plot.
 #' @param ext File extension (.pdf / .png).
+#' @param also.pdf Save plot in both png and pdf formats
 #' @param xlab X-axis label.
 #' @param plot Display the plot.
 #' @param suffix A suffix added to the filename. NULL by default.
@@ -139,7 +141,8 @@ qhistogram <- function(vec
 #' @examples weight <- rnorm(1000); qdensity(weight)
 
 qdensity <- function(vec
-                     , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'pdf')
+                     , also.pdf = FALSE
+                     , ext = MarkdownHelpers::ww.set.file.extension(def = 'png')
                      , xlab = FALSE, plot = TRUE
                      , suffix = NULL
                      , plotname = FixPlotName(substitute(vec), suffix)
@@ -172,7 +175,7 @@ qdensity <- function(vec
   file_name <- if (!isFALSE(filename)) { filename } else {
     FixPlotName(plotname, suffix, "dens", flag.nameiftrue(logX), flag.nameiftrue(logY), ext)
     }
-  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h)
+  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h, also.pdf = also.pdf)
   if (mdlink & save) qMarkdownImageLink(file_name)
   if (plot) p
 }
@@ -185,6 +188,7 @@ qdensity <- function(vec
 #' @description Draw and save a barplot.
 #' @param vec The variable to plot.
 #' @param ext File extension (.pdf / .png).
+#' @param also.pdf Save plot in both png and pdf formats
 #' @param plot Display the plot.
 #' @param suffix A suffix added to the filename. NULL by default.
 #' @param plotname The title of the plot and the name of the file (unless specified in `filename`).
@@ -216,7 +220,8 @@ qdensity <- function(vec
 #' qbarplot(weight3, filtercol = 1, hline = .5)
 
 qbarplot <- function(vec
-                     , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'pdf')
+                     , also.pdf = FALSE
+                     , ext = MarkdownHelpers::ww.set.file.extension(def = 'png')
                      , plot = TRUE
                      , suffix = NULL
                      , plotname = FixPlotName(substitute(vec), suffix)
@@ -271,7 +276,7 @@ qbarplot <- function(vec
   file_name <- if (!isFALSE(filename)) filename else {
     FixPlotName(plotname, suffix, "bar", flag.nameiftrue(logY), ext)
   }
-  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h, limitsize = limitsize)
+  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h, limitsize = limitsize, also.pdf = also.pdf)
   if (mdlink & save) qMarkdownImageLink(file_name)
   if (plot) p
 }
@@ -286,6 +291,7 @@ qbarplot <- function(vec
 #' @param fill Color (split) by along Y.
 #' @param color Color (split) by along Y.
 #' @param ext File extension (.pdf / .png).
+#' @param also.pdf Save plot in both png and pdf formats
 #' @param plot Display the plot.
 #' @param suffix A suffix added to the filename. NULL by default.
 #' @param plotname The title of the plot and the name of the file (unless specified in `filename`).
@@ -321,7 +327,8 @@ qbarplot.df <- function(df
                         , fill = colnames(df)[3]
                         , label = NULL
                         , color = 1
-                        , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'pdf')
+                        , also.pdf = FALSE
+                        , ext = MarkdownHelpers::ww.set.file.extension(def = 'png')
                         , plot = TRUE
                         , suffix = NULL
                         , plotname = FixPlotName(substitute(df), suffix)
@@ -362,7 +369,7 @@ qbarplot.df <- function(df
   file_name <- if (!isFALSE(filename)) filename else {
     FixPlotName(plotname, suffix, "bar", flag.nameiftrue(logY), ext)
     }
-  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h, limitsize = limitsize)
+  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h, limitsize = limitsize, also.pdf = also.pdf)
   if (mdlink & save) qMarkdownImageLink(file_name)
   if (plot) p
 }
@@ -374,6 +381,7 @@ qbarplot.df <- function(df
 #' @description Draw and save a pie chart
 #' @param vec The variable to plot.
 #' @param ext File extension (.pdf / .png).
+#' @param also.pdf Save plot in both png and pdf formats
 #' @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".
@@ -404,7 +412,8 @@ qbarplot.df <- function(df
 
 
 qpie <- function(vec = MyVec
-                 , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'pdf')
+                 , also.pdf = FALSE
+                 , ext = MarkdownHelpers::ww.set.file.extension(def = 'png')
                  , plot = TRUE, save = TRUE, mdlink = MarkdownHelpers::unless.specified('b.mdlink', def = FALSE)
                  , suffix = NULL
                  , plotname = FixPlotName(substitute(vec), suffix)
@@ -484,7 +493,7 @@ qpie <- function(vec = MyVec
   file_name <- if (!isFALSE(filename)) filename else {
     FixPlotName(plotname, suffix, "pie",  ext)
   }
-  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h)
+  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h, also.pdf = also.pdf)
   if (mdlink & save) qMarkdownImageLink(file_name)
 
   if (plot) p
@@ -499,7 +508,7 @@ qpie <- function(vec = MyVec
 #' @param plotname The title of the plot and the name of the file (unless specified in `filename`).
 #' @param filename Manually provided filename (optional). Default: parse from `plotname`,
 #' @param ext File extension (.pdf / .png).
-#' @param also.pdf also.pdf
+#' @param also.pdf Save plot in both png and pdf formats
 #' @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.
@@ -536,8 +545,8 @@ qboxplot <- function(df_XYcol_or_list
                      # , fill = c(NULL , 3)[1]
                      , palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4]
                      , hide.legend = FALSE
-                     , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'png')
                      , also.pdf = TRUE
+                     , ext = MarkdownHelpers::ww.set.file.extension(def = 'png')
                      , logY = FALSE #, logX = FALSE
                      , annotation_logticks_Y = logY
                      , xlab.angle = 90
@@ -588,7 +597,7 @@ qboxplot <- function(df_XYcol_or_list
 #' @param plotname Name of the plot
 #' @param filename Manually provided filename (optional). Default: parse from `plotname`,
 #' @param ext File extension (.pdf / .png).
-#' @param also.pdf also.pdf
+#' @param also.pdf Save plot in both png and pdf formats
 #' @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.
@@ -621,8 +630,8 @@ qviolin <- function(df_XYcol_or_list
                     , stat.method = NULL, stat.label.y.npc = "top", stat.label.x = 0.5
                     , palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4]
                     , hide.legend = FALSE
-                    , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'png')
                     , also.pdf = FALSE
+                    , ext = MarkdownHelpers::ww.set.file.extension(def = 'png')
                     , logY = FALSE #, logX = FALSE
                     , annotation_logticks_Y = logY
                     , xlab.angle = 45
@@ -682,7 +691,7 @@ qviolin <- function(df_XYcol_or_list
 #' @param filename Manually provided filename (optional). Default: parse from `plotname`,
 #' @param plot Display the plot.
 #' @param ext File extension (.pdf / .png).
-#' @param also.pdf also.pdf
+#' @param also.pdf Save plot in both png and pdf formats
 #' @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.
@@ -720,8 +729,8 @@ qstripchart <- function(df_XYcol_or_list
                         # , fill = c(NULL , 3)[1]
                         , palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4]
                         , hide.legend = FALSE
-                        , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'png')
                         , also.pdf = TRUE
+                        , ext = MarkdownHelpers::ww.set.file.extension(def = 'png')
                         , logY = FALSE #, logX = FALSE
                         , annotation_logticks_Y = logY
                         , xlab.angle = 90
@@ -775,7 +784,7 @@ qstripchart <- function(df_XYcol_or_list
 #' @param filename Manually provided filename (optional). Default: parse from `plotname`,
 #' @param col Color of the plot.
 #' @param ext File extension (.pdf / .png).
-#' @param also.pdf also.pdf
+#' @param also.pdf Save plot in both png and pdf formats
 #' @param logX Make X axis log10-scale.
 #' @param logY Make Y axis log10-scale.
 #' @param hline Draw a horizontal line on the plot, yintercept or FALSE
@@ -807,8 +816,8 @@ qscatter <- function(df_XYcol
                     , col = c(NULL , 3)[1]
                     , palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4]
                     , hide.legend = FALSE
-                    , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'png')
                     , also.pdf = TRUE
+                    , ext = MarkdownHelpers::ww.set.file.extension(def = 'png')
                     , logX = FALSE, logY = FALSE
                     , annotation_logticks_Y = logY
                     , annotation_logticks_X = logX
@@ -834,8 +843,8 @@ qscatter <- function(df_XYcol
 
 
   if (grid %in% c("xy", "x", "y")) p <- p + grids(axis = grid)
-  if (hline) p <- p + ggplot2::geom_hline(yintercept = hline)
-  if (vline) p <- p + ggplot2::geom_vline(xintercept = vline)
+  if (sum(hline)) p <- p + ggplot2::geom_hline(yintercept = hline) # sum is needed to deal with multiple lines (multiple values in if statement).
+  if (sum(vline)) p <- p + ggplot2::geom_vline(xintercept = vline)
   if (sum(abline)) p <- p + ggplot2::geom_abline(intercept = abline[1], slope = abline[2])
   if (add_contour_plot) p <- p + geom_density_2d()
   if (correlation_r2 %in% c("pearson", "spearman") ) p <- p + stat_cor(method = correlation_r2)
@@ -865,6 +874,7 @@ qscatter <- function(df_XYcol
 #' @description Draw and save a Venn Diagram using the `ggVennDiagram` package.
 #' @param list The variable to plot.
 #' @param ext File extension (.pdf / .png).
+#' @param also.pdf Save plot in both png and pdf formats
 #' @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".
@@ -884,7 +894,8 @@ qscatter <- function(df_XYcol
 #' @examples LetterSets <- list("One" = LETTERS[1:7], "Two" = LETTERS[3:12]); qvenn(LetterSets)
 
 qvenn <- function(list
-                  , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'pdf')
+                  , also.pdf = FALSE
+                  , ext = MarkdownHelpers::ww.set.file.extension(def = 'png')
                   , plot = TRUE, save = TRUE, mdlink = MarkdownHelpers::unless.specified('b.mdlink', def = FALSE)
                   , suffix = NULL
                   , plotname = FixPlotName(substitute(list), suffix)
@@ -909,7 +920,7 @@ qvenn <- function(list
   file_name <- if (!isFALSE(filename)) filename else {
     sppp(plotname, suffix, "venn", ext)
   }
-  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h)
+  if (save) qqSave(ggobj = p, title = plotname, fname = file_name, ext = ext, w = w, h = h, also.pdf = also.pdf)
   if (mdlink & save) qMarkdownImageLink(file_name)
   if (plot) p
 }
@@ -931,7 +942,8 @@ qvenn <- function(list
 #' @param w width of the plot.
 #' @param h height of the plot.
 #' @param ext File extension (.pdf / .png).
-#' @param also.pdf also.pdf
+#' @param also.pdf Save plot in both png and pdf formats
+#' @param bgcol Plot background color
 #' @param page page
 #' @param title title field for pdf file (saved into file metadata)
 #' @param fname fname
@@ -945,6 +957,7 @@ qvenn <- function(list
 qqSave <- function(ggobj, w =4, h = w
                    , ext = MarkdownHelpers::unless.specified('b.def.ext', def = 'png')
                    , also.pdf = FALSE
+                   , bgcol = 'white'
                    , page = c(F, "A4p", "A4l", "A5p", "A5l")[1]
                    , title = FALSE, fname = FALSE
                    , suffix = NULL, ...) {
@@ -963,6 +976,9 @@ qqSave <- function(ggobj, w =4, h = w
   }
   print(paste0(getwd(),"/", fname))
 
+  # Set the plot background to white
+  ggobj <- ggobj + theme(plot.background = element_rect(fill = bgcol, color = bgcol))
+
   if (also.pdf) {
     cowplot::save_plot(plot = ggobj, filename = fname2, base_width = w, base_height = h
                      , title = ww.ttl_field(title, creator = "ggExpress")
@@ -1069,7 +1085,7 @@ qA4_grid_plot <- function(plot_list
 #' @importFrom MarkdownHelpers llogit
 
 qMarkdownImageLink <- function(file_name = 'myplot.pdf') {
-  llogit(paste0("![", file_name, "]", "(", file_name, ")", collapse = ''))
+  MarkdownHelpers::llogit(paste0("![", file_name, "]", "(", file_name, ")", collapse = ''))
 }
 
 

diff --git a/R/ggExpress.R b/R/ggExpress.R
@@ -10,7 +10,6 @@
 # ____________________________________________________________________
 
 
-
 # _________________________________________________________________________________________________
 #' @title Quick Histogram Plotting
 #'
@@ -1086,7 +1085,7 @@ qA4_grid_plot <- function(plot_list
 #' @importFrom MarkdownHelpers llogit
 
 qMarkdownImageLink <- function(file_name = 'myplot.pdf') {
-  llogit(paste0("![", file_name, "]", "(", file_name, ")", collapse = ''))
+  MarkdownHelpers::llogit(paste0("![", file_name, "]", "(", file_name, ")", collapse = ''))
 }
 
 

diff --git a/man/qbarplot.Rd b/man/qbarplot.Rd
diff --git a/man/qbarplot.df.Rd b/man/qbarplot.df.Rd