diff --git a/boxplot.docx b/boxplot.docx
index f4bbdfb53923b40c73f270635a8afb4df61c4778..aadefd289ea35c656dc4fd554d0d4307f22b418c 100644
Binary files a/boxplot.docx and b/boxplot.docx differ
diff --git a/boxplot_examples.docx b/boxplot_examples.docx
index 78a78a4331e598a7709f662f03340dc7a3739d3f..ae0c6955213e723cde4fdeed5cb058a8be1dba95 100644
Binary files a/boxplot_examples.docx and b/boxplot_examples.docx differ
diff --git a/cute_little_R_functions.R b/cute_little_R_functions.R
index 731ef6ac6eca55fe6678ebdb143672407d00a988..f843e4732bde10f91cad72505d65272fecf10842 100644
--- a/cute_little_R_functions.R
+++ b/cute_little_R_functions.R
@@ -29,58 +29,58 @@
################################ OUTLINE ################################
-################ Object analysis 2
-######## fun_check() #### check class, type, length, etc., of objects 2
-######## fun_info() #### recover object information 8
-######## fun_head() #### head of the left or right of big 2D objects 10
-######## fun_tail() #### tail of the left or right of big 2D objects 11
-######## fun_comp_1d() #### comparison of two 1D datasets (vectors, factors, 1D tables) 13
-######## fun_comp_2d() #### comparison of two 2D datasets (row & col names, dimensions, etc.) 17
-######## fun_comp_list() #### comparison of two lists 23
-######## fun_test() #### test combinations of argument values of a function 25
-################ Object modification 28
-######## fun_name_change() #### check a vector of character strings and modify any string if present in another vector 28
-######## fun_df_remod() #### remodeling a data frame to have column name as a qualitative values and vice-versa 29
-######## fun_merge() #### merge the columns of two 2D objects, by common rows 32
-######## fun_round() #### rounding number if decimal present 36
-######## fun_mat_rotate() #### 90° clockwise matrix rotation 38
-######## fun_mat_num2color() #### convert a numeric matrix into hexadecimal color matrix 39
-######## fun_mat_op() #### assemble several matrices with operation 42
-######## fun_mat_inv() #### return the inverse of a square matrix 44
-######## fun_mat_fill() #### fill the empty half part of a symmetric square matrix 45
-######## fun_permut() #### progressively breaks a vector order 49
-################ Graphics management 59
-######## fun_width() #### window width depending on classes to plot 59
-######## fun_open() #### open a GUI or pdf graphic window 61
-######## fun_prior_plot() #### set graph param before plotting (erase axes for instance) 64
-######## fun_scale() #### select nice label numbers when setting number of ticks on an axis 68
-######## fun_post_plot() #### set graph param after plotting (axes redesign for instance) 73
-######## fun_close() #### close specific graphic windows 84
-################ Standard graphics 85
-######## fun_empty_graph() #### text to display for empty graphs 86
-################ gg graphics 87
-######## fun_gg_palette() #### ggplot2 default color palette 87
-######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle 89
-######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer 91
-######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally) 94
-######## fun_gg_bar() #### ggplot2 mean barplot + overlaid dots if required 130
-######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required 165
-######## fun_gg_prop() #### ggplot2 proportion barplot 165
-######## fun_gg_strip() #### ggplot2 stripchart + mean/median 165
-######## fun_gg_dot() #### ggplot2 categorial dotplot + mean/median 165
-######## fun_gg_violin() #### ggplot2 violins 165
-######## fun_gg_line() #### ggplot2 lines + background dots and error bars 165
-######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required 168
-######## fun_gg_empty_graph() #### text to display for empty graphs 181
-################ Graphic extraction 183
-######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs 183
-######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation 191
-################ Import 223
-######## fun_pack() #### check if R packages are present and import into the working environment 223
-######## fun_python_pack() #### check if python packages are present 225
-################ Print / Exporting results (text & tables) 227
-######## fun_report() #### print string or data object into output file 227
-######## fun_get_message() #### return messages of an expression (that can be exported) 230
+################ Object analysis 2
+######## fun_check() #### check class, type, length, etc., of objects 2
+######## fun_info() #### recover object information 8
+######## fun_head() #### head of the left or right of big 2D objects 10
+######## fun_tail() #### tail of the left or right of big 2D objects 11
+######## fun_comp_1d() #### comparison of two 1D datasets (vectors, factors, 1D tables) 13
+######## fun_comp_2d() #### comparison of two 2D datasets (row & col names, dimensions, etc.) 17
+######## fun_comp_list() #### comparison of two lists 23
+######## fun_test() #### test combinations of argument values of a function 25
+################ Object modification 28
+######## fun_name_change() #### check a vector of character strings and modify any string if present in another vector 28
+######## fun_df_remod() #### remodeling a data frame to have column name as a qualitative values and vice-versa 29
+######## fun_merge() #### merge the columns of two 2D objects, by common rows 32
+######## fun_round() #### rounding number if decimal present 36
+######## fun_mat_rotate() #### 90° clockwise matrix rotation 38
+######## fun_mat_num2color() #### convert a numeric matrix into hexadecimal color matrix 39
+######## fun_mat_op() #### assemble several matrices with operation 42
+######## fun_mat_inv() #### return the inverse of a square matrix 44
+######## fun_mat_fill() #### fill the empty half part of a symmetric square matrix 45
+######## fun_permut() #### progressively breaks a vector order 49
+################ Graphics management 59
+######## fun_width() #### window width depending on classes to plot 59
+######## fun_open() #### open a GUI or pdf graphic window 61
+######## fun_prior_plot() #### set graph param before plotting (erase axes for instance) 64
+######## fun_scale() #### select nice label numbers when setting number of ticks on an axis 68
+######## fun_post_plot() #### set graph param after plotting (axes redesign for instance) 73
+######## fun_close() #### close specific graphic windows 84
+################ Standard graphics 85
+######## fun_empty_graph() #### text to display for empty graphs 86
+################ gg graphics 87
+######## fun_gg_palette() #### ggplot2 default color palette 87
+######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle 89
+######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer 91
+######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally) 94
+######## fun_gg_bar() #### ggplot2 mean barplot + overlaid dots if required 130
+######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required 165
+######## fun_gg_prop() #### ggplot2 proportion barplot 165
+######## fun_gg_strip() #### ggplot2 stripchart + mean/median 165
+######## fun_gg_dot() #### ggplot2 categorial dotplot + mean/median 165
+######## fun_gg_violin() #### ggplot2 violins 165
+######## fun_gg_line() #### ggplot2 lines + background dots and error bars 165
+######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required 168
+######## fun_gg_empty_graph() #### text to display for empty graphs 181
+################ Graphic extraction 183
+######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs 183
+######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation 191
+################ Import 223
+######## fun_pack() #### check if R packages are present and import into the working environment 223
+######## fun_python_pack() #### check if python packages are present 225
+################ Print / Exporting results (text & tables) 227
+######## fun_report() #### print string or data object into output file 227
+######## fun_get_message() #### return messages of an expression (that can be exported) 230
################################ FUNCTIONS ################################
@@ -9374,3 +9374,1544 @@ return(output) # do not use cat() because the idea is to reuse the message
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# https://ggplot2-book.org/scales.html
+
+
+
+fun_gg_boxplot <- function(
+data1,
+y,
+categ,
+categ.class.order = NULL,
+categ.legend.name = NULL,
+categ.color = NULL,
+box.fill = FALSE,
+box.width = 0.5,
+box.space = 0.1,
+box.line.size = 0.5,
+box.notch = FALSE,
+box.alpha = 1,
+box.mean = TRUE,
+box.whisker.kind = "std",
+box.whisker.width = 0,
+dot.color = "black",
+dot.categ = NULL,
+dot.categ.class.order = NULL,
+dot.categ.legend.name = NULL,
+dot.tidy = TRUE,
+dot.tidy.bin.nb = 30,
+dot.jitter = 0.5,
+dot.size = 3,
+dot.alpha = 0.5,
+dot.border.size = 0.5,
+dot.border.color = NULL,
+x.lab = NULL,
+y.lab = NULL,
+y.lim = NULL,
+y.log = "no",
+y.tick.nb = NULL,
+y.inter.tick.nb = NULL,
+y.include.zero = FALSE,
+y.top.extra.margin = 0.05,
+y.bottom.extra.margin = 0.05,
+stat.disp = NULL,
+stat.disp.mean = FALSE,
+stat.size = 4,
+stat.dist = 2,
+vertical = TRUE,
+text.size = 12,
+text.angle = 0,
+title = "",
+title.text.size = 8,
+classic = TRUE,
+grid = FALSE,
+return = FALSE,
+plot = TRUE,
+add = NULL,
+warn.print = TRUE,
+lib.path = NULL
+){
+
+# DEBUGGING
+# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10)) ; data1 = obs1 ; y = "Time" ; categ = "Group1" ; categ.class.order = list(c("G", "H")) ; categ.legend.name = NULL ; categ.color = c("green") ; box.fill = FALSE ; box.width = 0.5 ; box.space = 0.1 ; box.notch = FALSE ; box.line.size = 0.5 ; box.alpha = 0.5 ; box.mean = TRUE ; box.whisker.kind = "std" ; box.whisker.width = 0.5 ; dot.color = "same" ; dot.categ = "Group1"; dot.categ.class.order = c("G", "H") ; dot.categ.legend.name = NULL ; dot.tidy = TRUE ; dot.tidy.bin.nb = 30 ; dot.jitter = 0.25 ; dot.size = 3 ; dot.alpha = 0.5 ; dot.border.size = 0.5 ; dot.border.color = NULL ; y.lim = NULL ; y.log = "no" ; y.tick.nb = NULL ; y.inter.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; stat.disp = NULL ; stat.disp.mean = FALSE ; stat.size = 4 ; stat.dist = 2 ; x.lab = NULL ; y.lab = NULL ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; return = TRUE ; plot = TRUE ; add = NULL ; warn.print = FALSE ; lib.path = NULL
+
+# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), Group2 = rep(c("A", "B"), time = 10), Group3 = rep(c("I", "J"), time = 10)) ; data1 = obs1 ; y = "Time" ; categ = c("Group1", "Group2") ; categ.class.order = list(c("G", "H"), c("A", "B")); categ.legend.name = NULL ; categ.color = c("green", "blue") ; box.fill = FALSE ; box.width = 0.5 ; box.space = 0.1 ; box.notch = FALSE ; box.line.size = 0.5 ; box.alpha = 0.5 ; box.mean = TRUE ; box.whisker.kind = "std" ; box.whisker.width = 0.5 ; dot.color = "black" ; dot.categ = "Group1" ; dot.categ.class.order = NULL ; dot.categ.legend.name = NULL ; dot.tidy = TRUE ; dot.tidy.bin.nb = 30 ; dot.jitter = 0.25 ; dot.size = 3 ; dot.alpha = 0.5 ; dot.border.size = 0.5 ; dot.border.color = NULL ; y.lim = NULL ; y.log = "no" ; y.tick.nb = NULL ; y.inter.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; stat.disp = NULL ; stat.disp.mean = FALSE ; stat.size = 4 ; stat.dist = 2 ; x.lab = NULL ; y.lab = NULL ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; return = FALSE ; plot = TRUE ; add = NULL ; warn.print = FALSE ; lib.path = NULL
+
+# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), Group2 = rep(c("A", "B"), time = 10)) ; data1 = obs1 ; y = "Time" ; categ = c("Group1") ; categ.class.order = list(c("H", "G")); categ.legend.name = NULL ; categ.color = c("blue") ; box.fill = FALSE ; box.width = 0.5 ; box.space = 0.1 ; box.notch = TRUE ; box.line.size = 1 ; box.alpha = 1 ; box.mean = FALSE ; box.whisker.kind = "max" ; box.whisker.width = 0 ; dot.color = "black" ; dot.categ = "Group1" ; dot.categ.class.order = NULL ; dot.categ.legend.name = NULL ; dot.tidy = TRUE ; dot.tidy.bin.nb = 30 ; dot.jitter = 0.25 ; dot.size = 3 ; dot.alpha = 0.5 ; dot.border.size = 0.5 ; dot.border.color = NULL ; y.lim = NULL ; y.log = "no" ; y.tick.nb = NULL ; y.inter.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; stat.disp = NULL ; stat.disp.mean = FALSE ; stat.size = 4 ; stat.dist = 2 ; x.lab = NULL ; y.lab = NULL ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; return = FALSE ; plot = TRUE ; add = NULL ; warn.print = FALSE ; lib.path = NULL
+
+
+
+
+
+# function name
+function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
+# end function name
+# required function checking
+req.function <- c(
+"fun_comp_2d",
+"fun_gg_just",
+"fun_gg_palette",
+"fun_name_change",
+"fun_pack",
+"fun_check",
+"fun_round",
+"fun_scale"
+)
+for(i1 in req.function){
+if(length(find(i1, mode = "function")) == 0){
+tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED ", i1, "() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
+stop(tempo.cat)
+}
+}
+# end required function checking
+# reserved words to avoid bugs (used in this function)
+reserved.words <- c("categ.check", "categ.color", "dot.color", "dot.categ", "dot.max", "dot.min", "group", "group.check", "MEAN", "tempo.categ1", "tempo.categ2", "text.max.pos", "text.min.pos", "x", "x.y", "y", "y.check", "y_from.dot.max", "ymax")
+# end reserved words to avoid bugs (used in this function)
+# primary argument checking
+arg.check <- NULL #
+text.check <- NULL #
+checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
+tempo <- fun_check(data = data1, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = y, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = categ, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+if( ! is.null(categ.class.order)){
+tempo <- fun_check(data = categ.class.order, class = "list", fun.name = function.name) ; eval(ee)
+}
+if( ! is.null(categ.legend.name)){
+tempo <- fun_check(data = categ.legend.name, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+}
+if( ! is.null(categ.color)){
+tempo1 <- fun_check(data = categ.color, class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name, print = FALSE)
+tempo2 <- fun_check(data = categ.color, class = "factor", na.contain = TRUE, fun.name = function.name, print = FALSE)
+if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+tempo.check.color <- fun_check(data = categ.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name, print = FALSE)$problem
+if(tempo.check.color == TRUE){
+tempo.cat <- paste0("ERROR IN ", function.name, ": categ.color MUST BE A FACTOR OR CHARACTER VECTOR OR INTEGER VECTOR") # integer possible because dealt above
+text.check <- c(text.check, tempo.cat)
+arg.check <- c(arg.check, TRUE)
+}
+}
+}
+tempo <- fun_check(data = box.fill, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = box.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = box.space, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = box.line.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = box.notch, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = box.alpha, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = box.mean, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = box.whisker.kind, options = c("no", "std", "max"), length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = box.whisker.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+if( ! is.null(dot.color)){
+tempo1 <- fun_check(data = dot.color, class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name, print = FALSE)
+tempo2 <- fun_check(data = dot.color, class = "factor", na.contain = TRUE, fun.name = function.name, print = FALSE)
+if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+tempo.check.color <- fun_check(data = dot.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name, print = FALSE)$problem
+if(tempo.check.color == TRUE){
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.color MUST BE A FACTOR OR CHARACTER VECTOR OR INTEGER VECTOR") # integer possible because dealt above
+text.check <- c(text.check, tempo.cat)
+arg.check <- c(arg.check, TRUE)
+}
+}
+}
+if( ! is.null(dot.categ)){
+tempo <- fun_check(data = dot.categ, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+}
+if( ! is.null(dot.categ.class.order)){
+tempo <- fun_check(data = dot.categ.class.order, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+}
+if( ! is.null(dot.categ.legend.name)){
+tempo <- fun_check(data = dot.categ.legend.name, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+}
+tempo <- fun_check(data = dot.tidy, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = dot.tidy.bin.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = dot.jitter, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = dot.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = dot.alpha, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = dot.border.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+if( ! is.null(dot.border.color)){
+tempo1 <- fun_check(data = dot.border.color, class = "vector", mode = "character", length = 1, fun.name = function.name, print = FALSE)
+tempo2 <- fun_check(data = dot.border.color, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name, print = FALSE)
+if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+# integer colors into gg_palette
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.color MUST BE A SINGLE CHARACTER STRING OF COLOR OR A SINGLE INTEGER VALUE") # integer possible because dealt above
+text.check <- c(text.check, tempo.cat)
+arg.check <- c(arg.check, TRUE)
+}
+}
+if( ! is.null(x.lab)){
+if(all(class(x.lab) %in% "expression")){ # to deal with math symbols
+tempo <- fun_check(data = x.lab, class = "expression", length = 1, fun.name = function.name) ; eval(ee)
+}else{
+tempo <- fun_check(data = x.lab, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+}
+}
+if( ! is.null(y.lab)){
+if(all(class(y.lab) %in% "expression")){ # to deal with math symbols
+tempo <- fun_check(data = y.lab, class = "expression", length = 1, fun.name = function.name) ; eval(ee)
+}else{
+tempo <- fun_check(data = y.lab, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+}
+}
+if( ! is.null(y.lim)){
+tempo <- fun_check(data = y.lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
+if(tempo$problem == FALSE & any(y.lim %in% c(Inf, -Inf))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": y.lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
+text.check <- c(text.check, tempo.cat)
+arg.check <- c(arg.check, TRUE)
+}
+}
+tempo <- fun_check(data = y.log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
+if( ! is.null(y.tick.nb)){
+tempo <- fun_check(data = y.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+if(tempo$problem == FALSE & y.tick.nb < 0){
+tempo.cat <- paste0("ERROR IN ", function.name, ": y.tick.nb ARGUMENT MUST BE A NON NULL POSITIVE INTEGER")
+text.check <- c(text.check, tempo.cat)
+arg.check <- c(arg.check, TRUE)
+}
+}
+if( ! is.null(y.inter.tick.nb)){
+tempo <- fun_check(data = y.inter.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+if(tempo$problem == FALSE & y.inter.tick.nb < 0){
+tempo.cat <- paste0("ERROR IN ", function.name, ": y.inter.tick.nb ARGUMENT MUST BE A NON NULL POSITIVE INTEGER")
+text.check <- c(text.check, tempo.cat)
+arg.check <- c(arg.check, TRUE)
+}
+}
+tempo <- fun_check(data = y.include.zero, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = y.top.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = y.bottom.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+if( ! is.null(stat.disp)){
+tempo <- fun_check(data = stat.disp, options = c("top", "above"), length = 1, fun.name = function.name) ; eval(ee)
+}
+tempo <- fun_check(data = stat.disp.mean, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = stat.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = stat.dist, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = vertical, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = text.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = title.text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = classic, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = grid, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = return, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+tempo <- fun_check(data = plot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+if( ! is.null(add)){
+tempo <- fun_check(data = add, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+if(tempo$problem == FALSE & ! grepl(pattern = "^\\+", add)){ # check that the add string start by +
+tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST START WITH \"+\": ", paste(unique(add), collapse = " "))
+text.check <- c(text.check, tempo.cat)
+arg.check <- c(arg.check, TRUE)
+}else if(tempo$problem == FALSE & ! grepl(pattern = "ggplot2::", add)){ #
+tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST CONTAIN \"ggplot2::\" IN FRONT OF EACH GGPLOT2 FUNCTION: ", paste(unique(add), collapse = " "))
+text.check <- c(text.check, tempo.cat)
+arg.check <- c(arg.check, TRUE)
+}else if(tempo$problem == FALSE & ! grepl(pattern = ")$", add)){ # check that the add string finished by )
+tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST FINISH BY \")\": ", paste(unique(add), collapse = " "))
+text.check <- c(text.check, tempo.cat)
+arg.check <- c(arg.check, TRUE)
+}
+}
+tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+if( ! is.null(lib.path)){
+tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+if(tempo$problem == FALSE & ! all(dir.exists(lib.path))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+text.check <- c(text.check, tempo.cat)
+arg.check <- c(arg.check, TRUE)
+}
+}
+if(any(arg.check) == TRUE){
+stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+}
+# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+# end primary argument checking
+# second round of checking and data preparation
+warn <- NULL
+warn.count <- 0
+if(any(duplicated(names(data1)))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": DUPLICATED COLUMN NAMES OF data1 ARGUMENT NOT ALLOWED:\n", paste(names(data1)[duplicated(names(data1))], collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+if( ! (y %in% names(data1))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": y ARGUMENT MUST BE A COLUMN NAME OF data1")
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else{
+tempo <- fun_check(data = data1[, y], data.name = "y COLUMN OF data1", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+}
+if(length(categ) > 2){
+tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT CANNOT HAVE MORE THAN 2 COLUMN NAMES OF data1")
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else if( ! all(categ %in% names(data1))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT MUST BE COLUMN NAMES OF data1. HERE IT IS:\n", paste(categ, collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+# reserved word checking
+if(any(names(data1) %in% reserved.words)){
+if(any(duplicated(names(data1)))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": DUPLICATED COLUMN NAMES OF data1 ARGUMENT NOT ALLOWED:\n", paste(names(data1)[duplicated(names(data1))], collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+if( ! is.null(dot.categ)){
+if(dot.categ %in% categ){
+reserved.words <- c(reserved.words, paste0(dot.categ, "_DOT")) # paste0(dot.categ, "_DOT") is added to the reserved words because in such situation, a new column will be added to data1 that is named paste0(dot.categ, "_DOT")
+}
+}
+tempo.output <- fun_name_change(names(data1), reserved.words)
+for(i3 in 1:length(tempo.output$ini)){ # a loop to be sure to take the good ones
+names(data1)[names(data1) == tempo.output$ini[i3]] <- tempo.output$post[i3]
+if(any(y == tempo.output$ini[i3])){
+y[y == tempo.output$ini[i3]] <- tempo.output$post[i3]
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") IN y ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i3], " HAS BEEN REPLACED BY ", tempo.output$post[i3], "\nBECAUSE RISK OF BUG AS SOME NAMES IN y ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# BEWARE: names of y argument potentially replaced
+if(any(categ == tempo.output$ini[i3])){
+categ[categ == tempo.output$ini[i3]] <- tempo.output$post[i3]
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") IN categ ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i3], " HAS BEEN REPLACED BY ", tempo.output$post[i3], "\nBECAUSE RISK OF BUG AS SOME NAMES IN categ ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# BEWARE: names of categ argument potentially replaced
+if( ! is.null(dot.categ)){
+if(any(dot.categ == tempo.output$ini[i3])){
+dot.categ[dot.categ == tempo.output$ini[i3]] <- tempo.output$post[i3]
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") IN dot.categ ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i3], " HAS BEEN REPLACED BY ", tempo.output$post[i3], "\nBECAUSE RISK OF BUG AS SOME NAMES IN dot.categ ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+}
+# BEWARE: names of dot.categ argument potentially replaced
+}
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") REGARDING COLUMN NAMES REPLACEMENT, THE NAMES\n", paste(tempo.output$ini, collapse = " "), "\nHAVE BEEN REPLACED BY\n", paste(tempo.output$post, collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# end reserved word checking
+# conversion of categ columns in data1 into factors
+for(i1 in 1:length(categ)){
+tempo1 <- fun_check(data = data1[, categ[i1]], data.name = paste0("categ NUMBER ", i1, " OF data1"), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name, print = FALSE)
+tempo2 <- fun_check(data = data1[, categ[i1]], data.name = paste0("categ NUMBER ", i1, " OF data1"), class = "factor", na.contain = TRUE, fun.name = function.name, print = FALSE)
+if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+tempo.cat <- paste0("ERROR IN ", function.name, ": ", paste0("categ NUMBER ", i1, " OF data1"), " MUST BE A FACTOR OR CHARACTER VECTOR")
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else if(tempo1$problem == FALSE){ # character vector
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") IN categ NUMBER ", i1, " IN data1, THE CHARACTER COLUMN HAS BEEN CONVERTED TO FACTOR, WITH LEVELS ACCORDING TO THE ALPHABETICAL ORDER")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+data1[, categ[i1]] <- factor(data1[, categ[i1]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
+}
+# OK: all the categ columns of data1 are factors from here
+# end conversion of categ columns in data1 into factors
+if( ! is.null(categ.class.order)){
+if(length(categ.class.order) != length(categ)){
+tempo.cat <- paste0("ERROR IN ", function.name, ": categ.class.order ARGUMENT MUST BE A LIST OF LENGTH EQUAL TO LENGTH OF categ\nHERE IT IS LENGTH: ", length(categ.class.order), " VERSUS ", length(categ))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else{
+for(i3 in 1:length(categ.class.order)){
+if(is.null(categ.class.order[[i3]])){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") THE categ.class.order COMPARTMENT ", i3, " IS NULL. ALPHABETICAL ORDER WILL BE APPLIED")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+data1[, categ[i3]] <- factor(as.character(data1[, categ[i3]])) # if already a factor, change nothing, if characters, levels according to alphabetical order
+categ.class.order[[i3]] <- levels(data1[, categ[i3]]) # character vector that will be used later
+}else{
+tempo <- fun_check(data = categ.class.order[[i3]], data.name = paste0("COMPARTMENT ", i3 , " OF categ.class.order ARGUMENT"), class = "vector", mode = "character", length = length(levels(data1[, categ[i1]])), fun.name = function.name) ; eval(ee) # length(data1[, categ[i1]) -> if data1[, categ[i1] was initially character vector, then conversion as factor after the NA removal, thus class number ok. If data1[, categ[i1] was initially factor, no modification after the NA removal, thus class number ok
+}
+if(any(duplicated(categ.class.order[[i3]]))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i3, " OF categ.class.order ARGUMENT CANNOT HAVE DUPLICATED CLASSES: ", paste(categ.class.order[[i3]], collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else if( ! (all(categ.class.order[[i3]] %in% unique(data1[, categ[i3]])) & all(unique(data1[, categ[i3]]) %in% categ.class.order[[i3]]))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i3, " OF categ.class.order ARGUMENT MUST BE CLASSES OF ELEMENT ", i3, " OF categ ARGUMENT\nHERE IT IS:\n", paste(categ.class.order[[i3]], collapse = " "), "\nFOR COMPARTMENT ", i3, " OF categ.class.order AND IT IS:\n", paste(unique(data1[, categ[i3]]), collapse = " "), "\nFOR COLUMN ", categ[i3], " OF data1")
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else{
+data1[, categ[i3]] <- factor(data1[, categ[i3]], levels = categ.class.order[[i3]]) # reorder the factor
+
+}
+}
+}
+}else{
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") THE categ.class.order SETTING IS NULL. ALPHABETICAL ORDER WILL BE APPLIED FOR ", paste(categ, collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+categ.class.order <- vector("list", length = length(categ))
+for(i2 in 1:length(categ.class.order)){
+categ.class.order[[i2]] <- levels(data1[, categ[i2]])
+}
+}
+# categ.class.order not NULL anymore
+if(is.null(categ.legend.name)){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") THE categ.legend.name SETTING IS NULL. NAMES OF categ WILL BE USED: ", paste(categ, collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+categ.legend.name <- categ[length(categ)] # if only categ1, then legend name of categ1, if length(categ) == 2, then legend name of categ2
+}
+# categ.legend.name not NULL anymore
+# management of categ.color
+if( ! is.null(categ.color)){
+# check the nature of color
+# integer colors into gg_palette
+tempo.check.color <- fun_check(data = categ.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name, print = FALSE)$problem
+if(tempo.check.color == FALSE){
+# convert integers into colors
+categ.color <- fun_gg_palette(max(categ.color, na.rm = TRUE))[categ.color]
+}
+# end integer colors into gg_palette
+if( ! (all(categ.color %in% colors() | grepl(pattern = "^#", categ.color)))){ # check that all strings of low.color start by #
+tempo.cat <- paste0("ERROR IN ", function.name, ": categ.color ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors(): ", paste(unique(categ.color), collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+if(any(is.na(categ.color))){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") categ.color ARGUMENT CONTAINS NA")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# end check the nature of color
+# check the length of color
+i0 <- length(categ) # if only categ1, then colors for classes of categ1, if length(categ) == 2, then colors for classes of categ2
+if(length(categ.color) == length(levels(data1[, categ[i0]]))){ # here length(categ.color) is equal to the different number of categ
+# data1[, categ[i0]] <- factor(data1[, categ[i0]]) # not required because sure that is is a factor
+data1 <- data.frame(data1, categ.color = data1[, categ[i0]])
+data1$categ.color <- factor(data1$categ.color, labels = categ.color)
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") IN ", categ[i0], " OF categ ARGUMENT, THE FOLLOWING COLORS:\n", paste(categ.color, collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(factor(data1[, categ[i0]])), collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}else if(length(categ.color) == length(data1[, categ[i0]])){# here length(categ.color) is equal to nrow(data1) -> Modif to have length(categ.color) equal to the different number of categ (length(categ.color) == length(levels(data1[, categ[i0]])))
+data1 <- data.frame(data1, categ.color = categ.color)
+tempo.check <- unique(data1[ , c(categ[i0], "categ.color")])
+if( ! (nrow(tempo.check) == length(unique(categ.color)) & nrow(tempo.check) == length(unique(data1[ , categ[i0]])))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": categ.color ARGUMENT HAS THE LENGTH OF data1 ROW NUMBER\nBUT IS INCORRECTLY ASSOCIATED TO EACH CLASS OF categ ", categ[i0], ":\n", paste(unique(mapply(FUN = "paste", data1[ ,categ[i0]], data1[ ,"categ.color"])), collapse = "\n"))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else{
+# data1[, categ[i0]] <- factor(data1[, categ[i0]]) # not required because sure that is is a factor
+categ.color <- unique(data1$categ.color[order(data1[, categ[i0]])]) # Modif to have length(categ.color) equal to the different number of categ (length(categ.color) == length(levels(data1[, categ[i0]])))
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") categ.color ARGUMENT HAS THE LENGTH OF data1 ROW NUMBER\nCOLORS HAVE BEEN RESPECTIVELY ASSOCIATED TO EACH CLASS OF categ ", categ[i0], " AS:\n", paste(levels(factor(data1[, categ[i0]])), collapse = " "), "\n", paste(categ.color, collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+}else if(length(categ.color) == 1){
+# data1[, categ[i0]] <- factor(data1[, categ[i0]]) # not required because sure that is is a factor
+data1 <- data.frame(data1, categ.color = categ.color)
+categ.color <- rep(categ.color, length(levels(data1[, categ[i0]])))
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") categ.color ARGUMENT HAS LENGTH 1, MEANING THAT ALL THE DIFFERENT CLASSES OF ", categ[i0], "\n", paste(levels(factor(data1[, categ[i0]])), collapse = " "), "\nWILL HAVE THE SAME COLOR\n", paste(categ.color, collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}else{
+tempo.cat <- paste0("ERROR IN ", function.name, ": categ.color ARGUMENT MUST BE (1) LENGTH 1, OR (2) THE LENGTH OF data1 NROWS, OR (3) THE LENGTH OF THE CLASSES IN THE categ ", categ[i0], " COLUMN. HERE IT IS COLOR LENGTH ", length(categ.color), " VERSUS CATEG LENGTH ", length(data1[, categ[i0]]), " AND CATEG CLASS LENGTH ", length(unique(data1[, categ[i0]])), "\nPRESENCE OF NA COULD BE THE PROBLEM")
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+}else{
+i0 <- length(categ) # if only categ1, then colors for classes of categ1, if length(categ) == 2, then colors for classes of categ2
+# data1[, categ[i0]] <- factor(data1[, categ[i0]]) # not required because sure that is is a factor
+categ.color <- fun_gg_palette(length(levels(data1[, categ[i0]])))
+data1 <- data.frame(data1, categ.color = data1[, categ[i0]])
+data1$categ.color <- factor(data1$categ.color, labels = categ.color)
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") NULL categ.color ARGUMENT -> COLORS RESPECTIVELY ATTRIBUTED TO EACH CLASS OF ", categ[i0], " IN data1:\n", paste(categ.color, collapse = " "), "\n", paste(levels(data1[, categ[i0]]), collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# categ.color not NULL anymore
+categ.color <- as.character(categ.color)
+# categ.color is a character string representing the diff classes
+data1$categ.color <- factor(data1$categ.color, levels = unique(categ.color)) # ok because if categ.color is a character string, the order make class 1, class 2, etc. unique() because no duplicates allowed
+# data1$categ.color is a factor with order of levels -> categ.color
+# end management of categ.color
+# management of dot.color
+if( ! is.null(dot.color)){
+# optional legend of dot colors
+if( ! is.null(dot.categ)){
+ini.dot.categ <- dot.categ
+if( ! dot.categ %in% names(data1)){ # no need to use all() because length(dot.categ) = 1
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.categ ARGUMENT MUST BE A COLUMN NAME OF data1. HERE IT IS:\n", dot.categ)
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else if(dot.categ %in% categ){ # no need to use all() because length(dot.categ) = 1
+# management of dot legend if dot.categ %in% categ (because legends with the same name are joined in ggplot2)
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") THE COLUMN NAME OF data1 INDICATED IN THE dot.categ ARGUMENT (", dot.categ, ") HAS BEEN REPLACED BY ", paste0(dot.categ, "_DOT"), " TO AVOID MERGED LEGEND BY GGPLOT2")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+data1 <- data.frame(data1, dot.categ = data1[, dot.categ]) # dot.categ is not a column name of data1 (checked above with reserved words)
+dot.categ <- paste0(dot.categ, "_DOT")
+names(data1)[names(data1) == "dot.categ"] <- dot.categ # paste0(dot.categ, "_DOT") is not a column name of data1 (checked above with reserved words)
+# tempo.cat <- paste0("ERROR IN ", function.name, ": dot.categ ARGUMENT CANNOT BE A COLUMN NAME OF data1 ALREADY SPECIFIED IN THE categ ARGUMENT:\n", dot.categ, "\nINDEED, dot.categ ARGUMENT IS MADE TO HAVE MULTIPLE DOT COLORS NOT RELATED TO THE BOXPLOT CATEGORIES")
+# stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+tempo1 <- fun_check(data = data1[, dot.categ], data.name = paste0(dot.categ, " COLUMN OF data1"), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name, print = FALSE)
+tempo2 <- fun_check(data = data1[, dot.categ], data.name = paste0(dot.categ, " COLUMN OF data1"), class = "factor", na.contain = TRUE, fun.name = function.name, print = FALSE)
+if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.categ COLUMN MUST BE A FACTOR OR CHARACTER VECTOR") #
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+data1[, dot.categ] <- factor(data1[, dot.categ]) # if already a factor, change nothing, if characters, levels according to alphabetical order
+# dot.categ column of data1 is factor from here
+if( ! is.null(dot.categ.class.order)){
+if(any(duplicated(dot.categ.class.order))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.categ.class.order ARGUMENT CANNOT HAVE DUPLICATED CLASSES: ", paste(dot.categ.class.order, collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else if( ! (all(dot.categ.class.order %in% levels(data1[, dot.categ])) & all(levels(data1[, dot.categ]) %in% dot.categ.class.order))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.categ.class.order ARGUMENT MUST BE CLASSES OF dot.categ ARGUMENT\nHERE IT IS:\n", paste(dot.categ.class.order, collapse = " "), "\nFOR dot.categ.class.order AND IT IS:\n", paste(levels(data1[, dot.categ]), collapse = " "), "\nFOR dot.categ COLUMN (", dot.categ, ") OF data1")
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else{
+data1[, dot.categ] <- factor(data1[, dot.categ], levels = dot.categ.class.order) # reorder the factor
+}
+}else{
+dot.categ.class.order <- levels(data1[, dot.categ])
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") THE dot.categ.class.order SETTING IS NULL. ALPHABETICAL ORDER WILL BE APPLIED FOR LEGEND DISPLAY: ", paste(dot.categ.class.order, collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# dot.categ.class.order not NULL anymore
+if(all(dot.color == "same") & length(dot.color) == 1){
+if( ! identical(ini.dot.categ, categ[length(categ)])){
+tempo.cat <- paste0("ERROR IN ", function.name, ":WHEN dot.color ARGUMENT IS \"same\", THE COLUMN NAME IN dot.categ ARGUMENT MUST BE IDENTICAL TO THE LAST COLUMN NAME IN categ ARGUMENT. HERE IT IS:\ndot.categ: ", paste(ini.dot.categ, collapse = " "), "\ncateg: ", paste(categ, collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else if( ! identical(unlist(categ.class.order[length(categ)]), dot.categ.class.order)){
+tempo.cat <- paste0("ERROR IN ", function.name, ":WHEN dot.color ARGUMENT IS \"same\",\nLAST COMPARTMENT OF categ.class.order ARGUMENT AND dot.categ.class.order ARGUMENT CANNOT BE DIFFERENT:\nLAST COMPARTMENT OF categ.class.order: ", paste(unlist(categ.class.order[length(categ)]), collapse = " "), "\ndot.categ.class.order: ", paste(dot.categ.class.order, collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+}
+if(identical(categ, ini.dot.categ) & ! identical(unlist(categ.class.order), dot.categ.class.order) & identical(sort(unlist(categ.class.order)), sort(dot.categ.class.order))){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") THE categ AND dot.categ ARGUMENT ARE IDENTICAL, BUT ORDER OF THE CLASSES IS NOT THE SAME:\ncateg.class.order: ", paste(unlist(categ.class.order), collapse = " "), "\ndot.categ.class.order: ", paste(dot.categ.class.order, collapse = " "), "\nNOTE THAT ORDER OF categ.class.order IS THE ONE USED FOR THE AXIS REPRESENTATION")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+if(is.null(dot.categ.legend.name)){
+dot.categ.legend.name <- if(ini.dot.categ %in% categ[length(categ)]){dot.categ}else{ini.dot.categ} #
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") THE dot.categ.legend.name SETTING IS NULL. VALUES OF dot.categ WILL BE USED: ", paste(dot.categ, collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# dot.categ.legend.name not NULL anymore
+}else{
+if( ! is.null(dot.categ.class.order)){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") THE dot.categ.class.order ARGUMENT IS NOT NULL, BUT THE dot.categ ARGUMENT IS\n-> dot.categ.class.order NOT CONSIDERED AS NO LEGEND WILL BE DRAWN")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+}
+# end optional legend of dot colors
+# check the nature of color
+# integer colors into gg_palette
+tempo.check.color <- fun_check(data = dot.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name, print = FALSE)$problem
+if(tempo.check.color == FALSE){
+# convert integers into colors
+dot.color <- fun_gg_palette(max(dot.color, na.rm = TRUE))[dot.color]
+}
+# end integer colors into gg_palette
+if(all(dot.color == "same") & length(dot.color) == 1){
+dot.color <- categ.color # same color of the dots as the corresponding box color
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") dot.color ARGUMENT HAS BEEN SET TO \"same\"\nTHUS, DOTS WILL HAVE THE SAME COLORS AS THE CORRESPONDING BOXPLOT")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}else if( ! (all(dot.color %in% colors() | grepl(pattern = "^#", dot.color)))){ # check that all strings of low.color start by #
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.color ARGUMENT MUST BE (1) A HEXADECIMAL COLOR VECTOR STARTING BY #, OR (2) COLOR NAMES GIVEN BY colors(), OR (3) INTEGERS, OR THE STRING\"same\"\nHERE IT IS: ", paste(unique(dot.color), collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+if(any(is.na(dot.color))){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") dot.color ARGUMENT CONTAINS NA")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# end check the nature of color
+# check the length of color
+if( ! is.null(dot.categ)){
+# optional legend of dot colors
+if(length(dot.color) > 1 & length(unique(data1[, dot.categ])) != length(dot.color)){
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.color ARGUMENT IS NOT THE SAME LENGTH AS LEVELS OF dot.categ COLUMN (", dot.categ, "):\ndot.color: ", paste(dot.color, collapse = " "), "\ndot.categ LEVELS: ", paste(levels(data1[, dot.categ]), collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else if(length(dot.color) == 1 & length(dot.categ.class.order) > 1){ # to deal with single color
+dot.color <- rep(dot.color, length(dot.categ.class.order))
+}
+data1 <- data.frame(data1, dot.color = data1[, dot.categ])
+data1$dot.color <- factor(data1$dot.color, labels = dot.color) # do not use labels = unique(dot.color). Otherwise, we can have green1 green2 when dot.color is c("green", "green")
+dot.color <- as.character(unique(data1$dot.color[order(data1[, dot.categ])])) # reorder the dot.color character vector
+if(length(dot.color) == 1 & length(dot.categ.class.order) > 1){ # to deal with single color
+dot.color <- rep(dot.color, length(dot.categ.class.order))
+}
+tempo.check <- unique(data1[ , c(dot.categ, "dot.color")])
+if(length(unique(data1[ , "dot.color"])) > 1 & ( ! (nrow(tempo.check) == length(unique(data1[ , "dot.color"])) & nrow(tempo.check) == length(unique(data1[ , dot.categ]))))){ # length(unique(data1[ , "dot.color"])) > 1 because if only one color, can be attributed to each class of dot.categ
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.color ARGUMENT IS INCORRECTLY ASSOCIATED TO EACH CLASS OF dot.categ (", dot.categ, ") COLUMN:\n", paste(unique(mapply(FUN = "paste", data1[ , dot.categ], data1[ ,"dot.color"])), collapse = "\n"))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else{
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") IN dot.categ ARGUMENT (", dot.categ, "), THE FOLLOWING COLORS Of DOTS:\n", paste(dot.color, collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(data1[, dot.categ]), collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# dot.color is a character string representing the diff classes of dot.categ
+# data1$dot.color is a factor with order of levels -> dot.categ
+# end optional legend of dot colors
+}else{
+i0 <- length(categ) # if only categ1, then colors for classes of categ1, if length(categ) == 2, then colors for classes of categ2
+if(length(dot.color) == length(levels(data1[, categ[i0]]))){ # here length(dot.color) is equal to the different number of categ
+# data1[, categ[i0]] <- factor(data1[, categ[i0]]) # not required because sure that is is a factor
+data1 <- data.frame(data1, dot.color = data1[, categ[i0]])
+data1$dot.color <- factor(data1$dot.color, labels = dot.color)
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") IN ", categ[i0], " OF categ ARGUMENT, THE FOLLOWING COLORS:\n", paste(dot.color, collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(factor(data1[, categ[i0]])), collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}else if(length(dot.color) == length(data1[, categ[i0]])){# here length(dot.color) is equal to nrow(data1) -> Modif to have length(dot.color) equal to the different number of categ (length(dot.color) == length(levels(data1[, categ[i0]])))
+data1 <- data.frame(data1, dot.color = dot.color)
+}else if(length(dot.color) == 1 & ! all(dot.color == "same")){
+# data1[, categ[i0]] <- factor(data1[, categ[i0]]) # not required because sure that is is a factor
+data1 <- data.frame(data1, dot.color = dot.color)
+dot.color <- rep(dot.color, length(levels(data1[, categ[i0]])))
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") dot.color ARGUMENT HAS LENGTH 1, MEANING THAT ALL THE DIFFERENT CLASSES OF ", categ[i0], "\n", paste(levels(factor(data1[, categ[i0]])), collapse = " "), "\nWILL HAVE THE SAME COLOR\n", paste(dot.color, collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}else{
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.color ARGUMENT MUST BE (1) LENGTH 1, OR (2) THE LENGTH OF data1 NROWS, OR (3) THE LENGTH OF THE CLASSES IN THE categ ", categ[i0], " COLUMN. HERE IT IS COLOR LENGTH ", length(dot.color), " VERSUS CATEG LENGTH ", length(data1[, categ[i0]]), " AND CATEG CLASS LENGTH ", length(unique(data1[, categ[i0]])), "\nPRESENCE OF NA COULD BE THE PROBLEM")
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+# end check the length of color
+dot.color <- as.character(dot.color)
+# dot.color is a character string representing the diff classes
+data1$dot.color <- factor(data1$dot.color, levels = unique(dot.color)) # ok because if dot.color is a character string, the order make class 1, class 2, etc. If dot.color is a column of data1, then levels will be created, without incidence, except if dot.categ specified (see below). unique() because no duplicates allowed
+# data1$dot.color is a factor with order of levels -> dot.color
+}
+# end optional legend of dot colors
+}else if(is.null(dot.color) & ! (is.null(dot.categ) & is.null(dot.categ.class.order) & is.null(dot.categ.legend.name))){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") dot.categ OR dot.categ.class.order OR dot.categ.legend.name ARGUMENT HAS BEEN SPECIFIED BUT dot.color ARGUMENT IS NULL (NO DOT PLOTTED)")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# dot.color either NULL (no dot plotted) or character string (potentially representing the diff classes of dot.categ)
+# data1$dot.color is either NA or a factor (with order of levels -> depending on dot.categ or categ[length(categ)], or other
+# end management of dot.color
+if(is.null(dot.color) & box.fill == FALSE & dot.alpha <= 0.025){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") THE FOLLOWING ARGUMENTS WERE SET AS:\ndot.color = NULL (NOT ALL DOTS BUT ONLY POTENTIAL OUTLIER DOTS DISPLAYED)\nbox.fill = FALSE (NO FILLING COLOR FOR BOTH BOXES AND POTENTIAL OUTLIER DOTS)\ndot.alpha = ", fun_round(dot.alpha, 4), "\n-> POTENTIAL OUTLIER DOTS MIGHT NOT BE VISIBLE BECAUSE ALMOST TRANSPARENT")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+if(is.null(dot.color) & box.fill == FALSE & dot.border.size == 0){
+tempo.cat <- paste0("ERROR IN ", function.name, ": THE FOLLOWING ARGUMENTS WERE SET AS:\ndot.color = NULL (NOT ALL DOTS BUT ONLY POTENTIAL OUTLIER DOTS DISPLAYED)\nbox.fill = FALSE (NO FILLING COLOR FOR BOTH BOXES AND POTENTIAL OUTLIER DOTS)\ndot.border.size = 0 (NO BORDER FOR POTENTIAL OUTLIER DOTS)\n-> THESE SETTINGS ARE NOT ALLOWED BECAUSE THE POTENTIAL OUTLIER DOTS WILL NOT BE VISIBLE")
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+if( ! is.null(dot.border.color)){
+tempo1 <- fun_check(data = dot.border.color, class = "vector", mode = "character", length = 1, fun.name = function.name, print = FALSE)
+tempo2 <- fun_check(data = dot.border.color, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name, print = FALSE)
+if(tempo1$problem == FALSE & tempo2$problem == TRUE & ! (all(dot.border.color %in% colors() | grepl(pattern = "^#", dot.border.color)))){ # check that all strings of low.color start by #
+tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.color ARGUMENT MUST BE (1) A HEXADECIMAL COLOR STRING STARTING BY #, OR (2) A COLOR NAME GIVEN BY colors(), OR (3) AN INTEGER VALUE\nHERE IT IS: ", paste(unique(dot.border.color), collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}else if(tempo1$problem == TRUE & tempo2$problem == FALSE){ # convert integers into colors
+dot.border.color <- fun_gg_palette(max(dot.border.color, na.rm = TRUE))[dot.border.color]
+}
+# end integer colors into gg_palette
+}
+if(y.log != "no"){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") y.log ARGUMENT SET TO ", y.log, ".\nVALUES FROM THE y ARGUMENT COLUMN OF THE data1 DATA FRAME MUST BE ALREADY ", toupper(y.log), " TRANSFORMED, AS THE y.log ARGUMENT JUST MODIFIES THE AXIS SCALE")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+if( ! is.null(y.lim)){
+if(any(y.lim <= 0)){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") y.lim ARGUMENT CAN SPAN ZERO OR NEGATIVE VALUES IF y.log ARGUMENT IS SET TO ", y.log, " BECAUSE THIS LATTER ARGUMENT DOES NOT TRANSFORM DATA, JUST MODIFIES THE AXIS SCALE")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}else if(any( ! is.finite(if(y.log == "log10"){10^y.lim}else{2^y.lim}))){
+tempo.cat <- paste0("ERROR IN ", function.name, ": y.lim ARGUMENT RETURNS INF WITH THE y.log ARGUMENT SET TO ", y.log, "\nAS SCALE COMPUTATION IS ", ifelse(y.log == "log10", 10, 2), "^y.lim:\n", paste(ifelse(y.log == "log10", 10, 2)^y.lim, collapse = " "), "\nARE YOU SURE THAT y.lim ARGUMENT HAS BEEN SPECIFIED WITH VALUES ALREADY IN LOG SCALE?\n", paste(y.lim, collapse = " "))
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+}
+}
+}
+# inactivated because y must already be log transformed data
+# if(y.log != "no" & y.include.zero == TRUE){
+# warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") y.log ARGUMENT SET TO ", y.log, " AND y.include.zero ARGUMENT SET TO TRUE -> y.include.zero ARGUMENT RESET TO FALSE BECAUSE NO 0 ALLOWED IN LOG SCALE")
+# warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+# }
+if(y.log != "no" & vertical == FALSE){
+vertical <- TRUE
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") BECAUSE OF A BUG IN ggplot2, CANNOT FLIP BOXS HORIZONTALLY WITH A Y.LOG SCALE -> vertical ARGUMENT RESET TO TRUE")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# end second round of checking and data preparation
+
+
+# package checking
+fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
+fun_pack(req.package = c("scales"), lib.path = lib.path)
+# end package checking
+
+
+
+# main code
+# na detection and removal (done now to be sure of the correct length of categ)
+column.check <- c(y, categ, "categ.color", if( ! is.null(dot.color)){"dot.color"}, dot.categ)
+if(any(is.na(data1[, column.check]))){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") NA DETECTED IN COLUMNS ", paste(column.check, collapse = " "), " OF data1 AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+for(i2 in 1:length(column.check)){
+if(any(is.na(data1[, column.check[i2]]))){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") COLUMN ", column.check[i2], " OF data1 CONTAINS NA")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+}
+removed.row.nb <- unlist(lapply(lapply(c(data1[column.check]), FUN = is.na), FUN = which))
+removed.rows <- data1[removed.row.nb, ]
+column.check <- column.check[ ! column.check == y] # remove y to keep quali columns
+if(length(removed.row.nb) != 0){
+for(i3 in 1:length(column.check)){
+if(any( ! unique(removed.rows[, column.check[i3]]) %in% unique(data1[, column.check[i3]]))){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") IN COLUMN ", column.check[i3], " OF data1, THE FOLLOWING CLASSES HAVE BEEN LOST DUE TO NA REMOVAL IN data1:\n", paste(unique(removed.rows[, column.check[i3]])[ ! unique(removed.rows[, column.check[i3]]) %in% unique(data1[, column.check[i3]])], collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+}
+data1 <- data1[-removed.row.nb, ]
+}
+for(i2 in 1:length(column.check)){
+if(any( ! levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]]))){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") IN COLUMN ", column.check[i2], " OF data1, THE FOLLOWING LEVELS ARE NOT REPRESENTED IN THE COLUMN:\n", paste(levels(data1[, column.check[i2]])[ ! levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])], collapse = " "))
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+if(column.check[i2] == "categ.color"){
+categ.color <- levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])] # remove the absent color in the character vector
+if(length(categ.color) == 1 & length(categ.class.order) > 1){ # to deal with single color
+categ.color <- rep(categ.color, length(categ.class.order))
+}
+data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = unique(categ.color))
+}else if(column.check[i2] == "dot.color"){
+dot.color <- levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])] # remove the absent color in the character vector
+if(length(dot.color) == 1 & length(dot.categ.class.order) > 1){ # to deal with single color
+dot.color <- rep(dot.color, length(dot.categ.class.order))
+}
+data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = unique(dot.color))
+}else{
+data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])])
+}
+}
+}
+}else{
+removed.row.nb <- NULL
+removed.rows <- NULL
+}
+# end na detection and removal (done now to be sure of the correct length of categ)
+
+
+# y coordinates recovery (create ini.box.coord, dot.coord and modify data1)
+if(length(categ) == 1){
+# width commputations
+box.width2 <- box.width
+box.space <- 0 # to inactivate the shrink that add space between grouped boxes, because no grouped boxes here
+# end width commputations
+# data1 check categ order for dots coordinates recovery
+data1 <- data.frame(data1, categ.check = data1[, categ[1]])
+data1$categ.check <- as.integer(data1$categ.check) # to check that data1[, categ[1]] and dot.coord$group are similar, during merging
+# end data1 check categ order for dots coordinates recovery
+# per box dots coordinates recovery
+tempo.gg.name <- "gg.indiv.plot."
+tempo.gg.count <- 0
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggplot())
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[1]), stroke = dot.border.size, size = dot.size, alpha = dot.alpha, shape = 21))
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = categ.legend.name, values = if(is.null(dot.color)){rep(NA, length(categ.color))}else{as.character(dot.color)})) # rep(NA, length(categ.color)) used because dot.color is NULL
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, fill = categ[1]), coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf})) # fill because this is what is used with geom_box # to easily have the equivalent of the grouped boxs
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = categ.legend.name, values = as.character(categ.color)))
+dot.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$data[[1]]
+ini.box.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$data[[2]]
+tempo.mean <- aggregate(x = dot.coord$y, by = list(dot.coord$group), FUN = mean, na.rm = TRUE)
+names(tempo.mean)[names(tempo.mean) == "x"] <- "MEAN"
+names(tempo.mean)[names(tempo.mean) == "Group.1"] <- "BOX"
+# if( ! is.null(dot.color)){
+if(is.null(dot.categ)){
+dot.coord <- data.frame(
+dot.coord[order(dot.coord$group, dot.coord$y), ],
+y.check = as.double(data1[order(data1$categ.check, data1[, y]), y]),
+categ.check = data1[order(data1$categ.check, data1[, y]), "categ.check"],
+dot.color = if(is.null(dot.color)){NA}else{data1[order(data1$categ.check, data1[, y]), "dot.color"]},
+tempo.categ1 = data1[order(data1$categ.check, data1[, y]), categ[1]]
+) # y.check to be sure that the order is the same between the y of data1 and the y of dot.coord
+names(dot.coord)[names(dot.coord) == "tempo.categ1"] <- categ[1]
+}else{
+dot.coord <- data.frame(
+dot.coord[order(dot.coord$group, dot.coord$y), ],
+y.check = as.double(data1[order(data1$categ.check, data1[, y]), y]),
+categ.check = data1[order(data1$categ.check, data1[, y]), "categ.check"],
+dot.color = if(is.null(dot.color)){NA}else{data1[order(data1$categ.check, data1[, y]), "dot.color"]},
+tempo.categ1 = data1[order(data1$categ.check, data1[, y]), categ[1]],
+tempo.categ3 = data1[order(data1$categ.check, data1[, y]), dot.categ]
+) # y.check to be sure that the order is the same between the y of data1 and the y of dot.coord
+names(dot.coord)[names(dot.coord) == "tempo.categ1"] <- categ[1]
+names(dot.coord)[names(dot.coord) == "tempo.categ3"] <- dot.categ
+}
+if( ! identical(dot.coord$y, dot.coord$y.check)){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": (dot.coord$y AND dot.coord$y.check) AS WELL AS (dot.coord$group AND dot.coord$categ.check) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}else{
+if( ! identical(tempo.mean[order(tempo.mean$BOX), ]$BOX, unique(dot.coord[order(dot.coord$group), ]$group))){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": (tempo.mean$BOX AND dot.coord$group) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}else{
+tempo.mean <- data.frame(tempo.mean[order(tempo.mean$BOX), ], unique(dot.coord[order(dot.coord$group), categ[1], drop = FALSE]))
+}
+}
+# }
+# end per box dots coordinates recovery
+}else if(length(categ) == 2){
+# width commputations
+box.width2 <- box.width / length(unique(data1[, categ[length(categ)]])) # real width of each box in x-axis unit, among the set of grouped box. Not relevant if no grouped boxs length(categ) == 1
+# end width commputations
+# data1 check categ order for dots coordinates recovery
+tempo.factor <- paste0(data1[order(data1[, categ[2]], data1[, categ[1]]), categ[2]], "_", data1[order(data1[, categ[2]], data1[, categ[1]]), categ[1]])
+data1 <- data.frame(data1[order(data1[, categ[2]], data1[, categ[1]]), ], categ.check = factor(tempo.factor, levels = unique(tempo.factor)))
+data1$categ.check <- as.integer(data1$categ.check)
+# end data1 check categ order for dots coordinates recovery
+# per box dots coordinates recovery
+tempo.gg.name <- "gg.indiv.plot."
+tempo.gg.count <- 0
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggplot())
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[2]), stroke = dot.border.size, size = dot.size, alpha = dot.alpha, shape = 21))
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = categ.legend.name, values = if(is.null(dot.color)){rep(NA, length(categ.color))}else{as.character(dot.color)})) # rep(NA, length(categ.color)) used because dot.color is NULL
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, fill = categ[2]), coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf})) # fill because this is what is used with geom_box # to easily have the equivalent of the grouped boxs
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = categ.legend.name, values = as.character(categ.color)))
+dot.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$data[[1]]
+ini.box.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$data[[2]]
+tempo.mean <- aggregate(x = dot.coord$y, by = list(dot.coord$group), FUN = mean, na.rm = TRUE)
+names(tempo.mean)[names(tempo.mean) == "x"] <- "MEAN"
+names(tempo.mean)[names(tempo.mean) == "Group.1"] <- "BOX"
+# if( ! is.null(dot.color)){
+if(is.null(dot.categ)){
+dot.coord <- data.frame(
+dot.coord[order(dot.coord$group, dot.coord$y), ],
+y.check = as.double(data1[order(data1$categ.check, data1[, y]), y]),
+categ.check = data1[order(data1$categ.check, data1[, y]), "categ.check"],
+dot.color = if(is.null(dot.color)){NA}else{data1[order(data1$categ.check, data1[, y]), "dot.color"]},
+tempo.categ1 = data1[order(data1$categ.check, data1[, y]), categ[1]],
+tempo.categ2 = data1[order(data1$categ.check, data1[, y]), categ[2]]
+) # y.check to be sure that the order is the same between the y of data1 and the y of dot.coord
+names(dot.coord)[names(dot.coord) == "tempo.categ1"] <- categ[1]
+names(dot.coord)[names(dot.coord) == "tempo.categ2"] <- categ[2]
+}else{
+dot.coord <- data.frame(
+dot.coord[order(dot.coord$group, dot.coord$y), ],
+y.check = as.double(data1[order(data1$categ.check, data1[, y]), y]),
+categ.check = data1[order(data1$categ.check, data1[, y]), "categ.check"],
+dot.color = if(is.null(dot.color)){NA}else{data1[order(data1$categ.check, data1[, y]), "dot.color"]},
+tempo.categ1 = data1[order(data1$categ.check, data1[, y]), categ[1]],
+tempo.categ2 = data1[order(data1$categ.check, data1[, y]), categ[2]],
+tempo.categ3 = data1[order(data1$categ.check, data1[, y]), dot.categ]
+) # y.check to be sure that the order is the same between the y of data1 and the y of dot.coord
+names(dot.coord)[names(dot.coord) == "tempo.categ1"] <- categ[1]
+names(dot.coord)[names(dot.coord) == "tempo.categ2"] <- categ[2]
+names(dot.coord)[names(dot.coord) == "tempo.categ3"] <- dot.categ
+}
+if( ! (identical(dot.coord$y, dot.coord$y.check) & identical(dot.coord$group, dot.coord$categ.check))){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": (dot.coord$y AND dot.coord$y.check) AS WELL AS (dot.coord$group AND dot.coord$categ.check) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}else{
+if( ! identical(tempo.mean[order(tempo.mean$BOX), ]$BOX, unique(dot.coord[order(dot.coord$group), ]$group))){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": (tempo.mean$BOX AND dot.coord$group) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}else{
+tempo.mean <- data.frame(tempo.mean[order(tempo.mean$BOX), ], unique(dot.coord[order(dot.coord$group), c(categ[1], categ[2])]))
+}
+}
+# }
+}else{
+tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": CODE INCONSISTENCY 2\n\n============\n\n")
+stop(tempo.cat)
+}
+# at that stage, categ color and dot color are correctly attributed in data1, box.coord and dot.coord
+# end y dot coordinates recovery (create ini.box.coord, dot.coord and modify data1)
+
+
+
+
+
+
+
+
+
+
+
+
+
+# stat output (will also serve for boxplot and mean display)
+ini.box.coord <- ini.box.coord[order(ini.box.coord$group), ]
+stat <- data.frame(MIN = ini.box.coord$ymin, QUART1 = ini.box.coord$lower, MEDIAN = ini.box.coord$middle, QUART3 = ini.box.coord$upper, MAX = ini.box.coord$ymax, NOTCHUPPER = ini.box.coord$notchupper, NOTCHLOWER = ini.box.coord$notchlower, OUTLIERS = ini.box.coord["outliers"], COLOR = ini.box.coord$fill, stringsAsFactors = TRUE) # ini.box.coord["outliers"] written like this because it is a list. X coordinates not put now because several features to set
+names(stat)[names(stat) == "outliers"] <- "OUTLIERS"
+tempo.mean <- tempo.mean[order(tempo.mean$BOX), ]
+if( ! identical(ini.box.coord$group, tempo.mean$BOX)){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": (ini.box.coord$group AND tempo.mean$BOX) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}else{
+stat <- data.frame(stat[c("MIN", "QUART1", "MEDIAN")], MEAN = tempo.mean$MEAN, stat[c("QUART3", "MAX", "NOTCHUPPER", "NOTCHLOWER", "OUTLIERS")], tempo.mean[colnames(tempo.mean) != "MEAN"], stat["COLOR"], stringsAsFactors = TRUE) # ini.box.coord["outliers"] written like this because it is a list
+}
+# end stat output (will also serve for boxplot and mean display)
+
+
+
+
+
+
+
+
+# ylim range
+if(is.null(y.lim)){
+if(any(data1[, y] %in% c(Inf, -Inf))){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") THE data1 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE y COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+y.lim <- range(data1[, y], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+}
+if(suppressWarnings(all(y.lim %in% c(Inf, -Inf)))){
+tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, " COMPUTED y.lim CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY\n\n================\n\n")
+stop(tempo.cat)
+}
+y.lim.order <- order(y.lim) # to deal with inverse axis
+y.lim <- sort(y.lim)
+y.lim[1] <- y.lim[1] - abs(y.lim[2] - y.lim[1]) * ifelse(diff(y.lim.order) > 0, y.bottom.extra.margin, y.top.extra.margin) # diff(y.lim.order) > 0 medians not inversed axis
+y.lim[2] <- y.lim[2] + abs(y.lim[2] - y.lim[1]) * ifelse(diff(y.lim.order) > 0, y.top.extra.margin, y.bottom.extra.margin) # diff(y.lim.order) > 0 medians not inversed axis
+if(y.include.zero == TRUE){ # no need to check y.log != "no" because done before
+y.lim <- range(c(y.lim, 0), na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+}
+y.lim <- y.lim[y.lim.order]
+if(any(is.na(y.lim))){
+tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": CODE INCONSISTENCY 4\n\n============\n\n")
+stop(tempo.cat)
+}
+# end ylim range
+
+
+
+
+
+
+# drawing
+# constant part
+tempo.gg.name <- "gg.indiv.plot."
+tempo.gg.count <- 0
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggplot())
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::xlab(if(is.null(x.lab)){categ[1]}else{x.lab}))
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ylab(if(is.null(y.lab)){y}else{y.lab}))
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(title))
+# text angle management
+tempo.just <- fun_gg_just(angle = text.angle, axis = ifelse(vertical == TRUE, "x", "y"))
+# end text angle management
+add.check <- TRUE
+if( ! is.null(add)){ # if add is NULL, then = 0
+if(grepl(pattern = "ggplot2::theme", add) == TRUE){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") \"ggplot2::theme\" STRING DETECTED IN THE add ARGUMENT -> INTERNAL GGPLOT2 THEME FUNCTIONS theme() AND theme_classic() HAVE BEEN INACTIVATED, TO BE USED BY THE USER")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+add.check <- FALSE
+}
+}
+if(add.check == TRUE & classic == TRUE){
+# BEWARE: not possible to add theme()several times. NO message but the last one overwrites the others
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme_classic(base_size = text.size))
+if(grid == TRUE){
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
+text = ggplot2::element_text(size = text.size),
+plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
+line = ggplot2::element_line(size = 0.5),
+axis.line.y.left = ggplot2::element_line(colour = "black"), # draw lines for the y axis
+axis.line.x.bottom = ggplot2::element_line(colour = "black"), # draw lines for the x axis
+panel.grid.major.x = if(vertical == TRUE){NULL}else{ggplot2::element_line(colour = "grey75")},
+panel.grid.major.y = if(vertical == TRUE){ggplot2::element_line(colour = "grey75")}else{NULL},
+axis.text.x = if(vertical == TRUE){ggplot2::element_text(angle = tempo.just$angle, hjust = tempo.just$hjust, vjust = tempo.just$vjust)}else{NULL},
+axis.text.y = if(vertical == TRUE){NULL}else{ggplot2::element_text(angle = tempo.just$angle, hjust = tempo.just$hjust, vjust = tempo.just$vjust)}
+))
+}else{
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
+text = ggplot2::element_text(size = text.size),
+plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
+line = ggplot2::element_line(size = 0.5),
+axis.line.y.left = ggplot2::element_line(colour = "black"),
+axis.line.x.bottom = ggplot2::element_line(colour = "black"),
+axis.text.x = if(vertical == TRUE){ggplot2::element_text(angle = tempo.just$angle, hjust = tempo.just$hjust, vjust = tempo.just$vjust)}else{NULL},
+axis.text.y = if(vertical == TRUE){NULL}else{ggplot2::element_text(angle = tempo.just$angle, hjust = tempo.just$hjust, vjust = tempo.just$vjust)}
+))
+}
+}else if(add.check == TRUE & classic == FALSE){
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
+text = ggplot2::element_text(size = text.size),
+plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
+line = ggplot2::element_line(size = 0.5),
+panel.background = ggplot2::element_rect(fill = "grey95"),
+axis.line.y.left = ggplot2::element_line(colour = "black"),
+axis.line.x.bottom = ggplot2::element_line(colour = "black"),
+panel.grid.major.x = ggplot2::element_line(colour = "grey75"),
+panel.grid.major.y = ggplot2::element_line(colour = "grey75"),
+panel.grid.minor.x = ggplot2::element_blank(),
+panel.grid.minor.y = ggplot2::element_blank(),
+strip.background = ggplot2::element_rect(fill = "white", colour = "black"),
+axis.text.x = if(vertical == TRUE){ggplot2::element_text(angle = tempo.just$angle, hjust = tempo.just$hjust, vjust = tempo.just$vjust)}else{NULL},
+axis.text.y = if(vertical == TRUE){NULL}else{ggplot2::element_text(angle = tempo.just$angle, hjust = tempo.just$hjust, vjust = tempo.just$vjust)}
+))
+}
+# Contrary to fun_gg_bar(), cannot plot the boxplot right now, because I need the dots plotted first
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, group = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), color = NA, width = box.width, fill = NA)) # this is to set the graph (i.e., a blanck boxplot to be able to use x coordinates to plot dots before boxes)
+# end constant part
+
+
+
+
+# x coordinates management (for random plotting and for stat display)
+# boxs
+tempo.graph.info <- ggplot2::ggplot_build(eval(parse(text = paste0(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), ' + ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, fill = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), width = box.width, notch = box.notch, coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf}) + ggplot2::scale_discrete_manual(aesthetics = "fill", name = categ.legend.name, values = as.character(categ.color))')))) # will be recovered later again, when ylim will be considered
+tempo.yx.ratio <- (tempo.graph.info$layout$panel_params[[1]]$y.range[2] - tempo.graph.info$layout$panel_params[[1]]$y.range[1]) / (tempo.graph.info$layout$panel_params[[1]]$x.range[2] - tempo.graph.info$layout$panel_params[[1]]$x.range[1])
+box.coord <- tempo.graph.info$data[[2]] # to have the summary statistics of the plot. Contrary to ini.box.plot, now integrates ylim Here because can be required for stat.disp when just box are plotted
+box.coord <- box.coord[order(box.coord$group), ]
+if(stat.disp.mean == TRUE){ # for mean display
+if( ! identical(tempo.mean$BOX, box.coord$group)){
+tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": tempo.mean$BOX AND box.coord$group DO NOT HAVE THE SAME VALUE ORDER\n\n============\n\n")
+stop(tempo.cat)
+}else{
+box.coord <- data.frame(box.coord, tempo.mean)
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") MEAN VALUES INSTEAD OF MEDIAN VALUES DISPLAYED")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+
+}
+}
+# width commputations
+width.ini <- c(box.coord$xmax - box.coord$xmin)[1] # all the box widths are equal here. Only the first one taken
+width.correct <- width.ini * box.space / 2
+if( ! identical(box.coord$group, stat$BOX)){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": (box.coord$group AND stat$BOX) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}else{
+stat <- data.frame(
+stat,
+X = box.coord$x,
+X_BOX_INF = box.coord$xmin + width.correct,
+X_BOX_SUP = box.coord$xmax - width.correct,
+X_NOTCH_INF = box.coord$x - (box.coord$x - (box.coord$xmin + width.correct)) / 2,
+X_NOTCH_SUP = box.coord$x + (box.coord$x - (box.coord$xmin + width.correct)) / 2,
+X_WHISK_INF = box.coord$x - (box.coord$x - (box.coord$xmin + width.correct)) * box.whisker.width,
+X_WHISK_SUP = box.coord$x + (box.coord$x - (box.coord$xmin + width.correct)) * box.whisker.width,
+tempo.mean[colnames(tempo.mean) != "MEAN"],
+stringsAsFactors = TRUE
+)
+stat$COLOR <- factor(stat$COLOR, levels = unique(categ.color))
+if( ! all(stat$NOTCHUPPER < stat$QUART3 & stat$NOTCHLOWER > stat$QUART1) & box.notch == TRUE){
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") SOME NOTCHES ARE BEYOND BOX HINGES. TRY ARGUMENT box.notch = FALSE")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+}
+dot.jitter <- c((box.coord$xmax - width.correct) - (box.coord$xmin + width.correct))[1] * dot.jitter # real dot.jitter. (box.coord$xmin + width.correct) - (box.coord$xmax - width.correct))[1] is the width of the box. Is equivalent to (box.coord$x - (box.coord$xmin + width.correct))[1] * 2
+# end width commputations
+# end boxs
+if( ! is.null(dot.color)){
+# random dots
+if(dot.tidy == FALSE){
+dot.coord.rd1 <- merge(dot.coord, box.coord[c("fill", "group", "x")], by = intersect("group", "group"), sort = FALSE) # rd for random. Send the coord of the boxs into the coord data.frame of the dots (in the column x.y). BEWARE: by = intersect("group", "group") because group is enough as only one value of x per group number in box.coord. Thus, no need to consider fill
+if(nrow(dot.coord.rd1) != nrow(dot.coord)){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": THE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.rd1 DATA FRAME. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}
+set.seed(1)
+sampled.dot.jitter <- if(nrow(dot.coord.rd1) == 1){runif(n = nrow(dot.coord.rd1), min = - dot.jitter / 2, max = dot.jitter / 2)}else{sample(x = runif(n = nrow(dot.coord.rd1), min = - dot.jitter / 2, max = dot.jitter / 2), size = nrow(dot.coord.rd1), replace = FALSE)}
+dot.coord.rd2 <- data.frame(dot.coord.rd1, dot.x = dot.coord.rd1$x.y + sampled.dot.jitter) # set the dot.jitter thanks to runif and dot.jitter range. Then, send the coord of the boxs into the coord data.frame of the dots (in the column x.y)
+set.seed(NULL)
+if(length(categ) == 1){
+tempo.data1 <- unique(data.frame(data1[categ[1]], group = as.integer(factor(as.numeric(data1[, categ[1]]))))) # categ[2] first if categ[2] is used to make the categories in ggplot and categ[1] is used to make the x-axis
+names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
+verif <- paste0(categ[1], ".check")
+}else if(length(categ) == 2){
+tempo.data1 <- unique(data.frame(data1[c(categ[1], categ[2])], group = as.integer(factor(paste0(as.numeric(data1[, categ[2]]), ".", as.numeric(data1[, categ[1]])))))) # categ[2] first if categ[2] is used to make the categories in ggplot and categ[1] is used to make the x-axis
+names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
+names(tempo.data1)[names(tempo.data1) == categ[2]] <- paste0(categ[2], ".check")
+verif <- c(paste0(categ[1], ".check"), paste0(categ[2], ".check"))
+}else{
+tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": CODE INCONSISTENCY 6\n\n============\n\n")
+stop(tempo.cat)
+}
+dot.coord.rd3 <- merge(dot.coord.rd2, tempo.data1, by = "group", sort = FALSE) # send the factors of data1 into coord
+if(nrow(dot.coord.rd3) != nrow(dot.coord) | ( ! fun_comp_2d(dot.coord.rd3[categ], dot.coord.rd3[verif])$identical.content)){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": THE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.rd3 DATA FRAME. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}
+# end random dots
+}
+# tidy dots
+# coordinates are recover during plotting (see dot.coord.tidy1 below)
+# end tidy dots
+}
+# end x coordinates management (for random plotting and for stat display)
+
+
+
+
+
+# boxplot display before dot display if box.fill = TRUE
+coord.names <- NULL
+# creation of the data frame for (main box + legend) and data frame for means
+if(box.notch == FALSE){
+for(i2 in 1:length(categ)){
+if(i2 == 1){
+tempo.polygon <- data.frame(GROUPX = c(t(stat[, c(categ[i2], categ[i2], categ[i2], categ[i2], categ[i2])])), stringsAsFactors = TRUE)
+}else{
+tempo.polygon <- cbind(tempo.polygon, c(t(stat[, c(categ[i2], categ[i2], categ[i2], categ[i2], categ[i2])])), stringsAsFactors = TRUE)
+}
+}
+names(tempo.polygon) <- categ
+tempo.polygon <- data.frame(X = c(t(stat[, c("X_BOX_INF", "X_BOX_SUP", "X_BOX_SUP", "X_BOX_INF", "X_BOX_INF")])), Y = c(t(stat[, c("QUART1", "QUART1", "QUART3", "QUART3", "QUART1")])), COLOR = c(t(stat[, c("COLOR", "COLOR", "COLOR", "COLOR", "COLOR")])), BOX = as.character(c(t(stat[, c("BOX", "BOX", "BOX", "BOX", "BOX")]))), tempo.polygon, stringsAsFactors = TRUE)
+}else{
+for(i2 in 1:length(categ)){
+if(i2 == 1){
+tempo.polygon <- data.frame(GROUPX = c(t(stat[, c(categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2])])), stringsAsFactors = TRUE)
+}else{
+tempo.polygon <- cbind(tempo.polygon, c(t(stat[, c(categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2], categ[i2])])), stringsAsFactors = TRUE)
+}
+}
+names(tempo.polygon) <- categ
+tempo.polygon <- data.frame(X = c(t(stat[, c("X_BOX_INF", "X_BOX_SUP", "X_BOX_SUP", "X_NOTCH_SUP", "X_BOX_SUP", "X_BOX_SUP", "X_BOX_INF", "X_BOX_INF", "X_NOTCH_INF", "X_BOX_INF", "X_BOX_INF")])), Y = c(t(stat[, c("QUART1", "QUART1", "NOTCHLOWER", "MEDIAN", "NOTCHUPPER", "QUART3", "QUART3", "NOTCHUPPER", "MEDIAN", "NOTCHLOWER", "QUART1")])), COLOR = c(t(stat[, c("COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR")])), BOX = as.character(c(t(stat[, c("BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX")]))), tempo.polygon, stringsAsFactors = TRUE)
+}
+tempo.polygon$COLOR <- factor(tempo.polygon$COLOR, levels = unique(categ.color))
+if( ! is.null(categ.class.order)){
+for(i2 in 1:length(categ)){
+tempo.polygon[, categ[i2]] <- factor(tempo.polygon[, categ[i2]], levels = categ.class.order[[i2]])
+}
+}
+tempo.diamon.mean <- data.frame(X = c(t(stat[, c("X", "X_NOTCH_INF", "X", "X_NOTCH_SUP", "X")])), Y = c(t(cbind(stat["MEAN"] - (stat[, "X"] - stat[, "X_NOTCH_INF"]) * tempo.yx.ratio, stat["MEAN"], stat["MEAN"] + (stat[, "X"] - stat[, "X_NOTCH_INF"]) * tempo.yx.ratio, stat["MEAN"], stat["MEAN"] - (stat[, "X"] - stat[, "X_NOTCH_INF"]) * tempo.yx.ratio))), COLOR = c(t(stat[, c("COLOR", "COLOR", "COLOR", "COLOR", "COLOR")])), GROUP = c(t(stat[, c("BOX", "BOX", "BOX", "BOX", "BOX")])), stringsAsFactors = TRUE)
+tempo.diamon.mean$COLOR <- factor(tempo.diamon.mean$COLOR, levels = unique(categ.color))
+# end creation of the data frame for (main box + legend) and data frame for means
+if(box.fill == TRUE){
+# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[length(categ)], fill = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), width = box.width, size = box.line.size, notch = box.notch, coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf}, alpha = box.alpha, outlier.shape = if( ! is.null(dot.color)){NA}else{21}, outlier.color = if( ! is.null(dot.color)){NA}else{dot.border.color}, outlier.fill = if( ! is.null(dot.color)){NA}else{NULL}, outlier.size = if( ! is.null(dot.color)){NA}else{dot.size}, outlier.stroke = if( ! is.null(dot.color)){NA}else{dot.border.size}, outlier.alpha = if( ! is.null(dot.color)){NA}else{dot.alpha})) # the color, size, etc. of the outliers are dealt here. outlier.color = NA to do not plot outliers when dots are already plotted. Finally, boxplot redrawn (see below)
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_polygon(
+data = tempo.polygon,
+mapping = ggplot2::aes_string(x = "X", y = "Y", group = "BOX", fill = categ[length(categ)], color = categ[length(categ)]),
+size = box.line.size,
+alpha = box.alpha
+))
+coord.names <- c(coord.names, "main.box")
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = QUART3, yend = MAX, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha)) #
+coord.names <- c(coord.names, "sup.whisker")
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = QUART1, yend = MIN, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha)) #
+coord.names <- c(coord.names, "inf.whisker")
+if(box.whisker.width > 0){
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = MAX, yend = MAX, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha, lineend = "round")) #
+coord.names <- c(coord.names, "sup.whisker.edge")
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = MIN, yend = MIN, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha, lineend = "round")) #
+coord.names <- c(coord.names, "inf.whisker.edge")
+}
+if(box.mean == TRUE){
+# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = stat, mapping = ggplot2::aes_string(x = "X", y = "MEAN", group = categ[length(categ)]), shape = 23, stroke = box.line.size * 2, fill = stat$COLOR, size = box.mean.size, color = "black", alpha = box.alpha)) # group used in aesthetic to do not have it in the legend
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_polygon(
+data = tempo.diamon.mean,
+mapping = ggplot2::aes(x = X, y = Y, group = GROUP),
+fill = tempo.diamon.mean[, "COLOR"],
+color = hsv(0, 0, 0, alpha = box.alpha), # outline of the polygon in black but with alpha
+size = box.line.size * 2,
+alpha = box.alpha
+))
+coord.names <- c(coord.names, "mean")
+}
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = if(box.notch == FALSE){X_BOX_INF}else{X_NOTCH_INF}, xend = if(box.notch == FALSE){X_BOX_SUP}else{X_NOTCH_SUP}, y = MEDIAN, yend = MEDIAN, group = categ[length(categ)]), color = "black", size = box.line.size * 2, alpha = box.alpha)) #
+coord.names <- c(coord.names, "median")
+}
+# end boxplot display before dot display if box.fill = TRUE
+
+
+
+
+
+
+# dot display
+if( ! is.null(dot.color)){
+if(dot.tidy == FALSE){
+if(is.null(dot.categ)){
+if(dot.border.size == 0){
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
+data = dot.coord.rd3,
+mapping = ggplot2::aes_string(x = "dot.x", y = "y", group = categ[length(categ)]),
+size = dot.size,
+shape = 19,
+color = dot.coord.rd3$dot.color,
+alpha = dot.alpha
+)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
+}else{
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
+data = dot.coord.rd3,
+mapping = ggplot2::aes_string(x = "dot.x", y = "y", group = categ[length(categ)]),
+shape = 21,
+stroke = dot.border.size,
+color = if(is.null(dot.border.color)){dot.coord.rd3$dot.color}else{rep(dot.border.color, nrow(dot.coord.rd3))},
+size = dot.size,
+fill = dot.coord.rd3$dot.color,
+alpha = dot.alpha
+)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
+}
+}else{
+if(dot.border.size == 0){
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
+data = dot.coord.rd3,
+mapping = ggplot2::aes_string(x = "dot.x", y = "y", alpha = dot.categ),
+size = dot.size,
+shape = 19,
+color = dot.coord.rd3$dot.color
+)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
+}else{
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
+data = dot.coord.rd3,
+mapping = ggplot2::aes_string(x = "dot.x", y = "y", alpha = dot.categ),
+size = dot.size,
+shape = 21,
+stroke = dot.border.size,
+color = if(is.null(dot.border.color)){dot.coord.rd3$dot.color}else{rep(dot.border.color, nrow(dot.coord.rd3))},
+fill = dot.coord.rd3$dot.color
+)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
+}
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "alpha", name = dot.categ.legend.name, values = rep(dot.alpha, length(dot.color)), guide = ggplot2::guide_legend(override.aes = list(fill = dot.color, color = if(is.null(dot.border.color)){dot.color}else{dot.border.color}, stroke = dot.border.size)))) # values are the values of color (which is the border color in geom_box. BEWARE: values = categ.color takes the numbers to make the colors if categ.color is a factor
+}
+}else if(dot.tidy == TRUE){
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_dotplot(
+data = dot.coord,
+mapping = ggplot2::aes_string(x = categ[1], y = "y", linetype = categ[length(categ)]),
+position = ggplot2::position_dodge(width = box.width),
+binaxis = "y",
+stackdir = "center",
+alpha = dot.alpha,
+fill = dot.coord[rev(order(dot.coord[, categ[1]], decreasing = TRUE)), "dot.color"],
+stroke = dot.border.size,
+color = if(is.null(dot.border.color)){dot.coord[rev(order(dot.coord[, categ[1]], decreasing = TRUE)), "dot.color"]}else{rep(dot.border.color, nrow(dot.coord))},
+# show.legend = FALSE,
+binwidth = (y.lim[2] - y.lim[1]) / dot.tidy.bin.nb
+)) # very weird behavior of geom_dotplot, (1) because with aes group = (to avoid legend), the dot plotting is not good in term of coordinates, and (2) because data1 seems reorderer according to x = categ[1] before plotting. Thus, I have to use fill = dot.coord[rev(order(dot.coord[, categ[1]], decreasing = TRUE)), "dot.color"] to have the good corresponding colors # show.legend option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
+if( ! is.null(dot.categ)){
+# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "linetype", name = dot.categ.legend.name, values = rep(1, length(categ.color)))) # values = rep("black", length(categ.color)) are the values of color (which is the border color of dots), and this modify the border color on the plot. BEWARE: values = categ.color takes the numbers to make the colors if categ.color is a factor
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "linetype", name = dot.categ.legend.name, values = rep(dot.border.size, length(dot.color)), guide = ggplot2::guide_legend(override.aes = list(fill = dot.color, color = if(is.null(dot.border.color)){dot.color}else{dot.border.color}, stroke = dot.border.size)))) # values are the values of color (which is the border color in geom_box. BEWARE: values = categ.color takes the numbers to make the colors if categ.color is a factor
+}else{
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "linetype", name = dot.categ.legend.name, values = rep(dot.border.size, length(dot.color)), guide = ggplot2::guide_legend(label = FALSE, override.aes = list(name = NA, fill = rep(NA, length(dot.color)), color = if(is.null(dot.border.color)){rep(NA, length(dot.color))}else{dot.border.color}, stroke = NA)))) # values are the values of color (which is the border color in geom_box. BEWARE: values = categ.color takes the numbers to make the colors if categ.color is a factor
+}
+# coordinates of tidy dots
+tempo.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$data # to have the tidy dot coordinates
+if(length(which(sapply(tempo.coord, FUN = nrow) == nrow(data1))) > 1){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": MORE THAN 2 COMPARTMENT WITH NROW EQUAL TO nrow(data1) IN THE tempo.coord LIST (FOR TIDY DOT COORDINATES). CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}else{
+dot.coord.tidy1 <- tempo.coord[[which(sapply(tempo.coord, FUN = nrow) == nrow(data1))]]
+}
+tempo.box.coord <- merge(box.coord, unique(dot.coord[, c("group", categ)]), by = intersect("group", "group"), sort = FALSE) # add the categ in box.coord. BEWARE: by = intersect("group", "group") because group is enough as only one value of x per group number in box.coord. Thus, no need to consider fill
+if(nrow(tempo.box.coord) != nrow(box.coord)){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": THE merge() FUNCTION DID NOT RETURN A CORRECT tempo.box.coord DATA FRAME. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}
+dot.coord.tidy2 <- merge(dot.coord.tidy1, tempo.box.coord[c("fill", "group", "x", categ)], by = intersect("group", "group"), sort = FALSE) # send the coord of the boxs into the coord data.frame of the dots (in the column x.y). BEWARE: by = intersect("group", "group") because group is enough as only one value of x per group number in box.coord. Thus, no need to consider fill
+if(nrow(dot.coord.tidy2) != nrow(dot.coord)){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": THE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.tidy2 DATA FRAME. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}
+if(length(categ) == 1){
+tempo.data1 <- unique(data.frame(data1[categ[1]], group = as.integer(factor(as.numeric(data1[, categ[1]]))))) # categ[2] first if categ[2] is used to make the categories in ggplot and categ[1] is used to make the x-axis
+names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
+verif <- paste0(categ[1], ".check")
+}else if(length(categ) == 2){
+tempo.data1 <- unique(data.frame(data1[c(categ[1], categ[2])], group = as.integer(factor(paste0(as.numeric(data1[, categ[2]]), ".", as.numeric(data1[, categ[1]])))))) # categ[2] first if categ[2] is used to make the categories in ggplot and categ[1] is used to make the x-axis
+names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
+names(tempo.data1)[names(tempo.data1) == categ[2]] <- paste0(categ[2], ".check")
+verif <- c(paste0(categ[1], ".check"), paste0(categ[2], ".check"))
+}else{
+tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": CODE INCONSISTENCY 7\n\n============\n\n")
+stop(tempo.cat)
+}
+dot.coord.tidy3 <- merge(dot.coord.tidy2, tempo.data1, by = "group", sort = FALSE) # send the factors of data1 into coord
+if(nrow(dot.coord.tidy3) != nrow(dot.coord) | ( ! fun_comp_2d(dot.coord.tidy3[categ], dot.coord.tidy3[verif])$identical.content)){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": THE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.tidy3 DATA FRAME. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}
+# end coordinates of tidy dots
+}
+coord.names <- c(coord.names, "dots")
+}
+# end dot display
+
+
+
+# boxplot display (if box.fill = FALSE, otherwise, already plotted above)
+if(box.fill == TRUE){
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = categ.legend.name, values = as.character(categ.color))) #, guide = ggplot2::guide_legend(override.aes = list(fill = levels(tempo.polygon$COLOR), color = "black")))) # values are the values of color (which is the border color in geom_box. BEWARE: values = categ.color takes the numbers to make the colors if categ.color is a factor
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = categ.legend.name, values = rep(hsv(0, 0, 0, alpha = box.alpha), length(categ.color)))) # , guide = ggplot2::guide_legend(override.aes = list(color = "black")))) # values are the values of color (which is the border color in geom_box. BEWARE: values = categ.color takes the numbers to make the colors if categ.color is a factor # outline of the polygon in black but with alpha
+}else{
+# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[length(categ)], fill = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), width = box.width, size = box.line.size, notch = box.notch, alpha = box.alpha, coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf}, outlier.shape = if( ! is.null(dot.color)){NA}else{21}, outlier.color = if( ! is.null(dot.color)){NA}else{if(dot.border.size == 0){NA}else{dot.border.color}}, outlier.fill = if( ! is.null(dot.color)){NA}else{NULL}, outlier.size = if( ! is.null(dot.color)){NA}else{dot.size}, outlier.stroke = if( ! is.null(dot.color)){NA}else{dot.border.size}, outlier.alpha = if( ! is.null(dot.color)){NA}else{dot.alpha})) # the color, size, etc. of the outliers are dealt here. outlier.color = NA to do not plot outliers when dots are already plotted
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_path(
+data = tempo.polygon,
+mapping = ggplot2::aes_string(x = "X", y = "Y", group = "BOX", color = categ[length(categ)]),
+size = box.line.size,
+alpha = box.alpha,
+lineend = "round",
+linejoin = "round"
+))
+coord.names <- c(coord.names, "main.box")
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = if(box.notch == FALSE){X_BOX_INF}else{X_NOTCH_INF}, xend = if(box.notch == FALSE){X_BOX_SUP}else{X_NOTCH_SUP}, y = MEDIAN, yend = MEDIAN, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size * 2, alpha = box.alpha)) #
+coord.names <- c(coord.names, "median")
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = QUART3, yend = MAX, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha)) #
+coord.names <- c(coord.names, "sup.whisker")
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = QUART1, yend = MIN, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha)) #
+coord.names <- c(coord.names, "inf.whisker")
+if(box.whisker.width > 0){
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = MAX, yend = MAX, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha, lineend = "round")) #
+coord.names <- c(coord.names, "sup.whisker.edge")
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = MIN, yend = MIN, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha, lineend = "round")) #
+coord.names <- c(coord.names, "inf.whisker.edge")
+}
+if(box.mean == TRUE){
+# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = stat, mapping = ggplot2::aes_string(x = "X", y = "MEAN", group = categ[length(categ)]), shape = 23, stroke = box.line.size * 2, color = stat$COLOR, size = box.mean.size, fill = NA, alpha = box.alpha)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_path(
+data = tempo.diamon.mean,
+mapping = ggplot2::aes(x = X, y = Y, group = GROUP),
+color = tempo.diamon.mean[, "COLOR"],
+size = box.line.size * 2,
+alpha = box.alpha,
+lineend = "round",
+linejoin = "round"
+))
+coord.names <- c(coord.names, "mean")
+}
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = categ.legend.name, values = rep(NA, length(categ.color)))) #, guide = ggplot2::guide_legend(override.aes = list(color = categ.color)))) # values are the values of color (which is the border color in geom_box. BEWARE: values = categ.color takes the numbers to make the colors if categ.color is a factor
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = categ.legend.name, values = as.character(categ.color))) # , guide = ggplot2::guide_legend(override.aes = list(color = as.character(categ.color))))) # values are the values of color (which is the border color in geom_box. BEWARE: values = categ.color takes the numbers to make the colors if categ.color is a factor
+
+}
+# end boxplot display (if box.fill = FALSE, otherwise, already plotted above)
+
+
+
+
+# stat display
+# layer after dots but ok, behind dots on the plot
+if( ! is.null(stat.disp)){
+if(stat.disp == "top"){
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "text", x = stat$X, y = y.lim[2], label = if(stat.disp.mean == FALSE){fun_round(stat$MEDIAN, 2)}else{fun_round(stat$MEAN, 2)}, size = stat.size, color = "black", hjust = ifelse(vertical == TRUE, 0.5, 1.1), vjust = ifelse(vertical == TRUE, 1.1, 0.5))) # beware: no need of order() for labels because box.coord$x set the order. For justification, see https://stackoverflow.com/questions/7263849/what-do-hjust-and-vjust-do-when-making-a-plot-using-ggplot
+}else if(stat.disp == "above"){
+# stat coordinates
+if( ! is.null(dot.color)){ # for text just above max dot
+if(dot.tidy == FALSE){
+tempo.stat.ini <- dot.coord.rd3
+}else if(dot.tidy == TRUE){
+tempo.stat.ini <- dot.coord.tidy3
+}
+stat.coord1 <- aggregate(x = tempo.stat.ini["y"], by = {x.env <- if(length(categ) == 1){list(tempo.stat.ini$group, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]])}else if(length(categ) == 2){list(tempo.stat.ini$group, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]], tempo.stat.ini[, categ[2]])} ; names(x.env) <- if(length(categ) == 1){c("group", "x.y", categ[1])}else if(length(categ) == 2){c("group", "x.y", categ[1], categ[2])} ; x.env}, FUN = min, na.rm = TRUE)
+names(stat.coord1)[names(stat.coord1) == "y"] <- "dot.min"
+stat.coord2 <- aggregate(x = tempo.stat.ini["y"], by = {x.env <- if(length(categ) == 1){list(tempo.stat.ini$group, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]])}else if(length(categ) == 2){list(tempo.stat.ini$group, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]], tempo.stat.ini[, categ[2]])} ; names(x.env) <- if(length(categ) == 1){c("group", "x.y", categ[1])}else if(length(categ) == 2){c("group", "x.y", categ[1], categ[2])} ; x.env}, FUN = max, na.rm = TRUE)
+names(stat.coord2) <- paste0(names(stat.coord2), "_from.dot.max")
+names(stat.coord2)[names(stat.coord2) == "y_from.dot.max"] <- "dot.max"
+stat.coord3 <- cbind(box.coord[order(box.coord$x), ], stat.coord1[order(stat.coord1$x.y), ], stat.coord2[order(stat.coord2$x.y), ]) # should be ok to use box.coord$x and stat.coord$x.y to assemble the two data frames because x coordinates of the boxs. Thus, we cannot have identical values
+if( ! all(identical(round(stat.coord3$x, 9), round(stat.coord3$x.y, 9)))){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": FUSION OF box.coord, stat.coord1 AND stat.coord2 ACCORDING TO box.coord$x, stat.coord1$x.y AND stat.coord2$x.y IS NOT CORRECT. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}
+text.coord <- stat.coord3[, c("x", "group", "dot.min", "dot.max")]
+names(text.coord)[names(text.coord) == "dot.min"] <- "text.min.pos"
+names(text.coord)[names(text.coord) == "dot.max"] <- "text.max.pos"
+box.coord <- box.coord[order(box.coord$x), ]
+text.coord <- text.coord[order(text.coord$x), ] # to be sure to have the two objects in the same order for x. BEWARE: cannot add identical(as.integer(text.coord$group), as.integer(box.coord$group)) because with error, the correspondence between x and group is not the same
+if( ! identical(text.coord$x, box.coord$x)){
+tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": text.coord AND box.coord DO NOT HAVE THE SAME x COLUMN CONTENT\n\n============\n\n")
+stop(tempo.cat)
+}
+}
+# end stat coordinates
+# stat display
+if(is.null(dot.color)){ # text just above boxs
+# performed twice: first for y values >=0, then y values < 0, because only a single value allowed for hjust anf vjust
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
+geom = "text",
+x = box.coord$x[box.coord$middle >= 0],
+y = box.coord$middle[box.coord$middle >= 0],
+label = if(stat.disp.mean == FALSE){fun_round(box.coord$middle, 2)[box.coord$middle >= 0]}else{fun_round(box.coord$MEAN, 2)[box.coord$MEAN >= 0]},
+size = stat.size,
+color = "black",
+hjust = ifelse(vertical == TRUE, 0.5, 0.5 - stat.dist),
+vjust = ifelse(vertical == TRUE, 0.5 - stat.dist, 0.5)
+)) # beware: no need of order() for labels because box.coord$x set the order
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
+geom = "text",
+x = box.coord$x[box.coord$middle < 0],
+y = box.coord$middle[box.coord$middle < 0],
+label = if(stat.disp.mean == FALSE){fun_round(box.coord$middle, 2)[box.coord$middle < 0]}else{fun_round(box.coord$MEAN, 2)[box.coord$MEAN < 0]},
+size = stat.size,
+color = "black",
+hjust = ifelse(vertical == TRUE, 0.5, 0.5 + stat.dist),
+vjust = ifelse(vertical == TRUE, 0.5 + stat.dist, 0.5)
+)) # beware: no need of order() for labels because box.coord$x set the order
+}else{ # text just above error boxs or dots
+# I checked that text.coord and box.coord have the same x and group column content. Thus, ok to use them together
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
+geom = "text",
+x = text.coord$x[box.coord$middle >= 0],
+y = text.coord$text.max.pos[box.coord$middle >= 0],
+label = if(stat.disp.mean == FALSE){fun_round(box.coord$middle, 2)[box.coord$middle >= 0]}else{fun_round(box.coord$MEAN, 2)[box.coord$MEAN >= 0]},
+size = stat.size,
+color = "black",
+hjust = ifelse(vertical == TRUE, 0.5, 0.5 - stat.dist),
+vjust = ifelse(vertical == TRUE, 0.5 - stat.dist, 0.5)
+)) # beware: no need of order() for labels because box.coord$x set the order
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
+geom = "text",
+x = text.coord$x[box.coord$middle < 0],
+y = text.coord$text.min.pos[box.coord$middle < 0],
+label = if(stat.disp.mean == FALSE){fun_round(box.coord$middle, 2)[box.coord$middle < 0]}else{fun_round(box.coord$MEAN, 2)[box.coord$MEAN < 0]},
+size = stat.size,
+color = "black",
+hjust = ifelse(vertical == TRUE, 0.5, 0.5 + stat.dist),
+vjust = ifelse(vertical == TRUE, 0.5 + stat.dist, 0.5)
+)) # beware: no need of order() for labels because box.coord$x set the order
+}
+# end stat display
+}else{
+tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": CODE INCONSISTENCY 9\n\n============\n\n")
+stop(tempo.cat)
+}
+}
+# end stat display
+
+
+
+# y scale management (cannot be before dot plot management)
+tempo.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$layout$panel_params[[1]]
+tempo.scale <- fun_scale(lim = y.lim, n = ifelse(is.null(y.tick.nb), length(tempo.coord$y.major_source), y.tick.nb))
+# for the ggplot2 bug with y.log, this does not work: eval(parse(text = ifelse(vertical == FALSE & y.log == "log10", "ggplot2::scale_x_continuous", "ggplot2::scale_y_continuous")))
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_y_continuous(
+breaks = tempo.scale,
+labels = if(y.log == "log10"){scales::trans_format("identity", scales::math_format(10^.x))}else if(y.log == "log2"){scales::trans_format("identity", scales::math_format(2^.x))}else if(y.log == "no"){ggplot2::waiver()}else{tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": CODE INCONSISTENCY 10\n\n============\n\n") ; stop(tempo.cat)},
+expand = c(0, 0),
+limits = NA,
+trans = ifelse(diff(y.lim) < 0, "reverse", "identity") # equivalent to ggplot2::scale_y_reverse()
+))
+if(vertical == TRUE){
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_cartesian(ylim = y.lim)) # clip = "off" to have secondary ticks outside plot region does not work
+}else{
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_flip(ylim = y.lim)) # clip = "off" to have secondary ticks outside plot region does not work
+}
+# secondary ticks (after ggplot2::coord_cartesian() or ggplot2::coord_flip())
+tempo.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$layout$panel_params[[1]]
+# no secondary ticks for log2. Play with y.lim
+if(y.log == "log10"){
+y.lim.order <- order(y.lim) # to deal with inverse axis
+ini.scipen <- options()$scipen
+options(scipen = -1000) # force scientific format
+power10.exp <- as.integer(substring(text = 10^y.lim, first = (regexpr(pattern = "\\+|\\-", text = 10^y.lim)))) # recover the power of 10. Example recover 08 from 1e+08
+mantisse <- as.numeric(substr(x = 10^y.lim, start = 1, stop = (regexpr(pattern = "\\+|\\-", text = 10^y.lim) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
+options(scipen = ini.scipen) # restore the initial scientific penalty
+tempo.tick.pos <- as.vector(outer(log10(2:10), 10^((power10.exp[1] - ifelse(diff(y.lim.order) > 0, 1, -1)):(power10.exp[2] + ifelse(diff(y.lim.order) > 0, 1, -1)))))
+tempo.tick.pos <- sort(tempo.tick.pos, decreasing = ifelse(diff(y.lim.order) > 0, FALSE, TRUE))
+tempo.tick.pos <- log10(tempo.tick.pos[tempo.tick.pos >= min(10^y.lim) & tempo.tick.pos <= max(10^y.lim)])
+if(any(is.na(tempo.tick.pos) | ! is.finite(tempo.tick.pos))){
+tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": CODE INCONSISTENCY 11\n\n============\n\n")
+stop(tempo.cat)
+}
+# if(vertical == TRUE){ # do not remove in case the bug is fixed
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", y = tempo.tick.pos, yend = tempo.tick.pos, x = tempo.coord$x.range[1], xend = tempo.coord$x.range[1] + diff(tempo.coord$x.range) / 80))
+# }else{ # not working because of the ggplot2 bug
+# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", x = tempo.tick.pos, xend = tempo.tick.pos, y = tempo.coord$y.range[1], yend = tempo.coord$y.range[1] + diff(tempo.coord$y.range) / 80))
+# }
+}else if(( ! is.null(y.inter.tick.nb)) & y.log == "no"){
+if(y.inter.tick.nb > 0){
+if(vertical == TRUE){
+ticks.pos <- suppressWarnings(as.numeric(tempo.coord$y.labels)) # too difficult to predict the behavior of tempo.coord$x.major_source depending on y.lim neg or not, inv or not
+if(any(is.na(ticks.pos))){
+tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": CODE INCONSISTENCY 12\n\n============\n\n")
+stop(tempo.cat)
+}
+tick.dist <- mean(diff(ticks.pos), na.rm = TRUE)
+minor.tick.dist <- tick.dist / (y.inter.tick.nb + 1)
+minor.tick.pos <- seq(ticks.pos[1] - tick.dist, ticks.pos[length(ticks.pos)] + tick.dist, by = minor.tick.dist)
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", y = minor.tick.pos, yend = minor.tick.pos, x = tempo.coord$x.range[1], xend = tempo.coord$x.range[1] + diff(tempo.coord$x.range) / 80))
+}else{
+ticks.pos <- suppressWarnings(as.numeric(tempo.coord$x.labels))# too difficult to predict the behavior of tempo.coord$x.major_source depending on y.lim neg or not, inv or not
+if(any(is.na(ticks.pos))){
+tempo.cat <- paste0("\n\n============\n\nINTERNAL CODE ERROR IN ", function.name, ": CODE INCONSISTENCY 13\n\n============\n\n")
+stop(tempo.cat)
+}
+tick.dist <- mean(diff(ticks.pos), na.rm = TRUE)
+minor.tick.dist <- tick.dist / (y.inter.tick.nb + 1)
+minor.tick.pos <- seq(ticks.pos[1] - tick.dist, ticks.pos[length(ticks.pos)] + tick.dist, by = minor.tick.dist)
+assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", y = minor.tick.pos, yend = minor.tick.pos, x = tempo.coord$y.range[1], xend = tempo.coord$y.range[1] + diff(tempo.coord$y.range) / 80))
+}
+}
+}
+# end secondary ticks (after ggplot2::coord_cartesian() or ggplot2::coord_flip())
+# end y scale management (cannot be before dot plot management)
+
+
+
+
+# drawing
+if(plot == TRUE){
+# following lines inactivated because of problem in warn.recov and message.recov
+# assign("env_fun_get_message", new.env())
+# assign("tempo.gg.name", tempo.gg.name, envir = env_fun_get_message)
+# assign("tempo.gg.count", tempo.gg.count, envir = env_fun_get_message)
+# assign("add", add, envir = env_fun_get_message)
+# two next line: for the moment, I cannot prevent the warning printing
+# warn.recov <- fun_get_message(paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}), kind = "warning", header = FALSE, print.no = FALSE, env = env_fun_get_message) # for recovering warnings printed by ggplot() functions
+# message.recov <- fun_get_message('print(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}))))', kind = "message", header = FALSE, print.no = FALSE, env = env_fun_get_message) # for recovering messages printed by ggplot() functions
+suppressMessages(suppressWarnings(print(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}))))))
+}else{
+# following lines inactivated because of problem in warn.recov and message.recov
+# message.recov <- NULL
+# warn.recov <- NULL
+warn.count <- warn.count + 1
+tempo.warn <- paste0("(", warn.count,") PLOT NOT SHOWN AS REQUESTED")
+warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+}
+# end drawing
+
+
+
+# outputs
+# following lines inactivated because of problem in warn.recov and message.recov
+# if( ! (is.null(warn) & is.null(warn.recov) & is.null(message.recov))){
+# warn <- paste0(warn, "\n\n", if(length(warn.recov) > 0 | length(message.recov) > 0){paste0(paste0("MESSAGES FROM ggplot2 FUNCTIONS: ", ifelse( ! is.null(warn.recov), unique(message.recov), ""), ifelse( ! is.null(message.recov), unique(message.recov), ""), collapse = "\n\n"), "\n\n")})
+# }else if( ! (is.null(warn) & is.null(warn.recov)) & is.null(message.recov)){
+# warn <- paste0(warn, "\n\n", if(length(warn.recov) > 0){paste0(paste0("MESSAGES FROM ggplot2 FUNCTIONS: ", unique(warn.recov), collapse = "\n\n"), "\n\n")})
+# }else if( ! (is.null(warn) & is.null(message.recov)) & is.null(warn.recov)){
+# warn <- paste0(warn, "\n\n", if(length(message.recov) > 0){paste0(paste0("MESSAGES FROM ggplot2 FUNCTIONS: ", unique(message.recov), collapse = "\n\n"), "\n\n")})
+# }
+if(warn.print == TRUE & ! is.null(warn)){
+warning(paste0("FROM ", function.name, " FUNCTION:\n\n", warn), call. = FALSE) # to recover the warning messages, use return = TRUE
+}
+if(return == TRUE){
+output <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))
+output$data <- output$data[-1] # remove the first data because corresponds to the initial empty boxplot
+if(length(output$data) != length(coord.names)){
+tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR IN ", function.name, ": length(output$data) AND length(coord.names) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED\n\n================\n\n")
+stop(tempo.cat)
+}else{
+names(output$data) <- coord.names
+}
+output <- list(data = data1, stat = stat, removed.row.nb = removed.row.nb, removed.rows = removed.rows, plot = output$data, axes = output$layout$panel_params[[1]], warn = paste0("\n", warn, "\n\n"))
+return(output)
+}
+# end outputs
+# end main code
+}
+
+
+
+
+
+
+
diff --git a/scatter.docx b/scatter.docx
index 99a93ea28492115d8bc534a4d559687ce0d021c9..160a03d7a851be23878216454ad22b3537665db6 100644
Binary files a/scatter.docx and b/scatter.docx differ