diff --git a/cute_checks.docx b/cute_checks.docx
index 78a5832c730270c07a8ba9bf061cab453f4ef6f0..d0e5be4afe0fd97bb13edff70971b79b6ccf0e05 100644
Binary files a/cute_checks.docx and b/cute_checks.docx differ
diff --git a/cute_little_R_functions.R b/cute_little_R_functions.R
index 57984ef6693d33d449bda3e8b5904fd8deffb5b6..e1cca2637ee679577e286966a6153963b653b58c 100644
--- a/cute_little_R_functions.R
+++ b/cute_little_R_functions.R
@@ -91,34 +91,36 @@
 ######## fun_check() #### check class, type, length, etc., of objects
 
 
-# Check OK: clear to go Apollo
+# Check r_debugging_tools-v1.2.R OK
+# Check fun_test() (see ) Ok
+# clear to go Apollo
 fun_check <- function(data, data.name = NULL, class = NULL, typeof = NULL, mode = NULL, length = NULL, prop = FALSE, double.as.integer.allowed = FALSE, options = NULL, all.options.in.data = FALSE, na.contain = FALSE, neg.values = TRUE, print = FALSE, fun.name = NULL){
 # AIM
 # check the class, type, mode and length of the data argument
 # mainly used to check the arguments of other functions
 # check also other kind of data parameters, is it a proportion? Is it type double but numbers without decimal part?
-# if options = NULL, then at least class or type or mode or length must be non null
+# if options == NULL, then at least class or type or mode or length argument must be non null
 # if options is non null, then class, type and mode must be NULL, and length can be NULL or specified
 # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
 # none
 # ARGUMENTS
 # data: object to test
-# data.name: name of the object to test. If NULL, use the name of the object assigned to the data argument
-# class: one of the class() result or "vector"
-# typeof: one of the typeof() result
-# mode: one of the mode() result (for non vector object)
-# length: length of the object
-# prop: logical, are the numeric values between 0 and 1 (proportion)? If TRUE, can be used alone, without considering class, etc.
-# double.as.integer.allowed: logical. If TRUE, no error is reported if argument is set to typeof = "integer" or class = "integer", while the reality is typeof = "double" or class = "numeric" but the numbers have a zero as modulo (remainder of a division). This means that i<-1 , which is typeof(i) -> "double" is considered as integer with double.as.integer.allowed = TRUE
-# options: a vector of possible values for data
-# all.options.in.data: If TRUE, all of the options must be present at least once in data, and nothing else. If FALSE, some of the options must be present in data, and nothing else
-# na.contain: can data contains NA?
-# neg.values: are negative numeric values authorized? BEWARE: only considered if set to FALSE, to check for non negative values when class is set to "numeric", "matrix", "array", "data.frame", "table", or typeof is set to "double", "integer", or mode is set to "numeric"
-# print: print the error message if $problem is TRUE? See the example section
-# fun.name: name of the function when fun_check() is used to check its argument. If non NULL, name will be added into the error message returned by fun_check()
+# data.name: character string indicating the name of the object to test. If NULL, use the name of the object assigned to the data argument
+# class: character string. Either one of the class() result or "vector" or NULL
+# typeof: character string. Either one of the typeof() result or NULL
+# mode: character string. Either one of the typeof() result (for non vector object) or NULL
+# length: numeric value indicating the length of the object. Not considered if NULL
+# prop: logical. Are the numeric values between 0 and 1 (proportion)? If TRUE, can be used alone, without considering class, etc.
+# double.as.integer.allowed: logical. If TRUE, no error is reported if argument is set to typeof == "integer" or class == "integer", while the reality is typeof == "double" or class == "numeric" but the numbers have a zero as modulo (remainder of a division). This means that i <- 1 , which is typeof(i) -> "double" is considered as integer with double.as.integer.allowed = TRUE
+# options: a vector of character strings indicating all the possible option values for data
+# all.options.in.data: logical. If TRUE, all of the options must be present at least once in data, and nothing else. If FALSE, some of the options must be present in data, and nothing else
+# na.contain: logical. Can data contain NA?
+# neg.values: logical. Are negative numeric values authorized? BEWARE: only considered if set to FALSE, to check for non negative values when class is set to "numeric", "matrix", "array", "data.frame", "table", or typeof is set to "double", "integer", or mode is set to "numeric"
+# print: logical. Print the error message if $problem is TRUE? See the example section
+# fun.name: character string indicating the name of the function when fun_check() is used to check its argument. If non NULL, name will be added into the error message returned by fun_check()
 # RETURN
 # a list containing:
-# $problem: logical. Is there any problem detected ?
+# $problem: logical. Is there any problem detected?
 # $text: the problem detected
 # $fun.name: name of the checked parameter
 # EXAMPLES
@@ -134,6 +136,13 @@ fun_check <- function(data, data.name = NULL, class = NULL, typeof = NULL, mode
 # data = expression(TEST) ; data.name = NULL ; class = "vector" ; typeof = NULL ; mode = NULL ; length = 1 ; prop = FALSE ; double.as.integer.allowed = FALSE ; options = NULL ; all.options.in.data = FALSE ; na.contain = FALSE ; neg.values = TRUE ; print = TRUE ; fun.name = NULL
 # function name: no used in this function for the error message, to avoid env colliding
 # argument checking
+# dealing with NA
+if(any(is.na(data.name)) | any(is.na(class)) | any(is.na(typeof)) | any(is.na(mode)) | any(is.na(length)) | any(is.na(prop)) | any(is.na(double.as.integer.allowed)) | any(is.na(all.options.in.data)) | any(is.na(na.contain)) | any(is.na(neg.values)) | any(is.na(print)) | any(is.na(fun.name))){
+tempo.cat <- paste0("\n\n================\n\nERROR IN fun_check(): NO ARGUMENT EXCEPT data AND options CAN HAVE NA VALUES\n\n================\n\n")
+stop(tempo.cat, call. = FALSE)
+}
+# end dealing with NA
+# dealing with NULL
 if( ! is.null(data.name)){
 if( ! (length(data.name) == 1 & class(data.name) == "character")){
 tempo.cat <- paste0("\n\n================\n\nERROR IN fun_check(): data.name ARGUMENT MUST BE A SINGLE CHARACTER ELEMENT AND NOT ", paste(data.name, collapse = " "), "\n\n================\n\n")
@@ -149,9 +158,10 @@ tempo.cat <- paste0("\n\n================\n\nERROR IN fun_check(): AT LEAST ONE
 stop(tempo.cat, call. = FALSE)
 }
 if( ! is.null(options) & ( ! is.null(class) | ! is.null(typeof) | ! is.null(mode) | prop == TRUE)){
-tempo.cat <- paste0("\n\n================\n\nERROR IN fun_check(): THE class, typeof, mode ARGUMENTS MUST BE NULL, AND prop FALSE, IF THE option ARGUMENT IS SPECIFIED\nTHE option ARGUMENT MUST BE NULL IF THE class AND/OR typeof AND/OR mode AND/OR prop ARGUMENT IS SPECIFIED\n\n================\n\n")
+tempo.cat <- paste0("\n\n================\n\nERROR IN fun_check(): THE class, typeof, mode ARGUMENTS MUST BE NULL, AND prop FALSE, IF THE options ARGUMENT IS SPECIFIED\nTHE options ARGUMENT MUST BE NULL IF THE class AND/OR typeof AND/OR mode AND/OR prop ARGUMENT IS SPECIFIED\n\n================\n\n")
 stop(tempo.cat, call. = FALSE)
 }
+# end dealing with NULL
 if( ! (all(class(neg.values) == "logical") & length(neg.values) == 1 & any(is.na(neg.values)) != TRUE)){
 tempo.cat <- paste0("\n\n================\n\nERROR IN fun_check(): THE neg.values ARGUMENT MUST BE TRUE OR FALSE ONLY\n\n================\n\n")
 stop(tempo.cat, call. = FALSE)
@@ -1389,13 +1399,11 @@ stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"),
 args <- names(formals(get(fun)))
 if( ! all(arg %in% args)){
 tempo.cat <- paste0("ERROR IN ", function.name, ": SOME OF THE STRINGS IN arg ARE NOT ARGUMENTS OF fun\nfun ARGUMENTS: ", paste(args, collapse = " "),"\nPROBLEMATIC STRINGS IN arg: ", paste(arg[ ! arg %in% args], collapse = " "))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
 }
 if(sum(sapply(val, FUN = length) > 1) > 43){
 tempo.cat <- paste0("ERROR IN ", function.name, ": CANNOT TEST MORE THAN 43 ARGUMENTS IF THEY ALL HAVE AT LEAST 2 VALUES EACH\nHERE THE NUMBER IS: ", sum(sapply(val, FUN = length) > 1))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
+stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
 }
 if( ! is.null(thread.nb) & is.null(res.path)){
 tempo.cat <- paste0("ERROR IN ", function.name, ": res.path ARGUMENT MUST BE SPECIFIED IF thread.nb ARGUMENT IS NOT NULL")
@@ -8195,7 +8203,7 @@ if(any(class(tempo.error) %in% c("gg", "ggplot"))){
 tempo.error <- try(suppressMessages(suppressWarnings(ggplot2::ggplot_build(tempo.error))), silent = TRUE)[1]
 }
 if(exists("tempo.error", inherit = FALSE) == TRUE){ # inherit = FALSE avoid the portee lexical and thus the declared word
-if((length(tempo.error) > 0 & ! any(grepl(x = tempo.error, pattern = "^Error|^error|^ERROR"))) | (length(tempo.error) == 0)){
+if( ! (all(class(tempo.error) == "try-error") & any(grepl(x = tempo.error, pattern = "^Error|^error|^ERROR")))){ # deal with NULL. Old code : if((length(tempo.error) > 0 & ! any(grepl(x = tempo.error, pattern = "^Error|^error|^ERROR"))) | (length(tempo.error) == 0) ){ but problem when tempo.error is a list but added this did not work: | ! all(class(tempo.error) == "character")
 tempo.error <- NULL
 }
 }else{
@@ -8282,1291 +8290,3 @@ return(output) # do not use cat() because the idea is to reuse the message
 
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally)
-
-
-
-# Check OK: clear to go Apollo
-fun_gg_scatter <- function(
-data1, 
-x, 
-y, 
-categ = NULL, 
-legend.name = NULL, 
-color = NULL, 
-geom = "geom_point", 
-alpha = 0.5, 
-dot.size = 2, 
-line.size = 0.5, 
-x.lim = NULL, 
-x.lab = NULL, 
-x.log = "no", 
-x.tick.nb = NULL, 
-x.inter.tick.nb = NULL, 
-x.include.zero = FALSE, 
-x.left.extra.margin = 0.05, 
-x.right.extra.margin = 0.05, 
-x.text.angle = 0, 
-y.lim = NULL, 
-y.lab = 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, 
-y.text.angle = 0, 
-text.size = 12, 
-title = "", 
-title.text.size = 12, 
-legend.show = TRUE, 
-legend.width = 0.5, 
-raster = FALSE, 
-raster.ratio = 1, 
-raster.threshold = NULL, 
-classic = TRUE, 
-grid = FALSE, 
-return = FALSE, 
-plot = TRUE, 
-add = NULL, 
-warn.print = TRUE, 
-lib.path = NULL
-){
-# DEBUGGING
-# set.seed(1) ; obs1 <- data.frame(km = rnorm(1000, 10, 3), time = rnorm(1000, 10, 3), group1 = rep(c("A1", "A2"), 500)) ; obs2 <-data.frame(km = rnorm(1000, 15, 3), time = rnorm(1000, 15, 3), group2 = rep(c("G1", "G2"), 500)) ; set.seed(NULL) ; obs1$km[2:3] <- NA ; data1 = list(L1 = obs1, L2 = obs2) ; x = list(L1 = "km", L2 = "km") ; y = list(L1 = "time", L2 = "time") ; categ = list(L1 = "group1", L2 = "group2") ; legend.name = NULL ; color = list(L1 = 4:5, L2 = 7:8) ; geom = list(L1 = "geom_point", L2 = "geom_point") ; alpha = list(L1 = 0.5, L2 = 0.5) ; dot.size = 3 ; line.size = 0.5 ; x.lim = NULL ; x.lab = "KM" ; x.log = "no" ; x.tick.nb = 10 ; x.inter.tick.nb = 1 ; x.left.extra.margin = 0 ; x.right.extra.margin = 0 ; y.lim = c(1, 25) ; y.lab = "TIME (s)" ; y.log = "no" ; y.tick.nb = 5 ; y.inter.tick.nb = 2 ; y.top.extra.margin = 0 ; y.bottom.extra.margin = 0 ; x.include.zero = TRUE ; y.include.zero = TRUE ; x.text.angle = 0 ; y.text.angle = 0 ; text.size = 12 ; title = "" ; title.text.size = 8 ; legend.show = TRUE ; legend.width = 0.5 ; classic = FALSE ; grid = FALSE ; raster = TRUE ; raster.ratio = 1 ; raster.threshold = NULL ; return = FALSE ; plot = TRUE ; add = NULL ; warn.print = TRUE ; lib.path = NULL
-# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")), L2 = data.frame(a = (1:6)*2, b = ((1:6)^2)*2, group = c("A1", "A1", "A1", "B1", "B1", "B1")), L3 = data.frame(a = (1:6)*3, b = ((1:6)^2)*3, group3 = c("A4", "A5", "A6", "A7", "B4", "B5"))) ; data1$L1$a[3] <- NA ; data1$L1$group[5] <- NA ; data1$L3$group3[4] <- NA ; x = list(L1 = names(data1$L1)[1], L2 = names(data1$L2)[1], L3 = NULL) ; y = list(L1 = names(data1$L1)[2], L2 = names(data1$L2)[2], L3 = "a") ; categ = list(L1 = "group", L2 = NULL, L3 = NULL) ; legend.name = NULL ; color = NULL ; geom = list(L1 = "geom_point", L2 = "geom_point", L3 = "geom_hline") ; alpha = list(L1 = 0.5, L2 = 0.5, L3 = 0.5) ; dot.size = 1 ; line.size = 0.5 ; x.lim = c(14, 4) ; x.lab = NULL ; x.log = "log10" ; x.tick.nb = 10 ; x.inter.tick.nb = 4 ; x.left.extra.margin = 0 ; x.right.extra.margin = 0 ; y.lim = c(60, 5) ; y.lab = NULL ; y.log = "log10" ; y.tick.nb = 10 ; y.inter.tick.nb = 2 ; y.top.extra.margin = 0 ; y.bottom.extra.margin = 0  ; x.include.zero = TRUE ; y.include.zero = TRUE ; x.text.angle = 0 ; y.text.angle = 0 ; text.size = 12 ; title = "" ; title.text.size = 8 ; legend.show = TRUE ; legend.width = 0.5 ; classic = FALSE ; grid = FALSE ; raster = FALSE ; raster.ratio = 1 ; raster.threshold = NULL ; return = FALSE ; plot = TRUE ; add = NULL ; warn.print = TRUE ; lib.path = NULL
-# data1 <- data.frame(km = 2:7, time = (2:7)^2, group = c("A", "A", "A", "B", "B", "B")) ; data1 ; x = "km"; y = "time"; categ = "group"; legend.name = NULL ; color = NULL ; geom = "geom_point"; alpha = 0.1 ; dot.size = 1 ; line.size = 0.5 ; x.lim = c(1,10) ; x.lab = NULL ; x.log = "log10" ; x.tick.nb = 10 ; x.inter.tick.nb = 4 ; x.left.extra.margin = 0 ; x.right.extra.margin = 0 ; y.lim = NULL ; y.lab = expression(paste("TIME (", 10^-20, " s)")) ; y.log = "log10" ; y.tick.nb = 10 ; y.inter.tick.nb = 2 ; y.top.extra.margin = 0 ; y.bottom.extra.margin = 0  ; x.include.zero = TRUE ; y.include.zero = TRUE ; x.text.angle = 0 ; y.text.angle = 0 ; text.size = 12 ; title = "" ; title.text.size = 8 ; legend.show = TRUE ; legend.width = 0.5 ; classic = FALSE ; grid = FALSE ; raster = FALSE ; raster.ratio = 1 ; raster.threshold = NULL ; return = FALSE ; plot = TRUE ; add = NULL ; warn.print = TRUE ; 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_check", 
-"fun_gg_just", 
-"fun_gg_palette", 
-"fun_gg_point_rast", 
-"fun_pack"
-)
-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("fake_x", "fake_y", "fake_categ", "color")
-# 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))
-tempo1 <- fun_check(data = data1, class = "data.frame", na.contain = TRUE, fun.name = function.name, print = FALSE)
-tempo2 <- fun_check(data = data1, class = "list", na.contain = TRUE, fun.name = function.name, print = FALSE)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A DATA FRAME OR A LIST OF DATA FRAMES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(x)){
-tempo1 <- fun_check(data = x, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name, print = FALSE)
-tempo2 <- fun_check(data = x, class = "list", na.contain = TRUE, fun.name = function.name, print = FALSE)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-if( ! is.null(y)){
-tempo1 <- fun_check(data = y, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name, print = FALSE)
-tempo2 <- fun_check(data = y, class = "list", na.contain = TRUE, fun.name = function.name, print = FALSE)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-if( ! is.null(categ)){
-tempo1 <- fun_check(data = categ, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name, print = FALSE)
-tempo2 <- fun_check(data = categ, class = "list", na.contain = TRUE, fun.name = function.name, print = FALSE)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-if( ! is.null(legend.name)){
-tempo1 <- fun_check(data = legend.name, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name, print = FALSE)
-tempo2 <- fun_check(data = legend.name, class = "list", na.contain = TRUE, fun.name = function.name, print = FALSE)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": legend.name ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-if( ! is.null(color)){
-tempo1 <- fun_check(data = color, class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name, print = FALSE)
-tempo2 <- fun_check(data = color, class = "list", na.contain = TRUE, fun.name = function.name, print = FALSE)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": color ARGUMENT MUST BE A VECTOR OF CHARACTER STRING OR A LIST OF CHARACTER VECTORS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-if( ! is.null(geom)){
-tempo1 <- fun_check(data = geom, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name, print = FALSE)
-tempo2 <- fun_check(data = geom, class = "list", na.contain = TRUE, fun.name = function.name, print = FALSE)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-tempo1 <- fun_check(data = alpha, prop = TRUE, length = 1, fun.name = function.name, print = FALSE)
-tempo2 <- fun_check(data = alpha, class = "list", na.contain = TRUE, fun.name = function.name, print = FALSE)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": alpha ARGUMENT MUST BE A SINGLE NUMERIC VALUE BETWEEN 0 AND 1 OR A LIST OF SUCH VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-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 = line.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-if( ! is.null(x.lim)){
-tempo <- fun_check(data = x.lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & any(x.lim %in% c(Inf, -Inf))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x.lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-if( ! is.null(x.lab)){
-if(all(class(x.lab) %in% "expression")){ # to deal with math symbols
-tempo <- fun_check(data = x.lab, class = "expression", length = 1, fun.name = function.name) ; eval(ee)
-}else{
-tempo <- fun_check(data = x.lab, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-}
-tempo <- fun_check(data = x.log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(x.tick.nb)){
-tempo <- fun_check(data = x.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & x.tick.nb < 0){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x.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(x.inter.tick.nb)){
-tempo <- fun_check(data = x.inter.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & x.inter.tick.nb < 0){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x.inter.tick.nb ARGUMENT MUST BE A NON NULL POSITIVE INTEGER")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-tempo <- fun_check(data = x.include.zero, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.left.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.right.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.text.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
-if( ! is.null(y.lim)){
-tempo <- fun_check(data = y.lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
-if(tempo$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)
-}
-}
-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)
-}
-}
-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)
-tempo <- fun_check(data = y.text.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
-# inactivated because x.lim and y.lim already log transformed
-# if(tempo$problem == FALSE & y.log == TRUE & xy.include.zero == TRUE){
-# warn.count <- warn.count + 1 ; tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": BOTH y.log AND xy.include.zero ARGUMENTS SET TO TRUE -> xy.include.zero ARGUMENT RESET TO FALSE")
-# warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-# }
-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 = 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 = legend.show, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(legend.width)){
-tempo <- fun_check(data = legend.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = raster, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = raster.ratio, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-if( ! is.null(raster.threshold)){
-tempo <- fun_check(data = raster.threshold, class = "vector", typeof = "integer", neg.values = FALSE, double.as.integer.allowed = TRUE, 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)
-}
-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){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-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
-# check list lengths (and names of data1 compartments if non name present)
-warn <- NULL
-warn.count <- 0
-if(all(class(data1) == "list")){
-if(length(data1) > 6){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": data1 ARGUMENT MUST BE A LIST OF 6 DATA FRAMES MAXIMUM (6 OVERLAYS MAX)\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-if(is.null(names(data1))){
-names(data1) <- paste0("L", 1:length(data1))
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": NULL NAME COMPARTMENT OF data1 LIST -> NAMES RESPECTIVELY ATTRIBUTED TO EACH COMPARTMENT:\n", paste(names(data1), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(x)){
-if( ! (all(class(x) == "list") & length(data1) == length(x))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": x ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}else{
-x <- vector("list", length(data1))
-}
-if( ! is.null(y)){
-if( ! (all(class(y) == "list") & length(data1) == length(y))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": y ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}else{
-y <- vector("list", length(data1))
-}
-if( ! is.null(categ)){
-if( ! (all(class(categ) == "list") & length(data1) == length(categ))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": categ ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-if( ! is.null(legend.name)){
-if( ! (all(class(legend.name) == "list") & length(data1) == length(legend.name))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": legend.name ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-if( ! is.null(color)){
-if( ! (all(class(color) == "list") & length(data1) == length(color))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": color ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-if( ! (all(class(geom) == "list") & length(data1) == length(geom))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": geom ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-if( ! (all(class(alpha) == "list") & length(data1) == length(alpha))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": alpha ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-# end check list lengths (and names of data1 compartments if non name present)
-# conversion into lists
-if(all(is.data.frame(data1))){
-data1 <- list(L1 = data1)
-if(all(class(x) == "list")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": x ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-x <- list(L1 = x)
-}
-if(all(class(y) == "list")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": y ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-y <- list(L1 = y)
-}
-if( ! is.null(categ)){
-if(all(class(categ) == "list")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": categ ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-categ <- list(L1 = categ)
-}
-}
-if( ! is.null(legend.name)){
-if(all(class(legend.name) == "list")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": legend.name ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-legend.name <- list(L1 = legend.name)
-}
-}
-if( ! is.null(color)){
-if(all(class(color) == "list")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": color ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-color <- list(L1 = color)
-}
-}
-if(all(class(geom) == "list")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": geom ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-geom <- list(L1 = geom)
-}
-if(all(class(alpha) == "list")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": alpha ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-alpha <- list(L1 = alpha)
-}
-}else if( ! all(sapply(data1, FUN = "class") == "data.frame")){ # if not a data frame, data1 can only be a list, as tested above
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": data1 ARGUMENT MUST BE A DATA FRAME OR A LIST OF DATA FRAMES\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-# data, x, y, geom, alpha are list now
-# if non NULL, categ, legend.name, color are list now
-# end conversion into lists
-# legend name filling
-if(is.null(legend.name) & ! is.null(categ)){
-legend.name <- categ
-}else if(is.null(legend.name) & is.null(categ)){
-legend.name <- vector("list", length(data1)) # null list
-}
-# legend.name not NULL anymore (list)
-# end legend name filling
-# ini categ for legend display
-fin.lg.disp <- vector("list", 6) # will be used at the end to display or not legends
-fin.lg.disp[] <- FALSE
-legend.disp <- vector("list", length(data1))
-if(is.null(categ) | legend.show == FALSE){
-legend.disp[] <- FALSE
-}else{
-for(i2 in 1:length(data1)){
-if(is.null(categ[[i2]])){
-legend.disp[[i2]] <- FALSE
-}else{
-legend.disp[[i2]] <- TRUE
-}
-}
-}
-# end ini categ for legend display
-# integer colors into gg_palette
-tempo.check.color <- NULL
-for(i1 in 1:length(data1)){
-if(any(is.na(color[[i1]]))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ": color ARGUMENT CANNOT CONTAIN NA\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-tempo.check.color <- c(tempo.check.color, fun_check(data = color[[i1]], data.name = ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name, print = FALSE)$problem)
-}
-tempo.check.color <- ! tempo.check.color # invert TRUE and FALSE because if integer, then problem = FALSE
-if(any(tempo.check.color == TRUE)){ # convert integers into colors
-tempo.integer <- unlist(color[tempo.check.color])
-tempo.color <- fun_gg_palette(max(tempo.integer, na.rm = TRUE))
-for(i1 in 1:length(data1)){
-if(tempo.check.color[i1] == TRUE){
-color[[i1]] <-tempo.color[color[[i1]]]
-}
-}
-}
-# end integer colors into gg_palette
-
-
-# second round of argument checking
-compart.null.color <- 0 # will be used to attribute a color when color is non NULL but a compartment of color is NULL
-data1.ini <- data1 # to report NA removal
-removed.row.nb <- vector("list", length = length(data1)) # to report NA removal
-removed.rows <- vector("list", length = length(data1)) # to report NA removal
-for(i1 in 1:length(data1)){
-tempo <- fun_check(data = data1[[i1]], data.name = ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-# reserved word checking
-if(any(names(data1[[i1]]) %in% reserved.words)){ # I do not use fun_name_change() because cannot control y before creating "fake_y". But ok because reserved are not that common
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": COLUMN NAMES OF ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), " ARGUMENT CANNOT BE ONE OF THESE WORDS\n", paste(reserved.words, collapse = " "), "\nTHESE ARE RESERVED FOR THE ", function.name, " FUNCTION\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-# end reserved word checking
-# check of geom now because required for y argument
-tempo <- fun_check(data = geom[[i1]], data.name = ifelse(length(geom) == 1, "geom", paste0("geom NUMBER ", i1)), options = c("geom_point", "geom_line", "geom_path", "geom_hline", "geom_vline"), length = 1, fun.name = function.name) ; eval(ee)
-# end check of geom now because required for y argument
-if(is.null(x[[i1]])){
-if(all(geom[[i1]] != "geom_hline")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(x) == 1, "x", paste0("x NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ": x ARGUMENT CANNOT BE NULL EXCEPT IF ", ifelse(length(geom) == 1, "x", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_hline\"\nHERE geom ARGUMENT IS: ", paste(geom[[i1]], collapse = " "), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-x[[i1]] <- "fake_x"
-data1[[i1]] <- cbind(data1[[i1]], fake_x = NA)
-data1[[i1]][, "fake_x"] <- as.numeric(data1[[i1]][, "fake_x"])
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": NULL ", ifelse(length(x) == 1, "x", paste0("x NUMBER ", i1)), " ARGUMENT ASSOCIATED TO ", ifelse(length(geom) == 1, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT ", geom[[i1]], " -> FAKE COLUMN ADDED TO DATA FRAME ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", NAMED \"fake_x\" FOR FINAL DRAWING")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(all(geom[[i1]] == "geom_hline")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(x) == 1, "x", paste0("x NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ": x ARGUMENT MUST BE NULL IF ", ifelse(length(geom) == 1, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_hline\"\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-tempo <- fun_check(data = x[[i1]], data.name = ifelse(length(x) == 1, "x", paste0("x NUMBER ", i1)), class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-if(is.null(y[[i1]])){
-if(all(geom[[i1]] != "geom_vline")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ": y ARGUMENT CANNOT BE NULL EXCEPT IF ", ifelse(length(geom) == 1, "y", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_vline\"\nHERE geom ARGUMENT IS: ", paste(geom[[i1]], collapse = " "), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-y[[i1]] <- "fake_y"
-data1[[i1]] <- cbind(data1[[i1]], fake_y = NA)
-data1[[i1]][, "fake_y"] <- as.numeric(data1[[i1]][, "fake_y"])
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": NULL ", ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), " ARGUMENT ASSOCIATED TO ", ifelse(length(geom) == 1, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT ", geom[[i1]], " -> FAKE COLUMN ADDED TO DATA FRAME ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", NAMED \"fake_y\" FOR FINAL DRAWING")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(all(geom[[i1]] == "geom_vline")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ": y ARGUMENT MUST BE NULL IF ", ifelse(length(geom) == 1, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_vline\"\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-tempo <- fun_check(data = y[[i1]], data.name = ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-if( ! (x[[i1]] %in% names(data1[[i1]]))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(x) == 1, "x", paste0("x NUMBER ", i1)), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-if( ! (y[[i1]] %in% names(data1[[i1]]))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-# na detection and removal (done now to be sure of the correct length of categ)
-if(x[[i1]] == "fake_x" & y[[i1]] == "fake_y"){ # because the code cannot accept to be both "fake_x" and "fake_y" at the same time
-tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 2\nTHE CODE CANNOT ACCEPT x AND y TO BE \"fake_x\" AND \"fake_y\" IN THE SAME DATA FRAME ", i1, " \n\n============\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-if(any(is.na(data1[[i1]][, c(if(x[[i1]] == "fake_x"){NULL}else{x[[i1]]}, if(y[[i1]] == "fake_y"){NULL}else{y[[i1]]})]))){
-tempo.removed.row.nb <- unlist(lapply(lapply(c(data1[[i1]][c(if(x[[i1]] == "fake_x"){NULL}else{x[[i1]]}, if(y[[i1]] == "fake_y"){NULL}else{y[[i1]]})]), FUN = is.na), FUN = which))
-removed.row.nb[[i1]] <- c(removed.row.nb[[i1]], tempo.removed.row.nb)
-# report of removed rows will be performed at the very end
-data1[[i1]] <- data1[[i1]][-tempo.removed.row.nb, ]
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": NA DETECTED IN COLUMN ", if(x[[i1]] == "fake_x"){""}else{ifelse(length(x) == 1, "x", paste0("x NUMBER ", i1))}, if(x[[i1]] != "fake_x" & y[[i1]] != "fake_y"){" AND "}, if(y[[i1]] == "fake_y"){""}else{ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1))}, " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ". CORRESPONDING ROWS HAVE BEEN REMOVED (SEE $removed.row.nb AND $removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# end na detection and removal (done now to be sure of the correct length of categ)
-tempo <- fun_check(data = data1[[i1]][, x[[i1]]], data.name = ifelse(length(x) == 1, "x OF data1", paste0("x NUMBER ", i1, " OF data1 NUMBER ", i1)), class = "vector", mode = "numeric", na.contain = ifelse(x[[i1]] == "fake_x", TRUE, FALSE), fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = data1[[i1]][, y[[i1]]], data.name = ifelse(length(y) == 1, "y OF data1", paste0("y NUMBER ", i1, " OF data1 NUMBER ", i1)), class = "vector", mode = "numeric", na.contain = ifelse(y[[i1]] == "fake_y", TRUE, FALSE), fun.name = function.name) ; eval(ee)
-if(( ! is.null(categ)) & ( ! is.null(categ[[i1]]))){ # if categ[[i1]] = NULL, fake_categ will be created later on
-tempo <- fun_check(data = categ[[i1]], data.name = ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)),, class = "vector", mode = "character", length = 1, fun.name = function.name)
-if( ! (categ[[i1]] %in% names(data1[[i1]]))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-# na detection and removal (done now to be sure of the correct length of categ)
-if(any(is.na(data1[[i1]][, categ[[i1]]]))){
-tempo.removed.row.nb <- unlist(lapply(lapply(c(data1[[i1]][categ[[i1]]]), FUN = is.na), FUN = which))
-removed.row.nb[[i1]] <- c(removed.row.nb[[i1]], tempo.removed.row.nb)
-# report of removed rows will be performed at the very end
-data1[[i1]] <- data1[[i1]][-tempo.removed.row.nb, ]
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": IN ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", THE CATEGORY COLUMN:\n", paste(categ[[i1]], collapse = " "), "\nCONTAINS NA")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# end na detection and removal (done now to be sure of the correct length of categ)
-tempo1 <- fun_check(data = data1[[i1]][, categ[[i1]]], data.name = ifelse(length(categ) == 1, "categ OF data1", paste0("categ NUMBER ", i1, " OF data1 NUMBER ", i1)), class = "vector", mode = "character", na.contain = FALSE, fun.name = function.name, print = FALSE)
-tempo2 <- fun_check(data = data1[[i1]][, categ[[i1]]], data.name = ifelse(length(categ) == 1, "categ OF data1", paste0("categ NUMBER ", i1, " OF data1 NUMBER ", i1)), class = "factor", na.contain = FALSE, fun.name = function.name, print = FALSE)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(categ) == 1, "categ OF data1", paste0("categ NUMBER ", i1, " OF data1 NUMBER ", i1)), " MUST BE A FACTOR OR CHARACTER VECTOR\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else if(tempo1$problem == FALSE){
-data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": IN ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", THE CHARACTER COLUMN HAS BEEN CONVERTED TO FACTOR")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-
-}
-# OK: all the non NULL categ columns of data1 are factors from here
-if(geom[[i1]] == "geom_vline" | geom[[i1]] == "geom_hline"){
-if(length(unique(data1[[i1]][, categ[[i1]]])) != nrow(data1[[i1]])){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(geom) == 1, "geom OF data1", paste0("geom NUMBER ", i1, " OF data1 NUMBER ", i1)), " ARGUMENT IS ", geom[[i1]], ", MEANING THAT ", ifelse(length(categ) == 1, "categ OF data1", paste0("categ NUMBER ", i1, " OF data1 NUMBER ", i1)), " MUST HAVE A DIFFERENT CLASS PER LINE OF data1 (ONE x VALUE PER CLASS)\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-}else if(( ! is.null(categ)) & is.null(categ[[i1]])){ # if categ[[i1]] = NULL, fake_categ will be created. BEWARE: is.null(categ[[i1]]) means no legend display (see above), because categ has not been precised. This also means a single color for data1[[i1]]
-if(length(color[[i1]]) > 1){ # 0 means is.null(color[[i1]]) and 1 is ok -> single color for data1[[i1]]
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": NULL ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " ARGUMENT BUT CORRESPONDING COLORS IN ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " HAS LENGTH OVER 1\n", paste(color[[i1]], collapse = " "), "\nWHICH IS NOT COMPATIBLE WITH NULL CATEG -> COLOR RESET TO A SINGLE COLOR")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-color[[i1]] <- NULL # will provide a single color below
-}
-categ[[i1]] <- "fake_categ"
-data1[[i1]] <- cbind(data1[[i1]], fake_categ = "")
-# inactivated because give a different color to different "Line_" categ while a single color for all the data1[[i1]] required. Thus, put back after the color management
-# if(geom[[i1]] == "geom_hline" | geom[[i1]] == "geom_vline"){
-# data1[[i1]][, "fake_categ"] <- paste0("Line_", 1:nrow(data1[[i1]]))
-# }else{
-data1[[i1]][, "fake_categ"] <- data1[[i1]][, "fake_categ"] # as.numeric("") create a vector of NA but class numeric
-# }
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": NULL ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " ARGUMENT -> FAKE COLUMN ADDED TO DATA FRAME ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", NAMED \"fake_categ\" FOR FINAL DRAWING")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(legend.name[[i1]])){
-tempo <- fun_check(data = legend.name[[i1]], data.name = ifelse(length(legend.name) == 1, "legend.name", paste0("legend.name NUMBER ", i1)),, class = "vector", mode = "character", length = 1, fun.name = function.name)
-}
-if( ! is.null(color)){ # if color is NULL, will be filled later on
-# check the nature of color
-if(is.null(color[[i1]])){
-compart.null.color <- compart.null.color + 1
-color[[i1]] <- grey(compart.null.color / 8) # cannot be more than 7 overlays. Thus 7 different greys. 8/8 is excluded because white dots
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": NULL COLOR IN ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", SINGLE COLOR ", paste(color[[i1]], collapse = " "), " HAS BEEN ATTRIBUTED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-tempo1 <- fun_check(data = color[[i1]], data.name = ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name, print = FALSE)
-tempo2 <- fun_check(data = color[[i1]], data.name = ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), class = "factor", na.contain = TRUE, fun.name = function.name, print = FALSE)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " MUST BE A FACTOR OR CHARACTER VECTOR OR INTEGER VECTOR\n\n================\n\n") # integer possible because dealt above
-stop(tempo.cat, call. = FALSE)
-}else if( ! (all(color[[i1]] %in% colors() | grepl(pattern = "^#", color[[i1]])))){ # check that all strings of low.color start by #
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors(): ", paste(unique(color[[i1]]), collapse = " "), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-if(any(is.na(color[[i1]]))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": IN ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", THE COLORS:\n", paste(unique(color[[i1]]), collapse = " "), "\nCONTAINS 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(categ) & length(color[[i1]]) != 1){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT MUST BE A SINGLE COLOR IF categ IS NULL\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else if( ! is.null(categ)){
-# No problem of NA management by ggplot2 because already removed
-if(categ[[i1]] == "fake_categ" & length(color[[i1]]) != 1){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT MUST BE A SINGLE COLOR IF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IS NULL\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else if(length(color[[i1]]) == length(unique(data1[[i1]][, categ[[i1]]]))){ # here length(color) is equal to the different number of categ
-data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": IN ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", THE FOLLOWING COLORS:\n", paste(color[[i1]], collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else if(length(color[[i1]]) == length(data1[[i1]][, categ[[i1]]])){# here length(color) is equal to nrow(data1[[i1]]) -> Modif to have length(color) equal to the different number of categ (length(color) == length(levels(data1[[i1]][, categ[[i1]]])))
-data1[[i1]] <- cbind(data1[[i1]], color = color[[i1]])
-tempo.check <- unique(data1[[i1]][ , c(categ[[i1]], "color")])
-if( ! (nrow(data1[[i1]]) == length(color[[i1]]) & nrow(tempo.check) == length(unique(data1[[i1]][ , categ[[i1]]])))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT HAS THE LENGTH OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), " COLUMN VALUES\nBUT IS INCORRECTLY ASSOCIATED TO EACH CLASS OF THIS categ:\n", paste(unique(mapply(FUN = "paste", data1[[i1]][ ,categ[[i1]]], data1[[i1]][ ,"color"])), collapse = "\n"), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
-color[[i1]] <- unique(color[[i1]][order(data1[[i1]][, categ[[i1]]])]) # Modif to have length(color) equal to the different number of categ (length(color) == length(levels(data1[[i1]][, categ[[i1]]])))
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count, ") FROM FUNCTION ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT HAS THE LENGTH OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), " COLUMN VALUES\nCOLORS HAVE BEEN RESPECTIVELY ASSOCIATED TO EACH CLASS OF categ AS:\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "), "\n", paste(color[[i1]], collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else if(length(color[[i1]]) == 1){
-data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
-color[[i1]] <- rep(color[[i1]], length(levels(data1[[i1]][, categ[[i1]]])))
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": IN ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", COLOR HAS LENGTH 1 MEANING THAT ALL THE DIFFERENT CLASSES OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), "\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "), "\nWILL HAVE THE SAME COLOR\n", paste(color[[i1]], collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else{
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT MUST BE (1) LENGTH 1, OR (2) THE LENGTH OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), " COLUMN VALUES, OR (3) THE LENGTH OF THE CLASSES IN THIS COLUMN. HERE IT IS COLOR LENGTH ", length(color[[i1]]), " VERSUS CATEG LENGTH ", length(data1[[i1]][, categ[[i1]]]), " AND CATEG CLASS LENGTH ", length(unique(data1[[i1]][, categ[[i1]]])), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-}
-if((geom[[i1]] == "geom_hline" | geom[[i1]] == "geom_vline") & ! is.null(categ[[i1]])){ # add here after the color management, to deal with the different lines to plot inside any data[[i1]]
-if(categ[[i1]] == "fake_categ"){
-data1[[i1]][, "fake_categ"] <- paste0("Line_", 1:nrow(data1[[i1]]))
-}
-}
-tempo <- fun_check(data = alpha[[i1]], data.name = ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-}
-if(length(data1) > 1){
-if(length(unique(unlist(x))) > 1){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": THE x ARGUMENT DOES NOT CONTAIN IDENTICAL COLUMN NAMES:\n", paste(unlist(x), collapse = " "), "\nX-AXIS OVERLAYING DIFFERENT VARIABLES?")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-if(length(data1) > 1){
-if(length(unique(unlist(y))) > 1){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": THE y ARGUMENT DOES NOT CONTAIN IDENTICAL COLUMN NAMES:\n", paste(unlist(y), collapse = " "), "\nY-AXIS OVERLAYING DIFFERENT VARIABLES?")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-if(sum(geom %in% "geom_point") > 3){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": geom ARGUMENT CANNOT HAVE MORE THAN THREE \"geom_point\" ELEMENTS\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else if(length(geom) - sum(geom %in% "geom_point") > 3){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": geom ARGUMENT CANNOT HAVE MORE THAN THREE LINE ELEMENTS\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-if(x.log != "no"){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": x.log ARGUMENT SET TO ", x.log, ".\nVALUES FROM THE x ARGUMENT COLUMN OF THE data1 DATA FRAME MUST BE ALREADY ", toupper(x.log), " TRANSFORMED, AS THE x.log ARGUMENT JUST MODIFIES THE AXIS SCALE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-if( ! is.null(x.lim)){
-if(any(x.lim <= 0)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": x.lim ARGUMENT CAN SPAN ZERO OR NEGATIVE VALUES IF x.log ARGUMENT IS SET TO ", x.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(x.log == "log10"){10^x.lim}else{2^x.lim}))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": x.lim ARGUMENT RETURNS INF WITH THE x.log ARGUMENT SET TO ", x.log, "\nAS SCALE COMPUTATION IS ", ifelse(x.log == "log10", 10, 2), "^x.lim:\n", paste(ifelse(x.log == "log10", 10, 2)^x.lim, collapse = " "), "\nARE YOU SURE THAT x.lim ARGUMENT HAS BEEN SPECIFIED WITH VALUES ALREADY IN LOG SCALE?\n", paste(x.lim, collapse = " "), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-}
-if(y.log != "no"){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": 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,") FROM FUNCTION ", function.name, ": 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("\n\n================\n\nERROR 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 = " "), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-}
-if( ! is.null(add)){
-if( ! grepl(pattern = "^\\+", add)){ # check that the add string start by +
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": add ARGUMENT MUST START WITH \"+\": ", paste(unique(add), collapse = " "), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else if( ! grepl(pattern = "ggplot2::", add)){ #
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": add ARGUMENT MUST CONTAIN \"ggplot2::\" IN FRONT OF EACH GGPLOT2 FUNCTION: ", paste(unique(add), collapse = " "), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else if( ! grepl(pattern = ")$", add)){ # check that the add string finished by )
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": add ARGUMENT MUST FINISH BY \")\": ", paste(unique(add), collapse = " "), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-# end second round of argument checking
-# end second round of checking and data preparation
-
-
-
-
-
-# package checking
-fun_pack(req.package = c("ggplot2", "gridExtra"), lib.path = lib.path)
-# packages Cairo and grid tested by fun_gg_point_rast()
-# end package checking
-
-
-# internal functions
-get_legend_fun <- function(myggplot, function.name = function.name){ # from https://stackoverflow.com/questions/12539348/ggplot-separate-legend-and-plot
-pdf(file = NULL)
-tmp <- ggplot2::ggplot_gtable(myggplot)
-# BEWARE with ggplot_gtable : open a blanck device https://stackoverflow.com/questions/17012518/why-does-this-r-ggplot2-code-bring-up-a-blank-display-device
-invisible(dev.off())
-leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
-if(length(leg) == 0){
-tempo.cat <- paste0("\n\n============\n\nERROR IN get_legend_fun() OF ", function.name, ": CODE INCONSISTENCY XX: length of leg object is null. Function get_legend_fun() should not be used\n\n============\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-legend <- tmp$grobs[[leg]]
-return(legend)
-}
-}
-# end internal functions
-
-
-
-# main code
-# axes management
-if(is.null(x.lim)){
-if(any(unlist(mapply(FUN = "[[", data1, x, SIMPLIFY = FALSE)) %in% c(Inf, -Inf))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": THE x COLUMN IN data1 CONTAINS -Inf OR Inf VALUES THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-x.lim <- suppressWarnings(range(unlist(mapply(FUN = "[[", data1, x, SIMPLIFY = FALSE)), 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. x.lim added here. If NULL, ok if x argument has values
-if(suppressWarnings(all(x.lim %in% c(Inf, -Inf)))){
-if(all(unlist(geom) == "geom_hline")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, " NOT POSSIBLE TO ONLY DRAW geom_hline KIND OF LINES IF x.lim ARGUMENT IS SET TO NULL, SINCE NO X-AXIS DEFINED (", ifelse(length(x) == 1, "x", paste0("x NUMBER ", i1)), " ARGUMENT MUST BE NULL FOR THESE KIND OF LINES)\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, " x.lim ARGUMENT MADE OF NA, -Inf OR Inf ONLY: ", paste(x.lim, collapse = " "), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-}
-x.lim.order <- order(x.lim) # to deal with inverse axis
-# print(x.lim.order)
-x.lim <- sort(x.lim)
-x.lim[1] <- x.lim[1] - abs(x.lim[2] - x.lim[1]) * ifelse(diff(x.lim.order) > 0, x.right.extra.margin, x.left.extra.margin) # diff(x.lim.order) > 0 means not inversed axis
-x.lim[2] <- x.lim[2] + abs(x.lim[2] - x.lim[1]) * ifelse(diff(x.lim.order) > 0, x.left.extra.margin, x.right.extra.margin) # diff(x.lim.order) > 0 means not inversed axis
-if(x.include.zero == TRUE){ # no need to check x.log != "no" because done before
-x.lim <- range(c(x.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
-}
-x.lim <- x.lim[x.lim.order]
-if(any(is.na(x.lim))){
-tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 3\n\n============\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-if(is.null(y.lim)){
-if(any(unlist(mapply(FUN = "[[", data1, y, SIMPLIFY = FALSE)) %in% c(Inf, -Inf))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": THE y COLUMN IN data1 CONTAINS -Inf OR Inf VALUES 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 <- suppressWarnings(range(unlist(mapply(FUN = "[[", data1, y, SIMPLIFY = FALSE)), 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 added here. If NULL, ok if y argument has values
-if(suppressWarnings(all(y.lim %in% c(Inf, -Inf)))){ # happen when y is only NULL
-if(all(unlist(geom) == "geom_vline")){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, " NOT POSSIBLE TO ONLY DRAW geom_vline KIND OF LINES IF y.lim ARGUMENT IS SET TO NULL, SINCE NO Y-AXIS DEFINED (", ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), " ARGUMENT MUST BE NULL FOR THESE KIND OF LINES)\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else{
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, " y.lim ARGUMENT MADE OF NA, -Inf OR Inf ONLY: ", paste(y.lim, collapse = " "), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-}
-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 means 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 means 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\nERROR IN ", function.name, ": CODE INCONSISTENCY 4\n\n============\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-# end axes management
-
-
-
-
-# create a fake categ if NULL to deal with legend display
-if(is.null(categ)){
-categ <- vector("list", length(data1))
-categ[] <- "fake_categ"
-for(i2 in 1:length(data1)){
-data1[[i2]] <- cbind(data1[[i2]], fake_categ = "")
-if(geom[[i2]] == "geom_hline" | geom[[i2]] == "geom_vline"){
-data1[[i2]][, "fake_categ"] <- paste0("Line_", 1:nrow(data1[[i2]]))
-}
-}
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": NULL categ ARGUMENT -> FAKE COLUMN ADDED TO EACH DATA FRAME IN data1, NAMED \"fake_categ\" AND FILLED WITH \"\"")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# end create a fake categ if NULL to deal with legend display
-
-
-
-
-# vector of color with length as in data1
-if(is.null(color)){
-color <- vector("list", length(data1))
-length.categ.list <- lapply(lapply(mapply(FUN = "[[", data1, categ, SIMPLIFY = FALSE), FUN = unique), FUN = function(x){length(x[ ! is.na(x)])})
-length.categ.list[sapply(categ, FUN = "==", "fake_categ")] <- 1 # when is.null(color), a single color for all the dots or lines of data[[i1]] that contain "fake_categ" category
-total.categ.length <- sum(unlist(length.categ.list), na.rm = TRUE)
-tempo.color <- fun_gg_palette(total.categ.length)
-tempo.count <- 0
-for(i3 in 1:length(data1)){
-color[[i3]] <- tempo.color[(1:length.categ.list[[i3]]) + tempo.count]
-tempo.count <- tempo.count + length.categ.list[[i3]]
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": NULL color ARGUMENT -> COLORS RESPECTIVELY ATTRIBUTED TO EACH CLASS OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i3)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i3)), ":\n", paste(unlist(color), collapse = " "), "\n", paste(names(data1), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end vector of color with length as in data1
-
-
-
-
-# last check
-for(i1 in 1:length(data1)){
-if(categ[[i1]] != "fake_categ" & length(color[[i1]]) != length(unique(data1[[i1]][, categ[[i1]]]))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, " LAST CHECK: ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT MUST HAVE THE LENGTH OF LEVELS OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), "\nHERE IT IS COLOR LENGTH ", length(color[[i1]]), " VERSUS CATEG LEVELS LENGTH ", length(unique(data1[[i1]][, categ[[i1]]])), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}else if(categ[[i1]] == "fake_categ" & length(color[[i1]]) != 1){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, " LAST CHECK: ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT MUST HAVE LENGTH 1 WHEN ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IS NULL\nHERE IT IS COLOR LENGTH ", length(color[[i1]]), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-# end last check
-
-
-
-
-
-# conversion of geom_hline and geom_vline
-for(i1 in 1:length(data1)){
-if(geom[[i1]] == "geom_hline" | geom[[i1]] == "geom_vline"){
-final.data.frame <- data.frame()
-for(i3 in 1:nrow(data1[[i1]])){
-tempo.data.frame <- rbind(data1[[i1]][i3, ], data1[[i1]][i3, ])
-if(geom[[i1]] == "geom_hline"){
-tempo.data.frame[, x[[i1]]] <- x.lim
-}else if(geom[[i1]] == "geom_vline"){
-tempo.data.frame[, y[[i1]]] <- y.lim
-}else{
-tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 5\n\n============\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-# 3 lines below inactivated because I put that above
-# if(is.null(categ[[i1]])){
-# data1[, "fake_categ"] <- paste0("Line_", i3)
-# }
-final.data.frame <- rbind(final.data.frame, tempo.data.frame)
-}
-data1[[i1]] <- final.data.frame
-geom[[i1]] <- "geom_line"
-if(length(color[[i1]]) == 1){
-color[[i1]] <- rep(color[[i1]], length(unique(data1[[i1]][ , categ[[i1]]])))
-}else if(length(color[[i1]]) != length(unique(data1[[i1]][ , categ[[i1]]]))){
-tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, " geom_hline AND geom_vline CONVERSION TO FIT THE XLIM AND YLIM LIMITS OF THE DATA: ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT MUST HAVE THE LENGTH OF LEVELS OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), "\nHERE IT IS COLOR LENGTH ", length(color[[i1]]), " VERSUS CATEG LEVELS LENGTH ", length(unique(data1[[i1]][, categ[[i1]]])), "\n\n================\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-}
-}
-# end conversion of geom_hline and geom_vline
-
-
-
-
-# kind of geom_point (vectorial or raster)
-scatter.kind <- vector("list", length = length(data1)) # list of same length as data1, that will be used to use either ggplot2::geom_point() (vectorial dot layer) or fun_gg_point_rast() (raster dot layer)
-fix.ratio <- FALSE
-if(is.null(raster.threshold)){
-if(raster == TRUE){
-scatter.kind[] <- "fun_gg_point_rast" # not important to fill everything: will be only used when geom == "geom_point"
-fix.ratio <- TRUE
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": RASTER PLOT GENERATED -> ASPECT RATIO OF THE PLOT REGION SET BY THE raster.ratio ARGUMENT (", fun_round(raster.ratio, 2), ") TO AVOID A BUG OF ELLIPSOID DOT DRAWING")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else{
-scatter.kind[] <- "ggplot2::geom_point"
-}
-}else{
-for(i2 in 1:length(data1)){
-if(geom[[i2]] == "geom_point"){
-if(nrow(data1[[i2]]) <= raster.threshold){
-scatter.kind[[i2]] <- "ggplot2::geom_point"
-}else{
-scatter.kind[[i2]] <- "fun_gg_point_rast"
-fix.ratio <- TRUE
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i2)), " LAYER AS RASTER (NOT VECTORIAL)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-}
-if(any(unlist(scatter.kind) == "fun_gg_point_rast")){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": RASTER PLOT GENERATED -> ASPECT RATIO OF THE PLOT REGION SET BY THE raster.ratio ARGUMENT (", fun_round(raster.ratio, 2), ") TO AVOID A BUG OF ELLIPSOID DOT DRAWING")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end kind of geom_point (vectorial or raster)
-
-
-
-
-# no need loop 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)){x[[1]]}else{x.lab}))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ylab(if(is.null(y.lab)){y[[1]]}else{y.lab}))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(title))
-# text angle management
-x.tempo.just <- fun_gg_just(angle = x.text.angle, axis = "x")
-y.tempo.just <- fun_gg_just(angle = y.text.angle, axis = "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,") FROM FUNCTION ", function.name, ": \"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.
-\nIT IS RECOMMENDED TO USE \"+ theme(aspect.ratio = raster.ratio)\" IF RASTER MODE IS ACTIVATED")
-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 several times theme(). 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
-legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
-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 = ggplot2::element_line(colour = "grey75"),
-panel.grid.major.y = ggplot2::element_line(colour = "grey75"),
-axis.text.x = ggplot2::element_text(angle = x.tempo.just$angle, hjust = x.tempo.just$hjust, vjust = x.tempo.just$vjust),
-axis.text.y = ggplot2::element_text(angle = y.tempo.just$angle, hjust = y.tempo.just$hjust, vjust = y.tempo.just$vjust), 
-aspect.ratio = if(fix.ratio == TRUE){raster.ratio}else{NULL} # for raster
-))
-}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), 
-legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
-axis.line.y.left = ggplot2::element_line(colour = "black"), 
-axis.line.x.bottom = ggplot2::element_line(colour = "black"), 
-axis.text.x = ggplot2::element_text(angle = x.tempo.just$angle, hjust = x.tempo.just$hjust, vjust = x.tempo.just$vjust),
-axis.text.y = ggplot2::element_text(angle = y.tempo.just$angle, hjust = y.tempo.just$hjust, vjust = y.tempo.just$vjust), 
-aspect.ratio = if(fix.ratio == TRUE){raster.ratio}else{NULL} # for raster
-))
-}
-}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), 
-legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
-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 = ggplot2::element_text(angle = x.tempo.just$angle, hjust = x.tempo.just$hjust, vjust = x.tempo.just$vjust),
-axis.text.y = ggplot2::element_text(angle = y.tempo.just$angle, hjust = y.tempo.just$hjust, vjust = y.tempo.just$vjust), 
-aspect.ratio = if(fix.ratio == TRUE){raster.ratio}else{NULL} # for raster
-# do not work -> legend.position = "none" # to remove the legend completely: https://www.datanovia.com/en/blog/how-to-remove-legend-from-a-ggplot/
-))
-}
-# end no need loop part
-
-
-
-# loop part
-point.count <- 0
-line.count <- 0
-lg.order <- vector(mode = "list", length = 6) # order of the legend
-lg.order <- lapply(lg.order, as.numeric) # order of the legend
-lg.color <- vector(mode = "list", length = 6) # color of the legend
-lg.alpha <- vector(mode = "list", length = 6) # order of the legend
-lg.alpha <- lapply(lg.alpha, as.numeric) # alpha of the legend
-for(i1 in 1:length(data1)){
-if(geom[[i1]] == "geom_point"){
-point.count <- point.count + 1
-if(point.count == 1){
-fin.lg.disp[[1]] <- legend.disp[[point.count + line.count]]
-lg.order[[1]] <- point.count + line.count
-lg.color[[1]] <- color[[i1]]
-lg.alpha[[1]] <- alpha[[i1]]
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = scatter.kind[[i1]]))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], fill = categ[[i1]]), size = dot.size, color = color[[i1]][i5], alpha = alpha[[i1]])) # beware: a single color allowed for color argument  outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_fill_manual(name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = as.character(color[[i1]]), guide = ggplot2::guide_legend(override.aes = list(colour = color[[i1]], linetype = 0)))) # values are the values of fill. order determines the order in the legend
-}
-if(point.count == 2){
-fin.lg.disp[[2]] <- legend.disp[[point.count + line.count]]
-lg.order[[2]] <- point.count + line.count
-lg.color[[2]] <- color[[i1]]
-lg.alpha[[2]] <- alpha[[i1]]
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = scatter.kind[[i1]]))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], shape = categ[[i1]]), size = dot.size, color = color[[i1]][i5], alpha = alpha[[i1]])) # beware: a single color allowed for color argument  outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_shape_manual(name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(19, length(color[[i1]])), guide = ggplot2::guide_legend(override.aes = list(colour = color[[i1]], linetype = 0)))) # values are the values of shape
-}
-if(point.count == 3){
-fin.lg.disp[[3]] <- legend.disp[[point.count + line.count]]
-lg.order[[3]] <- point.count + line.count
-lg.color[[3]] <- color[[i1]]
-lg.alpha[[3]] <- alpha[[i1]]
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = scatter.kind[[i1]]))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], stroke = categ[[i1]]), size = dot.size, color = color[[i1]][i5], alpha = alpha[[i1]])) # beware: a single color allowed for color argument  outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "stroke", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(0.5, length(color[[i1]])), guide = ggplot2::guide_legend(override.aes = list(colour = color[[i1]], linetype = 0)))) # values are the values of stroke
-}
-}else{
-line.count <- line.count + 1
-if(line.count == 1){
-fin.lg.disp[[4]] <- legend.disp[[point.count + line.count]]
-lg.order[[4]] <- point.count + line.count
-lg.color[[4]] <- color[[i1]]
-if(plot == TRUE & fin.lg.disp[[4]] == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list()) == 0 & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-lg.alpha[[4]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
-}else{
-lg.alpha[[4]] <- alpha[[i1]]
-}
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste("ggplot2::", geom[[i1]], sep ="")))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], linetype = categ[[i1]]), color = color[[i1]][i5], size = line.size, lineend = "round", alpha = alpha[[i1]])) # beware: a single color allowed for color argument  outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "linetype", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(1, length(color[[i1]])), guide = ggplot2::guide_legend(override.aes = list(colour = color[[i1]], shape = NA)))) # values are the values of linetype. 1 means solid. Regarding the alpha bug, I have tried different things without success: alpha in guide alone, in geom alone, in both, with different values 
-}
-if(line.count == 2){
-fin.lg.disp[[5]] <- legend.disp[[point.count + line.count]]
-lg.order[[5]] <- point.count + line.count
-lg.color[[5]] <- color[[i1]]
-if(plot == TRUE & fin.lg.disp[[5]] == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list()) == 0 & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-lg.alpha[[5]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
-}else{
-lg.alpha[[5]] <- alpha[[i1]]
-}
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste("ggplot2::", geom[[i1]], sep ="")))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], alpha = categ[[i1]]), color = color[[i1]][i5], size = line.size, lineend = "round")) # beware: a single color allowed for color argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "alpha", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(alpha[[i1]], length(color[[i1]])), guide = ggplot2::guide_legend(override.aes = list(colour = color[[i1]], shape = NA)))) # values are the values of linetype. 1 means solid. Regarding the alpha bug, I have tried different things without success: alpha in guide alone, in geom alone, in both, with different values 
-}
-if(line.count == 3){
-fin.lg.disp[[6]] <- legend.disp[[point.count + line.count]]
-lg.order[[6]] <- point.count + line.count
-lg.color[[6]] <- color[[i1]]
-if(plot == TRUE & fin.lg.disp[[6]] == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list()) == 0 & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-lg.alpha[[6]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
-}else{
-lg.alpha[[6]] <- alpha[[i1]]
-}
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste("ggplot2::", geom[[i1]], sep ="")))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], size = categ[[i1]]), color = color[[i1]][i5], alpha = alpha[[i1]], lineend = "round")) # beware: a single color allowed for color argument  outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "size", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(line.size, length(color[[i1]])), guide = ggplot2::guide_legend(override.aes = list(colour = color[[i1]], shape = NA)))) # values are the values of linetype. 1 means solid. Regarding the alpha bug, I have tried different things without success: alpha in guide alone, in geom alone, in both, with different values 
-}
-}
-}
-# end loop part
-
-
-
-
-# legend display
-tempo.legend.final <- ggplot2::guides(fill = if(fin.lg.disp[[1]] == TRUE){ggplot2::guide_legend(order = lg.order[[1]], override.aes = list(alpha = lg.alpha[[1]], color = lg.color[[1]]))}else{FALSE}, shape = if(fin.lg.disp[[2]] == TRUE){ggplot2::guide_legend(order = lg.order[[2]], override.aes = list(alpha = lg.alpha[[2]], color = lg.color[[2]]))}else{FALSE}, stroke = if(fin.lg.disp[[3]] == TRUE){ggplot2::guide_legend(order = lg.order[[3]], override.aes = list(alpha = lg.alpha[[2]], color = lg.color[[3]]))}else{FALSE}, linetype = if(fin.lg.disp[[4]] == TRUE){ggplot2::guide_legend(order = lg.order[[4]], override.aes = list(alpha = lg.alpha[[4]], color = lg.color[[4]]))}else{FALSE}, alpha = if(fin.lg.disp[[5]] == TRUE){ggplot2::guide_legend(order = lg.order[[5]], override.aes = list(alpha = lg.alpha[[5]], color = lg.color[[5]]))}else{FALSE}, size = if(fin.lg.disp[[6]] == TRUE){ggplot2::guide_legend(order = lg.order[[6]], override.aes = list(alpha = lg.alpha[[6]], color = lg.color[[6]]))}else{FALSE}) # clip = "off" to have secondary ticks outside plot region does not work
-if(legend.show == TRUE & any(unlist(legend.disp)) == TRUE & ! is.null(legend.width)){
-tempo.graph.info <- ggplot2::ggplot_build(eval(parse(text = paste0(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), ' + tempo.legend.final')))) # will be recovered later again, when ylim will be considered
-legend.final <- get_legend_fun(tempo.graph.info) # get legend
-fin.lg.disp[] <- FALSE # remove all the legends
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::guides(fill = if(fin.lg.disp[[1]] == TRUE){ggplot2::guide_legend(order = lg.order[[1]], override.aes = list(alpha = lg.alpha[[1]], color = lg.color[[1]]))}else{FALSE}, shape = if(fin.lg.disp[[2]] == TRUE){ggplot2::guide_legend(order = lg.order[[2]], override.aes = list(alpha = lg.alpha[[2]], color = lg.color[[2]]))}else{FALSE}, stroke = if(fin.lg.disp[[3]] == TRUE){ggplot2::guide_legend(order = lg.order[[3]], override.aes = list(alpha = lg.alpha[[2]], color = lg.color[[3]]))}else{FALSE}, linetype = if(fin.lg.disp[[4]] == TRUE){ggplot2::guide_legend(order = lg.order[[4]], override.aes = list(alpha = lg.alpha[[4]], color = lg.color[[4]]))}else{FALSE}, alpha = if(fin.lg.disp[[5]] == TRUE){ggplot2::guide_legend(order = lg.order[[5]], override.aes = list(alpha = lg.alpha[[5]], color = lg.color[[5]]))}else{FALSE}, size = if(fin.lg.disp[[6]] == TRUE){ggplot2::guide_legend(order = lg.order[[6]], override.aes = list(alpha = lg.alpha[[6]], color = lg.color[[6]]))}else{FALSE})) # without legend (added later)
-}else{
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), tempo.legend.final)
-}
-# end legend display
-
-
-
-
-
-# scale management
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_cartesian(xlim = x.lim, ylim = y.lim)) # clip = "off" to have secondary ticks outside plot region does not work
-# x-axis ticks and inv
-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 = x.lim, n = ifelse(is.null(x.tick.nb), length(tempo.coord$x.major_source), x.tick.nb))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_x_continuous(
-breaks = tempo.scale, 
-labels = if(x.log == "log10"){scales::trans_format("identity",  scales::math_format(10^.x))}else if(x.log == "log2"){scales::trans_format("identity",  scales::math_format(2^.x))}else if(x.log == "no"){ggplot2::waiver()}else{tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 6\n\n============\n\n") ; stop(tempo.cat, call. = FALSE)}, 
-expand = c(0, 0),
-limits = NA,
-trans = ifelse(diff(x.lim) < 0, "reverse", "identity") # equivalent to ggplot2::scale_x_reverse()
-))
-# end x-axis ticks and inv
-# y-axis ticks and inv
-# tempo.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$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))
-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\nERROR IN ", function.name, ": CODE INCONSISTENCY 7\n\n============\n\n") ; stop(tempo.cat, call. = FALSE)}, 
-expand = c(0, 0),
-limits = NA,
-trans = ifelse(diff(y.lim) < 0, "reverse", "identity") # equivalent to ggplot2::scale_y_reverse()
-))
-# end y-axis ticks and inv
-# x-axis 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]]
-x.lim.order <- order(x.lim) # to deal with inverse axis
-y.lim.order <- order(y.lim) # to deal with inverse axis
-# no secondary ticks for log2. Play with x.lim
-if(x.log == "log10"){
-y.range <- tempo.coord$y.range
-if(diff(y.lim.order) < 0){y.range <- -(y.range)}
-ini.scipen <- options()$scipen
-options(scipen = -1000) # force scientific format
-power10.exp <- as.integer(substring(text = 10^x.lim, first = (regexpr(pattern = "\\+|\\-", text = 10^x.lim)))) # recover the power of 10. Example recover 08 from 1e+08
-# print(x.lim)
-mantisse <- as.numeric(substr(x = 10^x.lim, start = 1, stop = (regexpr(pattern = "\\+|\\-", text = 10^x.lim) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
-options(scipen = ini.scipen) # restore the initial scientific penalty
-# print(power10.exp)
-tempo.tick.pos <- as.vector(outer(log10(2:10), 10^((power10.exp[1] - ifelse(diff(x.lim.order) > 0, 1, -1)):(power10.exp[2] + ifelse(diff(x.lim.order) > 0, 1, -1)))))
-tempo.tick.pos <- sort(tempo.tick.pos, decreasing = ifelse(diff(x.lim.order) > 0, FALSE, TRUE))
-tempo.tick.pos <- log10(tempo.tick.pos[tempo.tick.pos >= min(10^x.lim) & tempo.tick.pos <= max(10^x.lim)])
-if(any(is.na(tempo.tick.pos) | ! is.finite(tempo.tick.pos))){ 
-tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 8\n\n============\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-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 = y.range[1], yend = y.range[1] + diff(y.range) / 80))
-}else if(( ! is.null(x.inter.tick.nb)) & x.log == "no"){
-if(x.inter.tick.nb > 0){
-x.ticks.pos <- suppressWarnings(as.numeric(tempo.coord$x.labels)) # too difficult to predict the behavior of tempo.coord$x.major_source depending on x.lim neg or not, inv or not. Inv is respected
-if(any(is.na(x.ticks.pos))){
-tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 9\n\n============\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-y.range <- tempo.coord$y.range
-if(diff(y.lim.order) < 0){y.range <- -(y.range)}
-tick.dist <- mean(diff(x.ticks.pos), na.rm = TRUE)
-minor.tick.dist <- tick.dist / (x.inter.tick.nb + 1)
-minor.tick.pos <- seq(x.ticks.pos[1] - tick.dist, x.ticks.pos[length(x.ticks.pos)] + tick.dist, by = minor.tick.dist)
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", x = minor.tick.pos, xend = minor.tick.pos, y = y.range[1], yend = y.range[1] + diff(y.range) / 80))
-}
-}
-# end x-axis secondary ticks (after ggplot2::coord_cartesian() or ggplot2::coord_flip())
-# y-axis secondary ticks (after ggplot2::coord_cartesian() or ggplot2::coord_flip())
-# tempo.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$layout$panel_params[[1]]
-# no secondary ticks for log2. Play with y.lim
-if(y.log == "log10"){
-x.range <- tempo.coord$x.range
-if(diff(x.lim.order) < 0){x.range <- -(x.range)}
-ini.scipen <- options()$scipen
-options(scipen = -1000) # force scientific format
-power10.exp <- as.integer(substring(text = 10^y.lim, first = (regexpr(pattern = "\\+|\\-", text = 10^y.lim)))) # recover the power of 10. Example recover 08 from 1e+08
-mantisse <- as.numeric(substr(x = 10^y.lim, start = 1, stop = (regexpr(pattern = "\\+|\\-", text = 10^y.lim) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
-options(scipen = ini.scipen) # restore the initial scientific penalty
-tempo.tick.pos <- as.vector(outer(log10(2:10), 10^((power10.exp[1] - ifelse(diff(y.lim.order) > 0, 1, -1)):(power10.exp[2] + ifelse(diff(y.lim.order) > 0, 1, -1)))))
-tempo.tick.pos <- sort(tempo.tick.pos, decreasing = ifelse(diff(y.lim.order) > 0, FALSE, TRUE))
-tempo.tick.pos <- log10(tempo.tick.pos[tempo.tick.pos >= min(10^y.lim) & tempo.tick.pos <= max(10^y.lim)])
-if(any(is.na(tempo.tick.pos) | ! is.finite(tempo.tick.pos))){ 
-tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 10\n\n============\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", y = tempo.tick.pos, yend = tempo.tick.pos, x = x.range[1], xend = x.range[1] + diff(x.range) / 80))
-}else if(( ! is.null(y.inter.tick.nb)) & y.log == "no"){
-if(y.inter.tick.nb > 0){
-y.ticks.pos <- suppressWarnings(as.numeric(tempo.coord$y.labels)) # too difficult to predict the behavior of tempo.coord$y.major_source depending on y.lim neg or not, inv or not. Inv is respected
-if(any(is.na(y.ticks.pos))){
-tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 11\n\n============\n\n")
-stop(tempo.cat, call. = FALSE)
-}
-x.range <- tempo.coord$x.range
-if(diff(x.lim.order) < 0){x.range <- -(x.range)}
-tick.dist <- mean(diff(y.ticks.pos), na.rm = TRUE)
-minor.tick.dist <- tick.dist / (y.inter.tick.nb + 1)
-minor.tick.pos <- seq(y.ticks.pos[1] - tick.dist, y.ticks.pos[length(y.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 = x.range[1], xend = x.range[1] + diff(x.range) / 80))
-}
-}
-# end y-axis secondary ticks (after ggplot2::coord_cartesian() or ggplot2::coord_flip())
-# end scale management
-
-
-
-
-if(plot == TRUE){
-if(legend.show == TRUE & any(unlist(legend.disp)) == TRUE & ! is.null(legend.width)){ # not & any(unlist(fin.lg.disp)) == TRUE here because converted to FALSE
-suppressWarnings(gridExtra::grid.arrange(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "),if(is.null(add)){NULL}else{add}))), legend.final, ncol=2, widths=c(1, legend.width)))
-}else{
-suppressWarnings(print(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "),if(is.null(add)){NULL}else{add})))))
-}
-}else{
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": PLOT NOT SHOWN AS REQUESTED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-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 = " + "))))
-if(is.null(unlist(removed.row.nb))){
-removed.row.nb <- NULL
-removed.rows <- NULL
-}else{
-for(i3 in 1:length(data1)){
-if( ! is.null(removed.row.nb[[i3]])){
-removed.row.nb[[i3]] <- sort(removed.row.nb[[i3]])
-removed.rows[[i3]] <- data1.ini[[i3]][removed.row.nb[[i3]], ]
-}
-}
-}
-output <- list(data = output$data, removed.row.nb = removed.row.nb, removed.rows = removed.rows, axes = output$layout$panel_params[[1]], warn = paste0("\n", warn, "\n\n"))
-return(output)
-}
-}
-
-
-
diff --git a/cute_little_R_functions.docx b/cute_little_R_functions.docx
index 0bbf1a1df628543d47a84ccf878df8b6a30ccc48..2efd1a4be5f260b5dff66c004a06e3696156b094 100644
Binary files a/cute_little_R_functions.docx and b/cute_little_R_functions.docx differ