cute_little_R_functions.R 866 KB
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# kind: either "approx" (approximative), "strict" (strict) or "strict.cl" (strict clean). If "approx", use the scales::trans_breaks() function to provide an easy to read scale of approximately n ticks spanning the range of the lim argument. If "strict", cut the range of the lim argument into n + 1 equidistant part and return the n numbers at each boundary. This often generates numbers uneasy to read. If "strict.cl", provide an easy to read scale of exactly n ticks, but sometimes not completely spanning the range of the lim argument
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# lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
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# REQUIRED PACKAGES
# if kind = "approx":
# ggplot2
# scales
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# fun_round()
# RETURN
# a vector of numbers
# EXAMPLES
# approximate number of main ticks
# ymin = 2 ; ymax = 3.101 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "approx") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
# strict number of main ticks
# ymin = 2 ; ymax = 3.101 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "strict") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
# strict "clean" number of main ticks
# ymin = 2 ; ymax = 3.101 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "strict.cl") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
# approximate number of main ticks, scale inversion
# ymin = 3.101 ; ymax = 2 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "approx") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
# DEBUGGING
# n = 9 ; lim = c(2, 3.101) ; kind = "approx" ; lib.path = NULL # for function debugging
# n = 10 ; lim = c(1e-4, 1e6) ; kind = "approx" ; lib.path = NULL # for function debugging
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# end initial argument checking
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
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tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
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if(length(utils::find("fun_round", mode = "function")) == 0){
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tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_round() FUNCTION IS MISSING IN THE R ENVIRONMENT")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
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# end required function checking
# argument checking
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = n, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE & isTRUE(all.equal(n, 0))){ # isTRUE(all.equal(n, 0)) equivalent to n == 0 but deals with floats (approx ok)
tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT MUST BE A NON NULL AND POSITIVE INTEGER")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE) # 
}
tempo <- fun_check(data = lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE & all(diff(lim) == 0)){ # isTRUE(all.equal(diff(lim), rep(0, length(diff(lim))))) not used because we strictly need zero as a result
tempo.cat <- paste0("ERROR IN ", function.name, ": lim ARGUMENT HAS A NULL RANGE (2 IDENTICAL VALUES)")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}else if(tempo$problem == FALSE & any(lim %in% c(Inf, -Inf))){
tempo.cat <- paste0("ERROR IN ", function.name, ": lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
tempo <- fun_check(data = kind, options = c("approx", "strict", "strict.cl"), 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)
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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"))
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text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
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}
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if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# end argument checking with fun_check()
# 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 argument checking
# main code
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lim.rank <- rank(lim) # to deal with inverted axis
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lim <- sort(lim)
if(kind == "approx"){
# package checking
fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
fun_pack(req.package = c("scales"), lib.path = lib.path)
# end package checking
output <- ggplot2::ggplot_build(ggplot2::ggplot() + ggplot2::scale_y_continuous(
breaks = scales::trans_breaks(
trans = "identity", 
inv = "identity", 
n = n
), 
limits = lim
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))$layout$panel_params[[1]]$y$breaks # pretty() alone is not appropriate: tempo.pret <-  pretty(seq(lim[1] ,lim[2], length.out = n)) ; tempo.pret[tempo.pret > = lim[1] & tempo.pret < = lim[2]]. # in ggplot 3.3.0, tempo.coord$y.major_source replaced by tempo.coord$y$breaks
if( ! is.null(attributes(output))){ # layout$panel_params[[1]]$y$breaks can be characters (labels of the axis). In that case, it has attributes that corresponds to positions
output <- unlist(attributes(output))
}
output <- output[ ! is.na(output)]
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}else if(kind == "strict"){
output <- fun_round(seq(lim[1] ,lim[2], length.out = n), 2)
}else if(kind == "strict.cl"){
tempo.range <- diff(sort(lim))
tempo.max <- max(lim)
tempo.min <- min(lim)
mid <- tempo.min + (tempo.range/2) # middle of axis
tempo.inter <- tempo.range / (n + 1) # current interval between two ticks, between 0 and Inf
if(tempo.inter == 0){ # isTRUE(all.equal(tempo.inter, rep(0, length(tempo.inter)))) not used because we strictly need zero as a result
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tempo.cat <- paste0("ERROR IN ", function.name, ": THE INTERVAL BETWEEN TWO TICKS OF THE SCALE IS NULL. MODIFY THE lim OR n ARGUMENT")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
log10.abs.lim <- 200
log10.range <- (-log10.abs.lim):log10.abs.lim
log10.vec <- 10^log10.range
round.vec <- c(5, 4, 3, 2.5, 2, 1.25, 1)
dec.table <- outer(log10.vec, round.vec) # table containing the scale units (row: power of ten from -201 to +199, column: the 5, 2.5, 2, 1.25, 1 notches

 

# recover the number of leading zeros in tempo.inter
ini.scipen <- options()$scipen
options(scipen = -1000) # force scientific format
if(any(grepl(pattern = "\\+", x = tempo.inter))){ # tempo.inter > 1
power10.exp <- as.integer(substring(text = tempo.inter, first = (regexpr(pattern = "\\+", text = tempo.inter) + 1))) # recover the power of 10. Example recover 08 from 1e+08
mantisse <- as.numeric(substr(x = tempo.inter, start = 1, stop = (regexpr(pattern = "\\+", text = tempo.inter) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
}else if(any(grepl(pattern = "\\-", x = tempo.inter))){ # tempo.inter < 1
power10.exp <- as.integer(substring(text = tempo.inter, first = (regexpr(pattern = "\\-", text = tempo.inter)))) # recover the power of 10. Example recover 08 from 1e+08
mantisse <- as.numeric(substr(x = tempo.inter, start = 1, stop = (regexpr(pattern = "\\-", text = tempo.inter) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
}else{
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tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 1")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
tempo.scale <- dec.table[log10.range == power10.exp, ]
# new interval 
inter.select <- NULL
for(i1 in 1:length(tempo.scale)){
tempo.first.tick <- trunc((tempo.min + tempo.scale[i1]) / tempo.scale[i1]) * (tempo.scale[i1]) # this would be use to have a number not multiple of tempo.scale[i1]: ceiling(tempo.min) + tempo.scale[i1] * 10^power10.exp
tempo.last.tick <- tempo.first.tick + tempo.scale[i1] * (n - 1)
if((tempo.first.tick >= tempo.min) & (tempo.last.tick <= tempo.max)){
inter.select <- tempo.scale[i1]
break()
}
}
if(is.null(inter.select)){
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tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 2")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
options(scipen = ini.scipen) # restore the initial scientific penalty
# end new interval 
# centering the new scale 
tempo.mid <- trunc((mid + (-1:1) * inter.select) / inter.select) * inter.select # tempo middle tick closest to the middle axis
mid.tick <- tempo.mid[which.min(abs(tempo.mid - mid))]
if(isTRUE(all.equal(n, rep(1, length(n))))){ # isTRUE(all.equal(n, rep(1, length(n)))) is similar to n == 1 but deals with float
output <- mid.tick
}else if(isTRUE(all.equal(n, rep(2, length(n))))){ # isTRUE(all.equal(n, rep(0, length(n)))) is similar to n == 2 but deals with float
output <- mid.tick
tempo.min.dist <- mid.tick - inter.select - tempo.min
tempo.max.dist <- tempo.max - mid.tick + inter.select
if(tempo.min.dist <= tempo.max.dist){ # distance between lowest tick and bottom axis <= distance between highest tick and top axis. If yes, extra tick but at the top, otherwise at the bottom
output <- c(mid.tick, mid.tick + inter.select)
}else{
output <- c(mid.tick - inter.select, mid.tick)
}
}else if((n / 2 - trunc(n / 2)) > 0.1){ # > 0.1 to avoid floating point. Because result can only be 0 or 0.5. Thus, > 0.1 means odd number
output <- c(mid.tick - (trunc(n / 2):1) * inter.select, mid.tick, mid.tick + (1:trunc(n / 2)) * inter.select)
}else if((n / 2 - trunc(n / 2)) < 0.1){ # < 0.1 to avoid floating point. Because result can only be 0 or 0.5. Thus, < 0.1 means even number
tempo.min.dist <- mid.tick - trunc(n / 2) * inter.select - tempo.min
tempo.max.dist <- tempo.max - mid.tick + trunc(n / 2) * inter.select
if(tempo.min.dist <= tempo.max.dist){ # distance between lowest tick and bottom axis <= distance between highest tick and top axis. If yes, extra tick but at the bottom, otherwise at the top
output <- c(mid.tick - ((trunc(n / 2) - 1):1) * inter.select, mid.tick, mid.tick + (1:trunc(n / 2)) * inter.select)
}else{
output <- c(mid.tick - (trunc(n / 2):1) * inter.select, mid.tick, mid.tick + (1:(trunc(n / 2) - 1)) * inter.select)
}
}else{
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tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 3")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
# end centering the new scale 
# last check
if(min(output) < tempo.min){
output <- c(output[-1], max(output) + inter.select) # remove the lowest tick and add a tick at the top
}else if( max(output) > tempo.max){
output <- c(min(output) - inter.select, output[-length(output)])
}
if(min(output) < tempo.min | max(output) > tempo.max){
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tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 4")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
if(any(is.na(output))){
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tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 5 (NA GENERATION)")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
# end last check
}else{
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tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 6")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
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if(diff(lim.rank) < 0){
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output <- rev(output)
}
return(output)
}


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######## fun_inter_ticks() #### define coordinates of secondary ticks
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fun_inter_ticks <- function(lim, log = "log10", breaks = NULL, n = NULL, warn.print = TRUE){
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# AIM
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# define coordinates and values of secondary ticks
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# ARGUMENTS
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# lim: vector of 2 numbers indicating the limit range of the axis. Order of the 2 values matters (for inverted axis). If log argument is "log2" or "log10", values in lim must be already log transformed. Thus, negative or zero values are allowed
# log: either "log2" (values in the lim argument are log2 transformed) or "log10" (values in the lim argument are log10 transformed), or "no"
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# breaks: mandatory vector of numbers indicating the main ticks values/positions when log argument is "no". Ignored when log argument is "log2" or "log10"
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# n: number of secondary ticks between each main tick when log argument is "no". Ignored when log argument is "log2" or "log10"
# warn.print: logical. Print potential warning messages at the end of the execution? If FALSE, warning messages are never printed, but can still be recovered in the returned list
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# REQUIRED PACKAGES
# none
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# RETURN
# a list containing
# $log: value of the log argument used
# $coordinates: the coordinates of the secondary ticks on the axis, between the lim values
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# $values: the corresponding values associated to each coordinate (with log scale, 2^$values or 10^$values is equivalent to the labels of the axis)
# $warn: the potential warning messages. Use cat() for proper display. NULL if no warning
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# EXAMPLES
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# no log scale
# fun_inter_ticks(lim = c(-4,4), log = "no", breaks = c(-2, 0, 2), n = 3)
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# fun_inter_ticks(lim = c(10, 0), log = "no", breaks = c(10, 8, 6, 4, 2, 0), n = 4)
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# log2
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# fun_inter_ticks(lim = c(-4,4), log = "log2")
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# log10
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# fun_inter_ticks(lim = c(-2,3), log = "log10")
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# DEBUGGING
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# lim = c(2, 3.101) ; log = "no" ; breaks = NULL ; n = NULL ; warn.print = TRUE # for function debugging
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# lim = c(0, 26.5) ; log = "no" ; breaks = c(0, 10, 20) ; n = 3 # for function debugging
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# lim = c(10, 0); log = "no"; breaks = c(10, 8, 6, 4, 2, 0); n = 4 # for function debugging
# lim = c(-10, -20); log = "no"; breaks = c(-20, -15, -10); n = 4 # for function debugging
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# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
req.function <- c(
"fun_check"
)
for(i1 in req.function){
if(length(find(i1, mode = "function")) == 0){
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tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED ", i1, "() FUNCTION IS MISSING IN THE R ENVIRONMENT")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
}
# end required function checking
# argument primary checking
# arg with no default values
if(any(missing(lim))){
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tempo.cat <- paste0("ERROR IN ", function.name, "\nARGUMENT lim HAS NO DEFAULT VALUE AND REQUIRES ONE")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
# end arg with no default values
# using fun_check()
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(breaks)){
tempo <- fun_check(data = breaks, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
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}
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if( ! is.null(n)){
tempo <- fun_check(data = n, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
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}
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tempo <- fun_check(data = warn.print, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
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if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# end using fun_check()
# 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 argument primary checking
# second round of checking and data preparation
# dealing with NA
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if(any(is.na(lim)) | any(is.na(log)) | any(is.na(breaks)) | any(is.na(n)) | any(is.na(warn.print))){
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tempo.cat <- paste0("ERROR IN ", function.name, "\nNO ARGUMENT CAN HAVE NA VALUES")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
# end dealing with NA
# dealing with NULL
if(is.null(lim) | is.null(log)){
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tempo.cat <- paste0("ERROR IN ", function.name, "\nTHESE ARGUMENTS\nlim\nlog\nCANNOT BE NULL")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
# end dealing with NULL
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if(all(diff(lim) == 0)){ # isTRUE(all.equal(diff(lim), rep(0, length(diff(lim))))) not used because we strictly need zero as a result
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tempo.cat <- paste0("ERROR IN ", function.name, "\nlim ARGUMENT HAS A NULL RANGE (2 IDENTICAL VALUES): ", paste(lim, collapse = " "))
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}else if(any(lim %in% c(Inf, -Inf))){
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tempo.cat <- paste0("ERROR IN ", function.name, "\nlim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
if(log == "no" & is.null(breaks)){
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tempo.cat <- paste0("ERROR IN ", function.name, "\nbreaks ARGUMENT CANNOT BE NULL IF log ARGUMENT IS \"no\"")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
if( ! is.null(breaks)){
if(length(breaks) < 2){
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tempo.cat <- paste0("ERROR IN ", function.name, "\nbreaks ARGUMENT MUST HAVE 2 VALUES AT LEAST (OTHERWISE, INTER TICK POSITIONS CANNOT BE COMPUTED): ", paste(breaks, collapse = " "))
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
if( ! isTRUE(all.equal(diff(sort(breaks)), rep(diff(sort(breaks))[1], length(diff(sort(breaks))))))){ # isTRUE(all.equal(n, 0)) equivalent to n == 0 but deals with floats (approx ok)
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tempo.cat <- paste0("ERROR IN ", function.name, "\nbreaks ARGUMENT MUST HAVE EQUIDISTANT VALUES (OTHERWISE, EQUAL NUMBER OF INTER TICK BETWEEN MAIN TICKS CANNOT BE COMPUTED): ", paste(breaks, collapse = " "))
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
}
if( ! is.null(n)){
if(n <= 0){
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tempo.cat <- paste0("ERROR IN ", function.name, "\nn ARGUMENT MUST BE A POSITIVE AND NON NULL INTEGER: ", paste(n, collapse = " "))
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
}
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# end second round of checking and data preparation
# main code
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ini.warning.length <- options()$warning.length
options(warning.length = 8170)
on.exit(exp = options(warning.length = ini.warning.length))
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warn <- NULL
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warn.count <- 0
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lim.rank <- rank(lim) # to deal with inverse axis
if(log != "no"){
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ini.scipen <- options()$scipen
options(scipen = -1000) # force scientific format
power10.exp <- as.integer(substring(text = 10^lim, first = (regexpr(pattern = "\\+|\\-", text = 10^lim)))) # recover the power of 10, i.e., integer part of lim. Example recover 08 from 1e+08. Works for log2
# mantisse <- as.numeric(substr(x = 10^lim, start = 1, stop = (regexpr(pattern = "\\+|\\-", text = 10^lim) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
options(scipen = ini.scipen) # restore the initial scientific penalty
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tick.pos <- unique(as.vector(outer(2:10, ifelse(log == "log2", 2, 10)^((power10.exp[1] - ifelse(diff(lim.rank) > 0, 1, -1)):(power10.exp[2] + ifelse(diff(lim.rank) > 0, 1, -1)))))) # use log10(2:10) even if log2: it is to get log values between 0 and 1
tick.pos <- sort(tick.pos, decreasing = ifelse(diff(lim.rank) > 0, FALSE, TRUE))
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if(log == "log2"){
tick.values <- tick.pos[tick.pos >= min(2^lim) & tick.pos <= max(2^lim)]
tick.pos <- log2(tick.values)
}else if(log == "log10"){
tick.values <- tick.pos[tick.pos >= min(10^lim) & tick.pos <= max(10^lim)]
tick.pos <- log10(tick.values)
}
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}else{
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# if(length(breaks) > 1){ # not required because already checked above
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breaks.rank <- rank(c(breaks[1], breaks[length(breaks)]))
if(diff(breaks.rank) != diff(lim.rank)){
breaks <- sort(breaks, decreasing = ifelse(diff(lim.rank) < 0, TRUE, FALSE))
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warn.count <- warn.count + 1
tempo.warn <- paste0("(", warn.count,") VALUES IN breaks ARGUMENT NOT IN THE SAME ORDER AS IN lim ARGUMENT -> VALUES REORDERED AS IN lim: ", paste(breaks, collapse = " "))
warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
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breaks.rank <- rank(c(breaks[1], breaks[length(breaks)]))
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}
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# }
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main.tick.dist <- mean(diff(breaks), na.rm = TRUE)
tick.dist <- main.tick.dist / (n + 1)
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tempo.extra.margin <- max(abs(diff(breaks)), na.rm = TRUE)
tick.pos <- seq(
if(diff(breaks.rank) > 0){breaks[1] - tempo.extra.margin}else{breaks[1] + tempo.extra.margin}, 
if(diff(breaks.rank) > 0){breaks[length(breaks)] + tempo.extra.margin}else{breaks[length(breaks)] - tempo.extra.margin}, 
by = tick.dist
)
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tick.pos <- tick.pos[tick.pos >= min(lim) & tick.pos <= max(lim)]
tick.values <- tick.pos
}
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if(any(is.na(tick.pos) | ! is.finite(tick.pos))){ 
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tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, ": NA or Inf GENERATED FOR THE INTER TICK POSITIONS: ", paste(tick.pos, collapse = " "))
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
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if(length(tick.pos) == 0){
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warn.count <- warn.count + 1
tempo.warn <- paste0("(", warn.count,") NO INTER TICKS COMPUTED BETWEEN THEN LIMITS INDICATED: ", paste(lim, collapse = " "))
warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
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}
output <- list(log = log, coordinates = tick.pos, values = tick.values, warn = warn)
if(warn.print == TRUE & ! is.null(warn)){
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warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE) # to recover the warning messages, see $warn
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}
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return(output)
}


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######## fun_post_plot() #### set graph param after plotting (axes redesign for instance)


 


# Check OK: clear to go Apollo
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fun_post_plot <- function(x.side = 0, x.log.scale = FALSE, x.categ = NULL, x.categ.pos = NULL, x.lab = "", x.axis.size = 1.5, x.label.size = 1.5, x.dist.legend = 0.5, x.nb.inter.tick = 1, y.side = 0, y.log.scale = FALSE, y.categ = NULL, y.categ.pos = NULL, y.lab = "", y.axis.size = 1.5, y.label.size = 1.5, y.dist.legend = 0.5, y.nb.inter.tick = 1, text.angle = 90, tick.length = 0.5, sec.tick.length = 0.3, bg.color = NULL, grid.lwd = NULL, grid.col = "white", corner.text = "", corner.text.size = 1, just.label.add = FALSE, par.reset = FALSE, custom.par = NULL){
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# AIM
# redesign axis. If x.side = 0, y.side = 0, the function just adds text at topright of the graph and reset par() for next graphics and provides outputs (see below)
# provide also positions for legend or additional text on the graph
# use fun_prior_plot() before this function for initial inactivation of the axis drawings
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# fun_open() to reinitialize graph parameters if par.reset = TRUE and custom.par = NULL
# ARGUMENTS
# x.side: axis at the bottom (1) or top (3) of the region figure. Write 0 for no change
# x.log.scale: Log scale for the x-axis? Either TRUE or FALSE
# x.categ: character vector representing the classes (levels()) to specify when the x-axis is qualititative(stripchart, boxplot)
# x.categ.pos: position of the classes names (numeric vector of identical length than x.categ). If left NULL, this will be 1:length(levels())
# x.lab: label of the x-axis. If x.side == 0 and x.lab != "", then x.lab is printed
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# x.axis.size: positive numeric. Increase or decrease the size of the x axis numbers. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2. Also control the size of displayed categories
# x.label.size: positive numeric. Increase or decrease the size of the x axis legend text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
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# x.dist.legend: increase the number to move x-axis legends away in inches (first number of mgp argument of par() but in inches)
# x.nb.inter.tick: number of secondary ticks between main ticks on x-axis (only if not log scale). 0 means no secondary ticks
# y.side: axis at the left (2) or right (4) of the region figure. Write 0 for no change
# y.log.scale: Log scale for the y-axis? Either TRUE or FALSE
# y.categ: classes (levels()) to specify when the y-axis is qualititative(stripchart, boxplot)
# y.categ.pos: position of the classes names (numeric vector of identical length than y.categ). If left NULL, this will be 1:length(levels())
# y.lab: label of the y-axis. If y.side == 0 and y.lab != "", then y.lab is printed
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# y.axis.size: positive numeric. Increase or decrease the size of the y axis numbers. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2. Also control the size of displayed categories
# y.label.size: positive numeric. Increase or decrease the size of the y axis legend text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
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# y.dist.legend: increase the number to move y-axis legends away in inches (first number of mgp argument of par() but in inches)
# y.nb.inter.tick: number of secondary ticks between main ticks on y-axis (only if not log scale). 0 means non secondary ticks
# text.angle: angle of the text when axis is qualitative
# tick.length: length of the main ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc., 0 for no ticks)
# sec.tick.length: length of the secondary ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc., 0 for no ticks)
# bg.color: background color of the plot region. NULL for no color. BEWARE: cover/hide an existing plot !
# grid.lwd: if non NULL, activate the grid line (specify the line width)
# grid.col: grid line color (only if grid.lwd non NULL)
# corner.text: text to add at the top right corner of the window
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# corner.text.size: positive numeric. Increase or decrease the size of the text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
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# par.reset: to reset all the graphics parameters. BEWARE: TRUE can generate display problems, mainly in graphic devices with multiple figure regions
# just.label.add: just add axis labels (legend)? Either TRUE or FALSE. If TRUE, at least (x.side == 0 & x.lab != "") or (y.side == 0 & y.lab != "") must be set to display the corresponding x.lab or y.lab
# custom.par: list that provides the parameters that reset all the graphics parameters. BEWARE: if NULL and par.reset == TRUE, the default par() parameters are used
# RETURN
# a list containing: 
# $x.mid.left.dev.region: middle of the left margin of the device region, in coordinates of the x-axis
# $x.left.dev.region: left side of the left margin (including the potential margin of the device region), in coordinates of the x-axis
# $x.mid.right.dev.region: middle of the right margin of the device region, in coordinates of the x-axis
# $x.right.dev.region: right side of the right margin (including the potential margin of the device region), in coordinates of the x-axis
# $x.mid.left.fig.region: middle of the left margin of the figure region, in coordinates of the x-axis
# $x.left.fig.region: left side of the left margin, in coordinates of the x-axis
# $x.mid.right.fig.region: middle of the right margin of the figure region, in coordinates of the x-axis
# $x.right.fig.region: right side of the right margin, in coordinates of the x-axis
# $x.left.plot.region: left side of the plot region, in coordinates of the x-axis
# $x.right.plot.region: right side of the plot region, in coordinates of the x-axis
# $x.mid.plot.region: middle of the plot region, in coordinates of the x-axis
# $y.mid.bottom.dev.region: middle of the bottom margin of the device region, in coordinates of the y-axis
# $y.bottom.dev.region: bottom side of the bottom margin (including the potential margin of the device region), in coordinates of the y-axis
# $y.mid.top.dev.region: middle of the top margin of the device region, in coordinates of the y-axis
# $y.top.dev.region: top side of the top margin (including the potential margin of the device region), in coordinates of the y-axis
# $y.mid.bottom.fig.region: middle of the bottom margin of the figure region, in coordinates of the y-axis
# $y.bottom.fig.region: bottom of the bottom margin of the figure region, in coordinates of the y-axis
# $y.mid.top.fig.region: middle of the top margin of the figure region, in coordinates of the y-axis
# $y.top.fig.region: top of the top margin of the figure region, in coordinates of the y-axis
# $y.top.plot.region: top of the plot region, in coordinates of the y-axis
# $y.bottom.plot.region: bottom of the plot region, in coordinates of the y-axis
# $y.mid.plot.region: middle of the plot region, in coordinates of the y-axis
# $text: warning text
# EXAMPLES
# Example of log axis with log y-axis and unmodified x-axis:
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# prior.par <- fun_prior_plot(param.reinitial = TRUE, xlog.scale = FALSE, ylog.scale = TRUE, remove.label = TRUE, remove.x.axis = FALSE, remove.y.axis = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 0.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = TRUE) ; plot(1:100, log = "y") ; fun_post_plot(y.side = 2, y.log.scale = prior.par$ylog, x.lab = "Values", y.lab = "TEST", y.axis.size = 1.25, y.label.size = 1.5, y.dist.legend = 0.7, just.label.add = ! prior.par$ann)
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# Example of log axis with redrawn x-axis and y-axis:
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# prior.par <- fun_prior_plot(param.reinitial = TRUE) ; plot(1:100) ; fun_post_plot(x.side = 1, x.lab = "Values", y.side = 2, y.lab = "TEST", y.axis.size = 1, y.label.size = 2, y.dist.legend = 0.6)
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# Example of title easily added to a plot:
# plot(1:100) ; para <- fun_post_plot(corner.text = "TITLE ADDED") # try also: par(xpd = TRUE) ; text(x = para$x.mid.left.fig.region, y = para$y.mid.top.fig.region, labels = "TITLE ADDED", cex = 0.5)
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# example with margins in the device region:
# windows(5,5) ; fun_prior_plot(box.type = "o") ; par(mai=c(0.5,0.5,0.5,0.5), omi = c(0.25,0.25,1,0.25), xaxs = "i", yaxs = "i") ; plot(0:10) ; a <- fun_post_plot(x.side = 0, y.side = 0) ; x <- c(a$x.mid.left.dev.region, a$x.left.dev.region, a$x.mid.right.dev.region, a$x.right.dev.region, a$x.mid.left.fig.region, a$x.left.fig.region, a$x.mid.right.fig.region, a$x.right.fig.region, a$x.right.plot.region, a$x.left.plot.region, a$x.mid.plot.region) ; y <- c(a$y.mid.bottom.dev.region, a$y.bottom.dev.region, a$y.mid.top.dev.region, a$y.top.dev.region, a$y.mid.bottom.fig.region, a$y.bottom.fig.region, a$y.mid.top.fig.region, a$y.top.fig.region, a$y.top.plot.region, a$y.bottom.plot.region, a$y.mid.plot.region) ; par(xpd = NA) ; points(x = rep(5, length(y)), y = y, pch = 16, col = "red") ; text(x = rep(5, length(y)), y = y, c("y.mid.bottom.dev.region", "y.bottom.dev.region", "y.mid.top.dev.region", "y.top.dev.region", "y.mid.bottom.fig.region", "y.bottom.fig.region", "y.mid.top.fig.region", "y.top.fig.region", "y.top.plot.region", "y.bottom.plot.region", "y.mid.plot.region"), cex = 0.65, col = grey(0.25)) ; points(y = rep(5, length(x)), x = x, pch = 16, col = "blue") ; text(y = rep(5, length(x)), x = x, c("x.mid.left.dev.region", "x.left.dev.region", "x.mid.right.dev.region", "x.right.dev.region", "x.mid.left.fig.region", "x.left.fig.region", "x.mid.right.fig.region", "x.right.fig.region", "x.right.plot.region", "x.left.plot.region", "x.mid.plot.region"), cex = 0.65, srt = 90, col = grey(0.25))
# DEBUGGING
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# x.side = 0 ; x.log.scale = FALSE ; x.categ = NULL ; x.categ.pos = NULL ; x.lab = "" ; x.axis.size = 1.5 ; x.label.size = 1.5 ; x.dist.legend = 1 ; x.nb.inter.tick = 1 ; y.side = 0 ; y.log.scale = FALSE ; y.categ = NULL ; y.categ.pos = NULL ; y.lab = "" ; y.axis.size = 1.5 ; y.label.size = 1.5 ; y.dist.legend = 0.7 ; y.nb.inter.tick = 1 ; text.angle = 90 ; tick.length = 0.5 ; sec.tick.length = 0.3 ; bg.color = NULL ; grid.lwd = NULL ; grid.col = "white" ; corner.text = "" ; corner.text.size = 1 ; just.label.add = FALSE ; par.reset = FALSE ; custom.par = NULL # for function debugging
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# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
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tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
if(length(utils::find("fun_open", mode = "function")) == 0){
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tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_open() FUNCTION IS MISSING IN THE R ENVIRONMENT")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
# end required function checking
# argument checking
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = x.side, options = c(0, 1, 3), length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = x.log.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(x.categ)){
tempo <- fun_check(data = x.categ, class = "character", na.contain = TRUE, fun.name = function.name) ; eval(ee)
}
if( ! is.null(x.categ.pos)){
tempo <- fun_check(data = x.categ.pos, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
}
tempo <- fun_check(data = x.lab, class = "character", length = 1, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = x.axis.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = x.label.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = x.dist.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = x.nb.inter.tick, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = y.side, options = c(0, 2, 4), length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = y.log.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(y.categ)){
tempo <- fun_check(data = y.categ, class = "character", na.contain = TRUE, fun.name = function.name) ; eval(ee)
}
if( ! is.null(y.categ.pos)){
tempo <- fun_check(data = y.categ.pos, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
}
tempo <- fun_check(data = y.lab, class = "character", length = 1, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = y.axis.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = y.label.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = y.dist.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = y.nb.inter.tick, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = text.angle, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = sec.tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
if( ! is.null(bg.color)){
tempo <- fun_check(data = bg.color, class = "character", length = 1, fun.name = function.name) ; eval(ee)
if( ! (bg.color %in% colors() | grepl(pattern = "^#", bg.color))){ # check color
tempo.cat <- paste0("ERROR IN ", function.name, ": bg.color ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # OR A COLOR NAME GIVEN BY colors()")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
if( ! is.null(grid.lwd)){
tempo <- fun_check(data = grid.lwd, class = "vector", mode = "numeric", neg.values = FALSE, fun.name = function.name) ; eval(ee)
}
if( ! is.null(grid.col)){
tempo <- fun_check(data = grid.col, class = "character", length = 1, fun.name = function.name) ; eval(ee)
if( ! (grid.col %in% colors() | grepl(pattern = "^#", grid.col))){ # check color
tempo.cat <- paste0("ERROR IN ", function.name, ": grid.col ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # OR A COLOR NAME GIVEN BY colors()")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
tempo <- fun_check(data = corner.text, class = "character", length = 1, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = corner.text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = just.label.add, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = par.reset, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(custom.par)){
tempo <- fun_check(data = custom.par, typeof = "list", length = 1, fun.name = function.name) ; eval(ee)
}
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 argument checking
# main code
text <- NULL
par(tcl = -par()$mgp[2] * tick.length)
if(x.log.scale == TRUE){
grid.coord.x <- c(10^par("usr")[1], 10^par("usr")[2])
}else{
grid.coord.x <- c(par("usr")[1], par("usr")[2])
}
if(y.log.scale == TRUE){
grid.coord.y <- c(10^par("usr")[3], 10^par("usr")[4])
}else{
grid.coord.y <- c(par("usr")[3], par("usr")[4])
}
if( ! is.null(bg.color)){
rect(grid.coord.x[1], grid.coord.y[1], grid.coord.x[2], grid.coord.y[2], col = bg.color, border = NA)
}
if( ! is.null(grid.lwd)){
grid(nx = NA, ny = NULL, col = grid.col, lty = 1, lwd = grid.lwd)
}
if(x.log.scale == TRUE){
x.mid.left.dev.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
x.left.dev.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1]) # in x coordinates
x.mid.right.dev.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
x.right.dev.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2])) # in x coordinates
x.mid.left.fig.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
x.left.fig.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1]) # in x coordinates
x.mid.right.fig.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
x.right.fig.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2])) # in x coordinates
x.left.plot.region <- 10^par("usr")[1] # in x coordinates, left of the plot region (according to x scale)
x.right.plot.region <- 10^par("usr")[2] # in x coordinates, right of the plot region (according to x scale)
x.mid.plot.region <- 10^((par("usr")[2] + par("usr")[1]) / 2) # in x coordinates, right of the plot region (according to x scale)
}else{
x.mid.left.dev.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
x.left.dev.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1]) # in x coordinates
x.mid.right.dev.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
x.right.dev.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2])) # in x coordinates
x.mid.left.fig.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
x.left.fig.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1]) # in x coordinates
x.mid.right.fig.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
x.right.fig.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2])) # in x coordinates
x.left.plot.region <- par("usr")[1] # in x coordinates, left of the plot region (according to x scale)
x.right.plot.region <- par("usr")[2] # in x coordinates, right of the plot region (according to x scale)
x.mid.plot.region <- (par("usr")[2] + par("usr")[1]) / 2 # in x coordinates, right of the plot region (according to x scale)
}
if(y.log.scale == TRUE){
y.mid.bottom.dev.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (par("omd")[3] / 2)) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
y.bottom.dev.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * par("omd")[3]) # in y coordinates
y.mid.top.dev.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
y.top.dev.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4])) # in y coordinates
y.mid.bottom.fig.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] / 2) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
y.bottom.fig.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3]) # in y coordinates
y.mid.top.fig.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
y.top.fig.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4])) # in y coordinates
y.top.plot.region <- 10^par("usr")[4] # in y coordinates, top of the plot region (according to y scale)
y.bottom.plot.region <- 10^par("usr")[3] # in y coordinates, bottom of the plot region (according to y scale)
y.mid.plot.region <- (par("usr")[3] + par("usr")[4]) / 2 # in x coordinates, right of the plot region (according to x scale)
}else{
y.mid.bottom.dev.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (par("omd")[3] / 2)) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
y.bottom.dev.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * par("omd")[3]) # in y coordinates
y.mid.top.dev.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
y.top.dev.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4])) # in y coordinates
y.mid.bottom.fig.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] / 2) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
y.bottom.fig.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3]) # in y coordinates
y.mid.top.fig.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
y.top.fig.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4])) # in y coordinates
y.top.plot.region <- par("usr")[4] # in y coordinates, top of the plot region (according to y scale)
y.bottom.plot.region <- par("usr")[3] # in y coordinates, bottom of the plot region (according to y scale)
y.mid.plot.region <- ((par("usr")[3] + par("usr")[4]) / 2) # in x coordinates, right of the plot region (according to x scale)
}
if(any(sapply(FUN = all.equal, c(1, 3), x.side) == TRUE)){
par(xpd=FALSE, xaxt="s")
if(is.null(x.categ) & x.log.scale == TRUE){
if(any(par()$xaxp[1:2] == 0)){ # any(sapply(FUN = all.equal, par()$xaxp[1:2], 0) == TRUE) not used because we strictly need zero as a result. Beware: write "== TRUE", because the result is otherwise character and a warning message appears using any()
if(par()$xaxp[1] == 0){ # isTRUE(all.equal(par()$xaxp[1], 0)) not used because we strictly need zero as a result
par(xaxp = c(10^-30, par()$xaxp[2:3])) # because log10(par()$xaxp[1] == 0) == -Inf
}
if(par()$xaxp[2] == 0){ # isTRUE(all.equal(par()$xaxp[1], 0)) not used because we strictly need zero as a result
par(xaxp = c(par()$xaxp[1], 10^-30, par()$xaxp[3])) # because log10(par()$xaxp[2] == 0) == -Inf
}
}
axis(side = x.side, at = c(10^par()$usr[1], 10^par()$usr[2]), labels=rep("", 2), lwd=1, lwd.ticks = 0) # draw the axis line
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mtext(side = x.side, text = x.lab, line = x.dist.legend / 0.2, las = 0, cex = x.label.size)
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par(tcl = -par()$mgp[2] * sec.tick.length) # length of the secondary ticks are reduced
suppressWarnings(rug(10^outer(c((log10(par("xaxp")[1]) -1):log10(par("xaxp")[2])), log10(1:10), "+"), ticksize = NA, side = x.side)) # ticksize = NA to allow the use of par()$tcl value
par(tcl = -par()$mgp[2] * tick.length) # back to main ticks
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axis(side = x.side, at = c(1e-15, 1e-14, 1e-13, 1e-12, 1e-11, 1e-10, 1e-9, 1e-8, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10), labels = expression(10^-15, 10^-14, 10^-13, 10^-12, 10^-11, 10^-10, 10^-9, 10^-8, 10^-7, 10^-6, 10^-5, 10^-4, 10^-3, 10^-2, 10^-1, 10^0, 10^1, 10^2, 10^3, 10^4, 10^5, 10^6, 10^7, 10^8, 10^9, 10^10), lwd = 0, lwd.ticks = 1, cex.axis = x.axis.size)
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x.text <- 10^par("usr")[2]
}else if(is.null(x.categ) & x.log.scale == FALSE){
axis(side=x.side, at=c(par()$usr[1], par()$usr[2]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
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axis(side=x.side, at=round(seq(par()$xaxp[1], par()$xaxp[2], length.out=par()$xaxp[3]+1), 2), cex.axis = x.axis.size) # axis(side=x.side, at=round(seq(par()$xaxp[1], par()$xaxp[2], length.out=par()$xaxp[3]+1), 2), labels = format(round(seq(par()$xaxp[1], par()$xaxp[2], length.out=par()$xaxp[3]+1), 2), big.mark=','), cex.axis = x.axis.size) # to get the 1000 comma separator
mtext(side = x.side, text = x.lab, line = x.dist.legend / 0.2, las = 0, cex = x.label.size)
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if(x.nb.inter.tick > 0){
inter.tick.unit <- (par("xaxp")[2] - par("xaxp")[1]) / par("xaxp")[3]
par(tcl = -par()$mgp[2] * sec.tick.length) # length of the ticks are reduced
suppressWarnings(rug(seq(par("xaxp")[1] - 10 * inter.tick.unit, par("xaxp")[2] + 10 * inter.tick.unit, by = inter.tick.unit / (1 + x.nb.inter.tick)), ticksize = NA, x.side)) # ticksize = NA to allow the use of par()$tcl value
par(tcl = -par()$mgp[2] * tick.length) # back to main ticks
}
x.text <- par("usr")[2]
}else if(( ! is.null(x.categ)) & x.log.scale == FALSE){
if(is.null(x.categ.pos)){
x.categ.pos <- 1:length(x.categ)
}else if(length(x.categ.pos) != length(x.categ)){
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tempo.cat <- paste0("ERROR IN ", function.name, ": x.categ.pos MUST BE THE SAME LENGTH AS x.categ")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
par(xpd = TRUE)
if(isTRUE(all.equal(x.side, 1))){ #isTRUE(all.equal(x.side, 1)) is similar to x.side == 1 but deals with float
segments(x0 = x.left.plot.region, x1 = x.right.plot.region, y0 = y.bottom.plot.region, y1 = y.bottom.plot.region) # draw the line of the axis
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text(x = x.categ.pos, y = y.mid.bottom.fig.region, labels = x.categ, srt = text.angle, cex = x.axis.size)
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}else if(isTRUE(all.equal(x.side, 3))){ #isTRUE(all.equal(x.side, 1)) is similar to x.side == 3 but deals with float
segments(x0 = x.left.plot.region, x1 = x.right.plot.region, y0 = y.top.plot.region, y1 = y.top.plot.region) # draw the line of the axis
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text(x = x.categ.pos, y = y.mid.top.fig.region, labels = x.categ, srt = text.angle, cex = x.axis.size)
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}else{
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tempo.cat <- paste0("ERROR IN ", function.name, ": ARGUMENT x.side CAN ONLY BE 1 OR 3")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
par(xpd = FALSE)
x.text <- par("usr")[2]
}else{
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tempo.cat <- paste0("ERROR IN ", function.name, ": PROBLEM WITH THE x.side (", x.side ,") OR x.log.scale (", x.log.scale,") ARGUMENTS")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
}else{
x.text <- par("usr")[2]
}
if(any(sapply(FUN = all.equal, c(2, 4), y.side) == TRUE)){
par(xpd=FALSE, yaxt="s")
if(is.null(y.categ) & y.log.scale == TRUE){
if(any(par()$yaxp[1:2] == 0)){ # any(sapply(FUN = all.equal, par()$yaxp[1:2], 0) == TRUE) not used because we strictly need zero as a result. Beware: write "== TRUE", because the result is otherwise character and a warning message appears using any()
if(par()$yaxp[1] == 0){ # strict zero needed
par(yaxp = c(10^-30, par()$yaxp[2:3])) # because log10(par()$yaxp[1] == 0) == -Inf
}
if(par()$yaxp[2] == 0){ # strict zero needed
par(yaxp = c(par()$yaxp[1], 10^-30, par()$yaxp[3])) # because log10(par()$yaxp[2] == 0) == -Inf
}
}
axis(side=y.side, at=c(10^par()$usr[3], 10^par()$usr[4]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
par(tcl = -par()$mgp[2] * sec.tick.length) # length of the ticks are reduced
suppressWarnings(rug(10^outer(c((log10(par("yaxp")[1])-1):log10(par("yaxp")[2])), log10(1:10), "+"), ticksize = NA, side = y.side)) # ticksize = NA to allow the use of par()$tcl value
par(tcl = -par()$mgp[2] * tick.length) # back to main tick length
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axis(side = y.side, at = c(1e-15, 1e-14, 1e-13, 1e-12, 1e-11, 1e-10, 1e-9, 1e-8, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10), labels = expression(10^-15, 10^-14, 10^-13, 10^-12, 10^-11, 10^-10, 10^-9, 10^-8, 10^-7, 10^-6, 10^-5, 10^-4, 10^-3, 10^-2, 10^-1, 10^0, 10^1, 10^2, 10^3, 10^4, 10^5, 10^6, 10^7, 10^8, 10^9, 10^10), lwd = 0, lwd.ticks = 1, cex.axis = y.axis.size)
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y.text <- 10^(par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
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mtext(side = y.side, text = y.lab, line = y.dist.legend / 0.2, las = 0, cex = y.label.size)
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}else if(is.null(y.categ) & y.log.scale == FALSE){
axis(side=y.side, at=c(par()$usr[3], par()$usr[4]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
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axis(side=y.side, at=round(seq(par()$yaxp[1], par()$yaxp[2], length.out=par()$yaxp[3]+1), 2), cex.axis = y.axis.size)
mtext(side = y.side, text = y.lab, line = y.dist.legend / 0.2, las = 0, cex = y.label.size)
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if(y.nb.inter.tick > 0){
inter.tick.unit <- (par("yaxp")[2] - par("yaxp")[1]) / par("yaxp")[3]
par(tcl = -par()$mgp[2] * sec.tick.length) # length of the ticks are reduced
suppressWarnings(rug(seq(par("yaxp")[1] - 10 * inter.tick.unit, par("yaxp")[2] + 10 * inter.tick.unit, by = inter.tick.unit / (1 + y.nb.inter.tick)), ticksize = NA, side=y.side)) # ticksize = NA to allow the use of par()$tcl value
par(tcl = -par()$mgp[2] * tick.length) # back to main tick length
}
y.text <- (par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
}else if(( ! is.null(y.categ)) & y.log.scale == FALSE){
if(is.null(y.categ.pos)){
y.categ.pos <- 1:length(y.categ)
}else if(length(y.categ.pos) != length(y.categ)){
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tempo.cat <- paste0("ERROR IN ", function.name, ": y.categ.pos MUST BE THE SAME LENGTH AS y.categ")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
axis(side = y.side, at = y.categ.pos, labels = rep("", length(y.categ)), lwd=0, lwd.ticks=1) # draw the line of the axis
par(xpd = TRUE)
if(isTRUE(all.equal(y.side, 2))){ #isTRUE(all.equal(y.side, 2)) is similar to y.side == 2 but deals with float
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text(x = x.mid.left.fig.region, y = y.categ.pos, labels = y.categ, srt = text.angle, cex = y.axis.size)
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}else if(isTRUE(all.equal(y.side, 4))){ # idem
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text(x = x.mid.right.fig.region, y = y.categ.pos, labels = y.categ, srt = text.angle, cex = y.axis.size)
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}else{
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tempo.cat <- paste0("ERROR IN ", function.name, ": ARGUMENT y.side CAN ONLY BE 2 OR 4")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
par(xpd = FALSE)
y.text <- (par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
}else{
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tempo.cat <- paste0("ERROR IN ", function.name, ": PROBLEM WITH THE y.side (", y.side ,") OR y.log.scale (", y.log.scale,") ARGUMENTS")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
}else{
y.text <- (par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
}
par(xpd=NA)
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text(x = x.mid.right.fig.region, y = y.text, corner.text, adj=c(1, 1.1), cex = corner.text.size) # text at the topright corner. Replace x.right.fig.region by x.text if text at the right edge of the plot region
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if(just.label.add == TRUE & isTRUE(all.equal(x.side, 0)) & x.lab != ""){
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text(x = x.mid.plot.region, y = y.mid.bottom.fig.region, x.lab, adj=c(0.5, 0.5), cex = x.label.size) # x label
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}
if(just.label.add == TRUE & isTRUE(all.equal(y.side, 0)) & y.lab != ""){
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text(x = y.mid.plot.region, y = x.mid.left.fig.region, y.lab, adj=c(0.5, 0.5), cex = y.label.size) # x label
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}
par(xpd=FALSE)
if(par.reset == TRUE){
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tempo.par <- fun_open(pdf = FALSE, return.output = TRUE)
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invisible(dev.off()) # close the new window
if( ! is.null(custom.par)){
if( ! names(custom.par) %in% names(tempo.par$ini.par)){
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tempo.cat <- paste0("ERROR IN ", function.name, ": custom.par ARGUMENT SHOULD HAVE THE NAMES OF THE COMPARTMENT LIST COMING FROM THE par() LIST")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
par(custom.par)
text <- c(text, "\nGRAPH PARAMETERS SET TO VALUES DEFINED BY custom.par ARGUMENT\n")
}else{
par(tempo.par$ini.par)
text <- c(text, "\nGRAPH PARAMETERS RESET TO par() DEFAULT VALUES\n")
}
}
output <- list(x.mid.left.dev.region = x.mid.left.dev.region, x.left.dev.region = x.left.dev.region, x.mid.right.dev.region = x.mid.right.dev.region, x.right.dev.region = x.right.dev.region, x.mid.left.fig.region = x.mid.left.fig.region, x.left.fig.region = x.left.fig.region, x.mid.right.fig.region = x.mid.right.fig.region, x.right.fig.region = x.right.fig.region, x.left.plot.region = x.left.plot.region, x.right.plot.region = x.right.plot.region, x.mid.plot.region = x.mid.plot.region, y.mid.bottom.dev.region = y.mid.bottom.dev.region, y.bottom.dev.region = y.bottom.dev.region, y.mid.top.dev.region = y.mid.top.dev.region, y.top.dev.region = y.top.dev.region, y.mid.bottom.fig.region = y.mid.bottom.fig.region, y.bottom.fig.region = y.bottom.fig.region, y.mid.top.fig.region = y.mid.top.fig.region, y.top.fig.region = y.top.fig.region, y.top.plot.region = y.top.plot.region, y.bottom.plot.region = y.bottom.plot.region, y.mid.plot.region = y.mid.plot.region, text = text)
return(output)
}


######## fun_close() #### close specific graphic windows


# Check OK: clear to go Apollo
fun_close <- function(kind = "pdf", return.text = FALSE){
# AIM
# close only specific graphic windows (devices)
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# ARGUMENTS:
# kind: vector, among c("windows", "quartz", "x11", "X11", "pdf", "bmp", "png", "tiff"), indicating the kind of graphic windows (devices) to close. BEWARE: either "windows", "quartz", "x11" or "X11" means that all the X11 GUI graphics devices will be closed, whatever the OS used
# return.text: print text regarding the kind parameter and the devices that were finally closed?
# RETURN
# text regarding the kind parameter and the devices that were finally closed
# EXAMPLES
# windows() ; windows() ; pdf() ; dev.list() ; fun_close(kind = c("pdf", "x11"), return.text = TRUE) ; dev.list()
# DEBUGGING
# kind = c("windows", "pdf") ; return.text = FALSE # for function debugging
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
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tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
# end required function checking
# argument checking
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = kind, options = c("windows", "quartz", "x11", "X11", "pdf", "bmp", "png", "tiff"), fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = return.text, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
text <- paste0("THE REQUIRED KIND OF GRAPHIC DEVICES TO CLOSE ARE ", paste(kind, collapse = " "))
if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
if(any(kind %in% c("windows", "quartz", "x11", "X11"))){
tempo <- kind %in% c("windows", "quartz", "x11", "X11")
kind[tempo] <- "windows" # term are replaced by what is displayed when using a <- dev.list() ; names(a)
}
}else if(Sys.info()["sysname"] == "Linux"){
if(any(kind %in% c("windows", "quartz", "x11", "X11"))){
tempo.device <- suppressWarnings(try(X11(), silent = TRUE))[] # open a X11 window to try to recover the X11 system used
if( ! is.null(tempo.device)){
text <- paste0(text, "\nCANNOT CLOSE GUI GRAPHIC DEVICES AS REQUIRED BECAUSE THIS LINUX SYSTEM DOES NOT HAVE IT")
}else{
tempo <- kind %in% c("windows", "quartz", "x11", "X11")
kind[tempo] <- names(dev.list()[length(dev.list())]) # term are replaced by what is displayed when using a <- dev.list() ; names(a)
invisible(dev.off()) # close the X11 opened by tempo
}
}
}else{ # for macOS
if(any(kind %in% c("windows", "quartz", "x11", "X11"))){
tempo <- kind %in% c("windows", "quartz", "x11", "X11")
kind[tempo] <- "quartz" # term are replaced by what is displayed when using a <- dev.list() ; names(a)
}
}
kind <- unique(kind)
if(length(dev.list()) != 0){
for(i in length(names(dev.list())):1){
if(names(dev.list())[i] %in% kind){
text <- paste0(text, "\n", names(dev.list())[i], " DEVICE NUMBER ", dev.list()[i], " HAS BEEN CLOSED")
invisible(dev.off(dev.list()[i]))
}
}
}
if(return.text == TRUE){
return(text)
}
}


################ Standard graphics


######## fun_empty_graph() #### text to display for empty graphs


 


# Check OK: clear to go Apollo
fun_empty_graph <- function(text = NULL, text.size = 1, title = NULL, title.size = 1.5){
# AIM
# display an empty plot with a text in the middle of the window (for instance to specify that no plot can be drawn)
# ARGUMENTS
# text: character string of the message to display
# text.size: numeric value of the text size
# title: character string of the graph title
# title.size: numeric value of the title size (in points)
# REQUIRED PACKAGES
# none
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# RETURN
# an empty plot
# EXAMPLES
# simple example
# fun_empty_graph(text = "NO GRAPH")
# white page
# fun_empty_graph() # white page
# all the arguments
# fun_empty_graph(text = "NO GRAPH", text.size = 2, title = "GRAPH1", title.size = 1)
# DEBUGGING
# text = "NO GRAPH" ; title = "GRAPH1" ; text.size = 1
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
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tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
# end required function checking
# 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))
if( ! is.null(text)){
tempo <- fun_check(data = text, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
}
tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(title)){
tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
}
tempo <- fun_check(data = title.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
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 argument checking
# main code
ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
par(ann=FALSE, xaxt="n", yaxt="n", mar = rep(1, 4), bty = "n", xpd = NA)
plot(1, 1, type = "n") # no display with type = "n"
x.left.dev.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1])
y.top.dev.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4]))
if( ! is.null(text)){
text(x = 1, y = 1, labels = text, cex = text.size)
}
if( ! is.null(title)){
text(x = x.left.dev.region, y = y.top.dev.region, labels = title, adj=c(0, 1), cex = title.size)
}
par(ini.par)
}


################ gg graphics


######## fun_gg_palette() #### ggplot2 default color palette


 


# Check OK: clear to go Apollo
fun_gg_palette <- function(n, kind = "std"){
# AIM
# provide colors used by ggplot2
# the interest is to use another single color that is not the red one used by default
# for ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
# ARGUMENTS
# n: number of groups on the graph
# kind: either "std" for standard gg colors, "dark" for darkened gg colors, or "light" for pastel gg colors
# REQUIRED PACKAGES
# none
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# RETURN
# the vector of hexadecimal colors
# EXAMPLES
# output of the function
# fun_gg_palette(n = 2)
# the ggplot2 palette when asking for 7 different colors
# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7))
# selection of the 5th color of the ggplot2 palette made of 7 different colors
# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7)[5])
# the ggplot2 palette made of 7 darkened colors
# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7, kind = "dark"))
# the ggplot2 palette made of 7 lighten colors
# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7, kind = "light"))
# DEBUGGING
# n = 0
# kind = "std"
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
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tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
# end required function checking
# argument checking
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = n, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE & isTRUE(all.equal(n, 0))){ # isTRUE(all.equal(n, 0))) is similar to n == 0 but deals with float
tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT MUST BE A NON ZERO INTEGER. HERE IT IS: ", paste(n, collapse = " "))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
tempo <- fun_check(data = kind, options = c("std", "dark", "light"), length = 1, fun.name = function.name) ; eval(ee)
}
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 argument checking
# main code
hues = seq(15, 375, length = n + 1)
hcl(h = hues, l = if(kind == "std"){65}else if(kind == "dark"){35}else if(kind == "light"){85}, c = 100)[1:n]
}


######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle


 


# Check OK: clear to go Apollo
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fun_gg_just <- function(angle, pos, kind = "axis"){
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# AIM
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# provide correct justification for text labeling, depending on the chosen angle
# WARNING
# vjust sometimes does not work depending on the angle, which explain the if(pos == "top") and if(pos == "right") in the code
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# ARGUMENTS
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# angle: integer value of the text angle, using the same rules as in ggplot2. Positive values for counterclockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Negative values for clockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc. 
# pos: where text is? Either "top", "right", "bottom" or "left" of the elements to justify from
# kind: kind of text? Either "axis" or "text". In the first case, the pos argument refers to the axis position, and in the second to annotated text (using ggplot2::annotate() or ggplot2::geom_text())
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# REQUIRED PACKAGES
# none
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# RETURN
# a list containing:
# $angle: the submitted angle (value potentially reduced to fit the [-360 ; 360] interval, e.g., 460 -> 100, without impact on the final angle displayed)
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# $pos: the selected position (argument pos)
# $kind: the selected kind of text (argument kind)
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# $hjust: the horizontal justification
# $vjust: the vertical justification
# EXAMPLES
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# fun_gg_just(angle = 45, pos = "bottom")
# fun_gg_just(angle = (360*2 + 45), pos = "left")