cute_little_R_functions.R 697 KB
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GOBACK <- FALSE
}
}else{
cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FINAL WHILE LOOP | LOOP COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4)))
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print.count.loop <- logical(length = print.count)
print.count.loop[length(print.count.loop)] <- TRUE # counter to speedup
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count.loop <- 0 # 
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pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # selection of random positions. BEWARE: n = pos.selec.seq.max because already - 1 (see above) but is connected to tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
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tempo.cor.loop <- tempo.cor
tempo.date.loop <- Sys.time()
tempo.time.loop <- as.numeric(tempo.date.loop)
while(tempo.cor > cor.limit){
count <- count + 1
count.loop <- count.loop + 1
pos2 <- pos[count.loop]
tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
tempo.cor <- abs(cor(x = data1[tempo.pos], y = data2, use = "pairwise.complete.obs", method = cor.method))
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if(print.count.loop[count.loop]){
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count.loop <- 0
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pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # BEWARE: never forget to resample here
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tempo.time <- as.numeric(Sys.time())
tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - tempo.time.loop))
final.loop <- (tempo.time - tempo.time.loop) / (tempo.cor.loop - tempo.cor) * (tempo.cor - cor.limit) # tempo.cor.loop - tempo.cor always positive and tempo.cor decreases progressively starting from tempo.cor.loop
final.exp <- as.POSIXct(final.loop, origin = tempo.date.loop)
cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "WHILE LOOP | LOOP NB: ", format(count.loop, big.mark=","), " | COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4), " | TIME SPENT: ", tempo.lapse, " | EXPECTED END: ", final.exp))
}
}
}
}
tempo.time <- as.numeric(Sys.time())
tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "WHILE/FOR LOOPS END | LOOP COUNT: ", format(count, big.mark=","), " | NB OF ROUNDS: ", round, " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4), " | TOTAL SPENT TIME: ", tempo.lapse))
}
tempo.cor <- ifelse(neg.cor == TRUE, -tempo.cor, tempo.cor)
}
}
cat("\n\n")
if(warn.print == TRUE & ! is.null(warn)){
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warning(warn, call. = FALSE)
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cat("\n\n")
}
output <- list(data = data1[tempo.pos], warn = warn, cor = if(is.null(data2)){cor(ini.pos, tempo.pos, method = "spearman")}else{tempo.cor}, count = count)
return(output)
}


################ Graphics management


# this order can be used:
# fun_width()
# fun_open()
# fun_prior_plot() # not for ggplot2
# plot() or any other plotting
# fun_post_plot() if fun_prior_plot() has been used # not for ggplot2
# fun_close()


######## fun_width() #### window width depending on classes to plot


# Check OK: clear to go Apollo
fun_width <- function(class.nb, inches.per.class.nb = 1, ini.window.width = 7, inch.left.space, inch.right.space, boundarie.space = 0.5){
# AIM
# rescale the width of a window to open depending on the number of classes to plot
# can be used for height, considering that it is as if it was a width
# this order can be used:
# fun_width()
# fun_open()
# fun_prior_plot() # not for ggplot2
# plot() or any other plotting
# fun_post_plot() if fun_prior_plot() has been used # not for ggplot2
# fun_close()
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# ARGUMENTS
# class.nb: number of class to plot
# inches.per.class.nb: number of inches per unit of class.nb. 2 means 2 inches for each boxplot for instance
# ini.window.width:initial window width in inches
# inch.left.space: left horizontal margin of the figure region (in inches)
# inch.right.space: right horizontal margin of the figure region (in inches)
# boundarie.space: space between the right and left limits of the plotting region and the plot (0.5 means half a class width)
# RETURN
# the new window width in inches
# EXAMPLES
# fun_width(class.nb = 10, inches.per.class.nb = 0.2, ini.window.width = 7, inch.left.space = 1, inch.right.space = 1, boundarie.space = 0.5)
# DEBUGGING
# class.nb = 10 ; inches.per.class.nb = 0.2 ; ini.window.width = 7 ; inch.left.space = 1 ; inch.right.space = 1 ; boundarie.space = 0.5 # 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){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# 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 = class.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = inches.per.class.nb, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = ini.window.width, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = inch.left.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = inch.right.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = boundarie.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, 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
range.max <- class.nb + boundarie.space # the max range of the future plot
range.min <- boundarie.space # the min range of the future plot
window.width <- inch.left.space + inch.right.space + inches.per.class.nb * (range.max - range.min)
return(window.width)
}


######## fun_open() #### open a GUI or pdf graphic window


# Check OK: clear to go Apollo
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fun_open <- function(pdf.disp = TRUE, fun.path = "working.dir", pdf.name.file = "graph", width.fun = 7, height.fun = 7, paper = "special", no.pdf.overwrite = TRUE, return.output = FALSE){
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# AIM
# open a pdf or screen (GUI) graphic window
# BEWARE: on Linux, use pdf.disp = TRUE, if (GUI) graphic window is not always available, meaning that X is not installed (clusters for instance). Use X11() in R to test if available
# this order can be used:
# fun_width()
# fun_open()
# fun_prior_plot() # not for ggplot2
# plot() or any other plotting
# fun_post_plot() if fun_prior_plot() has been used # not for ggplot2
# fun_close()
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# ARGUMENTS:
# pdf.disp: use pdf or not
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# fun.path: where the pdf is saved (do not terminate by / or \\). Write "working.dir" if working directory is required (default)
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# pdf.name.file: name of the pdf file containing the graphs (the .pdf extension is added by the function)
# width.fun: width of the windows (in inches)
# height.fun: height of the windows (in inches)
# paper: paper argument of the pdf function (paper format). Only used for pdf(). Either "a4", "letter", "legal", "us", "executive", "a4r", "USr" or "special". If "special", means that width.fun and height.fun specify the paper size
# no.pdf.overwrite: existing pdf can be overwritten ? Only used if pdf.disp = TRUE
# return.output: return output ? If TRUE but function not assigned, the output list is displayed
# RETURN
# a list containing:
# $pdf.loc: path of the pdf created
# $ini.par: initial par() parameters (to reset in a new graph)
# $zone.ini: initial window spliting (to reset in a new graph)
# EXAMPLES
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# fun_open(pdf.disp = FALSE, fun.path = "C:/Users/Gael/Desktop", pdf.name.file = "graph", width.fun = 7, height.fun = 7, paper = "special", no.pdf.overwrite = TRUE, return.output = TRUE)
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# DEBUGGING
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# pdf.disp = TRUE ; fun.path = "C:/Users/Gael/Desktop" ; pdf.name.file = "graphs" ; width.fun = 7 ; height.fun = 7 ; paper = "special" ; no.pdf.overwrite = TRUE ; return.output = TRUE # for function debugging
# pdf.disp = TRUE ; fun.path = "/pasteur/homes/gmillot/" ; pdf.name.file = "graphs" ; width.fun = 7 ; height.fun = 7 ; paper = "special" ; no.pdf.overwrite = TRUE ; return.output = TRUE # for function debugging
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# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end required function checking
# argument checking
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = pdf.disp, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = fun.path, class = "character", length = 1, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = pdf.name.file, class = "character", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = width.fun, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = height.fun, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = fun.path, class = "character", length = 1, fun.name = function.name) ; eval(ee)
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tempo <- fun_check(data = paper, options = c("a4", "letter", "legal", "us", "executive", "a4r", "USr", "special", "A4", "LETTER", "LEGAL", "US"), length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data =no.pdf.overwrite, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = return.output, 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
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if(fun.path == "working.dir"){
fun.path <- getwd()
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}else{
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if(grepl(x = fun.path, pattern = ".+/$")){
fun.path <- substr(fun.path, 1, nchar(fun.path) - 1) # remove the last /
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}
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if(dir.exists(fun.path) == FALSE){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": fun.path ARGUMENT DOES NOT CORRESPOND TO EXISTING DIRECTORY\n\n================\n\n")
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stop(tempo.cat, call. = FALSE)
}
}
# par.ini recovery
# cannot use pdf(file = NULL), because some small differences between pdf() and other devices. For instance, differences with windows() for par()$fin, par()$pin and par()$plt
if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
open.fail <- NULL
windows()
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
invisible(dev.off()) # close the new window
}else if(Sys.info()["sysname"] == "Linux"){
if(pdf.disp == TRUE){
tempo.code <- 0
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while(file.exists(paste0(fun.path, "/recover_ini_par", tempo.code, ".pdf")) == TRUE){
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tempo.code <- tempo.code + 1
}
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pdf(width = width.fun, height = height.fun, file=paste0(fun.path, "/recover_ini_par", tempo.code, ".pdf"), paper = paper)
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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
invisible(dev.off()) # close the pdf windows
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file.remove(paste0(fun.path, "/recover_ini_par", tempo.code, ".pdf")) # remove the pdf file
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}else{
# test if X11 can be opened
if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THIS FUNCTION CANNOT BE USED ON LINUX IF A Rplots.pdf FILE ALREADY EXISTS HERE: ", getwd(), "\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else{
open.fail <- suppressWarnings(try(X11(), silent = TRUE))[] # try to open a X11 window. If open.fail == NULL, no problem, meaning that the X11 window is opened. If open.fail != NULL, a pdf can be opened here paste0(getwd(), "/Rplots.pdf")
if(is.null(open.fail)){
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
invisible(dev.off()) # close the new window
}else if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
file.remove(paste0(getwd(), "/Rplots.pdf")) # remove the pdf file
tempo.cat <- ("\n\n================\n\nPROBLEM IN fun_open(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET).\nTO OVERCOME THIS, PLEASE SET pdf.disp ARGUMENT TO TRUE AND RERUN\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
}
}
}else{
open.fail <- NULL
quartz()
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
invisible(dev.off()) # close the new window
}
# end par.ini recovery 
zone.ini <- matrix(1, ncol=1) # to recover the initial parameters for next figure region when device region split into several figure regions
if(pdf.disp == TRUE){
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pdf.loc <- paste0(fun.path, "/", pdf.name.file, ".pdf")
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if(file.exists(pdf.loc) == TRUE & no.pdf.overwrite == TRUE){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": pdf.loc FILE ALREADY EXISTS AND CANNOT BE OVERWRITTEN DUE TO no.pdf.overwrite ARGUMENT SET TO TRUE: ", pdf.loc, "\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else{
pdf(width = width.fun, height = height.fun, file=pdf.loc, paper = paper)
}
}else if(pdf.disp == FALSE){
pdf.loc <- NULL
if(Sys.info()["sysname"] == "Windows"){ # .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
windows(width = width.fun, height = height.fun, rescale="fixed")
}else if(Sys.info()["sysname"] == "Linux"){
if( ! is.null(open.fail)){
tempo.cat <- "\n\n================\n\nPROBLEM IN fun_open(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET).\nTO OVERCOME THIS, PLEASE SET pdf.disp ARGUMENT TO TRUE AND RERUN\n\n================\n\n"
stop(tempo.cat, call. = FALSE)
}else{
X11(width = width.fun, height = height.fun)
}
}else{
quartz(width = width.fun, height = height.fun)
}
}
if(return.output == TRUE){
output <- list(pdf.loc = pdf.loc, ini.par = ini.par, zone.ini = zone.ini)
return(output)
}
}


######## fun_prior_plot() #### set graph param before plotting (erase axes for instance)


# Check OK: clear to go Apollo
fun_prior_plot <- function(param.reinitial = FALSE, xlog.scale = FALSE, ylog.scale = FALSE, remove.label = TRUE, remove.x.axis = TRUE, remove.y.axis = TRUE, std.x.range = TRUE, std.y.range = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 3.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = FALSE){
# AIM
# very convenient to erase the axes for post plot axis redrawing using fun_post_plot()
# reinitialize and set the graphic parameters before plotting
# CANNOT be used if no graphic device already opened
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# ARGUMENTS
# param.reinitial: reinitialize graphic parameters before applying the new ones, as defined by the other arguments? Either TRUE or FALSE
# xlog.scale: Log scale for the x-axis? Either TRUE or FALSE. If TRUE, erases the x-axis, except legend, for further drawing by fun_post_plot()(xlog argument of par())
# ylog.scale: Log scale for the y-axis? Either TRUE or FALSE. If TRUE, erases the y-axis, except legend, for further drawing by fun_post_plot()(ylog argument of par())
# remove.label: remove labels (axis legend) of the two axes? Either TRUE or FALSE (ann argument of par())
# remove.x.axis: remove x-axis except legend? Either TRUE or FALSE (control the xaxt argument of par()). Automately set to TRUE if xlog.scale == TRUE
# remove.y.axis: remove y-axis except legend? Either TRUE or FALSE (control the yaxt argument of par()). Automately set to TRUE if ylog.scale == TRUE
# std.x.range: standard range on the x-axis? TRUE (no range extend) or FALSE (4% range extend). Controls xaxs argument of par() (TRUE is xaxs = "i", FALSE is xaxs = "r")
# std.y.range: standard range on the y-axis? TRUE (no range extend) or FALSE (4% range extend). Controls yaxs argument of par() (TRUE is yaxs = "i", FALSE is yaxs = "r")
# down.space: lower vertical margin (in inches, mai argument of par())
# left.space: left horizontal margin (in inches, mai argument of par())
# up.space: upper vertical margin between plot region and grapical window (in inches, mai argument of par())
# right.space: right horizontal margin (in inches, mai argument of par())
# orient: scale number orientation (las argument of par()). 0, always parallel to the axis; 1, always horizontal; 2, always perpendicular to the axis; 3, always vertical
# dist.legend: numeric value that moves axis legends away in inches (first number of mgp argument of par() but in inches thus / 0.2)
# tick.length: length of the ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc. 0 means no tick
# box.type: bty argument of par(). Either "o", "l", "7", "c", "u", "]", the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box
# amplif.label: increase or decrease the size of the text in legends
# amplif.axis: increase or decrease the size of the scale numbers in axis
# display.extend: extend display beyond plotting region? Either TRUE or FALSE (xpd argument of par() without NA)
# return.par: return graphic parameter modification?
# RETURN
# return graphic parameter modification
# EXAMPLES
# fun_prior_plot(param.reinitial = FALSE, xlog.scale = FALSE, ylog.scale = FALSE, remove.label = TRUE, remove.x.axis = TRUE, remove.y.axis = TRUE, std.x.range = TRUE, std.y.range = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 4.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = FALSE)
# DEBUGGING
# param.reinitial = FALSE ; xlog.scale = FALSE ; ylog.scale = FALSE ; remove.label = TRUE ; remove.x.axis = TRUE ; remove.y.axis = TRUE ; std.x.range = TRUE ; std.y.range = TRUE ; down.space = 1 ; left.space = 1 ; up.space = 1 ; right.space = 1 ; orient = 1 ; dist.legend = 4.5 ; tick.length = 0.5 ; box.type = "n" ; amplif.label = 1 ; amplif.axis = 1 ; display.extend = FALSE ; return.par = 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){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# 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 = param.reinitial, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = xlog.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = ylog.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = remove.label, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = remove.x.axis, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = remove.y.axis, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = std.x.range, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = std.y.range, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = down.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = left.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = up.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = right.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = orient, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = dist.legend, 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 = box.type, options = c("o", "l", "7", "c", "u", "]", "n"), length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = amplif.label, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = amplif.axis, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = display.extend, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = return.par, 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
if(is.null(dev.list())){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THIS FUNCTION CANNOT BE USED IF NO GRAPHIC DEVICE ALREADY OPENED (dev.list() IS CURRENTLY NULL)\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# par.ini recovery
# cannot use pdf(file = NULL), because some small differences between pdf() and other devices. For instance, differences with windows() for par()$fin, par()$pin and par()$plt
if(param.reinitial == TRUE){
if( ! all(names(dev.cur()) == "null device")){
active.wind.nb <- dev.cur()
}else{
active.wind.nb <- 0
}
if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
windows()
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
invisible(dev.off()) # close the new window
}else if(Sys.info()["sysname"] == "Linux"){
if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THIS FUNCTION CANNOT BE USED ON LINUX WITH param.reinitial SET TO TRUE IF A Rplots.pdf FILE ALREADY EXISTS HERE: ", getwd(), "\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else{
open.fail <- suppressWarnings(try(X11(), silent = TRUE))[] # try to open a X11 window. If open.fail == NULL, no problem, meaning that the X11 window is opened. If open.fail != NULL, a pdf can be opened here paste0(getwd(), "/Rplots.pdf")
if(is.null(open.fail)){
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
invisible(dev.off()) # close the new window
}else if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
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
invisible(dev.off()) # close the new window
file.remove(paste0(getwd(), "/Rplots.pdf")) # remove the pdf file
}else{
tempo.cat <- ("\n\n================\n\nPROBLEM IN fun_prior_plot(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET).\nTO OVERCOME THIS, PLEASE USE PDF GRAPHIC INTERFACES AND RERUN\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
}
}else{ # macOS
quartz()
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)
invisible(dev.off()) # close the new window
}
if( ! all(names(dev.cur()) == "null device")){
dev.set(active.wind.nb) # go back to the active windows if exists
par(ini.par) # apply the initial par to current window
}
}
# end par.ini recovery
if(remove.x.axis == TRUE){
par(xaxt = "n") # suppress the y-axis label
}else{
par(xaxt = "s")
}
if(remove.y.axis == TRUE){
par(yaxt = "n") # suppress the y-axis label
}else{
par(yaxt = "s")
}
if(std.x.range == TRUE){
par(xaxs = "i")
}else{
par(xaxs = "r")
}
if(std.y.range == TRUE){
par(yaxs = "i")
}else{
par(yaxs = "r")
}
par(mai = c(down.space, left.space, up.space, right.space), ann = ! remove.label, las = orient, mgp = c(dist.legend/0.2, 1, 0), xpd = display.extend, bty= box.type, cex.lab = amplif.label, cex.axis = amplif.axis)
par(tcl = -par()$mgp[2] * tick.length) # tcl gives the length of the ticks as proportion of line text, knowing that mgp is in text lines. So the main ticks are a 0.5 of the distance of the axis numbers by default. The sign provides the side of the tick (negative for outside of the plot region)
if(xlog.scale == TRUE){
par(xaxt = "n", xlog = TRUE) # suppress the x-axis label
}else{
par(xlog = FALSE)
}
if(ylog.scale == TRUE){
par(yaxt = "n", ylog = TRUE) # suppress the y-axis label
}else{
par(ylog = FALSE)
}
if(return.par == TRUE){
tempo.par <- par()
return(tempo.par)
}
}


######## fun_scale() #### select nice label numbers when setting number of ticks on an axis


 


# Check OK: clear to go Apollo
fun_scale <- function(n, lim, kind = "approx", lib.path = NULL){
# AIM
# attempt to select nice scale numbers when setting n ticks on a lim axis range
# ARGUMENTS
# n: desired number of main ticks on the axis (integer more than 0)
# lim: vector of 2 numbers indicating the limit range of the axis. Order of the 2 values matters (for inverted axis). Can be log transformed values
# 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
# lib.path: absolute path of the required packages, if not in the default folders
# 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){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# 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)
if(tempo$problem == FALSE & ! all(dir.exists(lib.path))){
tempo.cat <- paste0("ERROR IN ", function.name, ": \nDIRECTORY PATH INDICATED IN THE lib.path PARAMETER DOES NOT EXISTS: ", lib.path)
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# end argument checking with fun_check()
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
lim.order <- order(lim) # to deal with inverted axis
lim <- sort(lim)
if(kind == "approx"){
# package checking
fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
fun_pack(req.package = c("scales"), lib.path = lib.path)
# end package checking
output <- ggplot2::ggplot_build(ggplot2::ggplot() + ggplot2::scale_y_continuous(
breaks = scales::trans_breaks(
trans = "identity", 
inv = "identity", 
n = n
), 
limits = lim
))$layout$panel_params[[1]]$y.major_source # 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]]
}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
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": THE INTERVAL BETWEEN TWO TICKS OF THE SCALE IS NULL. MODIFY THE lim OR n ARGUMENT\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
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{
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 1\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
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)){
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 2\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
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{
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 3\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
# 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){
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 4\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
if(any(is.na(output))){
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 5 (NA GENERATION)\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
# end last check
}else{
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 6\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
if(diff(lim.order) < 0){
output <- rev(output)
}
return(output)
}


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


 


# Check OK: clear to go Apollo
fun_post_plot <- function(x.side = 0, x.log.scale = FALSE, x.categ = NULL, x.categ.pos = NULL, x.lab = "", x.axis.magnific = 1.5, x.label.magnific = 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.magnific = 1.5, y.label.magnific = 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 = "", magnific.corner.text = 1, just.label.add = FALSE, par.reset = FALSE, custom.par = NULL){
# 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
# x.axis.magnific: increase or decrease the value to increase or decrease the size of the x axis numbers. Also control the size of displayed categories
# x.label.magnific: increase or decrease the value to increase or decrease the size of the x axis legend
# 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
# y.axis.magnific: increase or decrease the value to increase or decrease the size of the y axis numbers. Also control the size of displayed categories
# y.label.magnific: increase or decrease the value to increase or decrease the size of the y axis legend
# 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
# magnific.corner.text: increase or decrease the size of the text
# 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
# $text: warning text
# EXAMPLES
# Example of log axis with log y-axis and unmodified x-axis:
# prior.par <- fun_prior_plot(param.reinitial = TRUE, xlog.scale = FALSE, ylog.scale = TRUE, remove.label = TRUE, remove.x.axis = FALSE, remove.y.axis = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 0.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = TRUE) ; plot(1:100, log = "y") ; fun_post_plot(y.side = 2, y.log.scale = prior.par$ylog, x.lab = "Values", y.lab = "TEST", y.axis.magnific = 1.25, y.label.magnific = 1.5, y.dist.legend = 0.7, just.label.add = ! prior.par$ann)
# Example of log axis with redrawn x-axis and y-axis:
# prior.par <- fun_prior_plot(param.reinitial = TRUE) ; plot(1:100) ; fun_post_plot(x.side = 1, x.lab = "Values", y.side = 2, y.lab = "TEST", y.axis.magnific = 1, y.label.magnific = 2, y.dist.legend = 0.6)
# example with margins in the device region:
# windows(5,5) ; fun_prior_plot(box.type = "o") ; par(mai=c(0.5,0.5,0.5,0.5), omi = c(0.25,0.25,1,0.25), xaxs = "i", yaxs = "i") ; plot(0:10) ; a <- fun_post_plot(x.side = 0, y.side = 0) ; x <- c(a$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
# x.side = 0 ; x.log.scale = FALSE ; x.categ = NULL ; x.categ.pos = NULL ; x.lab = "" ; x.axis.magnific = 1.5 ; x.label.magnific = 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.magnific = 1.5 ; y.label.magnific = 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 = "" ; magnific.corner.text = 1 ; just.label.add = FALSE ; par.reset = FALSE ; custom.par = NULL # 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){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(length(utils::find("fun_open", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_open() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# 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)
tempo <- fun_check(data = x.axis.magnific, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = x.label.magnific, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
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)
tempo <- fun_check(data = y.axis.magnific, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = y.label.magnific, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
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)
tempo <- fun_check(data = magnific.corner.text, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
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
mtext(side = x.side, text = x.lab, line = x.dist.legend / 0.2, las = 0, cex = x.label.magnific)
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()$mgp[2] * tick.length) # back to main ticks
axis(side = x.side, at = c(1e-15, 1e-14, 1e-13, 1e-12, 1e-11, 1e-10, 1e-9, 1e-8, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10), labels = expression(10^-15, 10^-14, 10^-13, 10^-12, 10^-11, 10^-10, 10^-9, 10^-8, 10^-7, 10^-6, 10^-5, 10^-4, 10^-3, 10^-2, 10^-1, 10^0, 10^1, 10^2, 10^3, 10^4, 10^5, 10^6, 10^7, 10^8, 10^9, 10^10), lwd = 0, lwd.ticks = 1, cex.axis = x.axis.magnific)
x.text <- 10^par("usr")[2]
}else if(is.null(x.categ) & x.log.scale == FALSE){
axis(side=x.side, at=c(par()$usr[1], par()$usr[2]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
axis(side=x.side, at=round(seq(par()$xaxp[1], par()$xaxp[2], length.out=par()$xaxp[3]+1), 2), cex.axis = x.axis.magnific) # 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.magnific) # to get the 1000 comma separator
mtext(side = x.side, text = x.lab, line = x.dist.legend / 0.2, las = 0, cex = x.label.magnific)
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()$mgp[2] * tick.length) # back to main ticks
}
x.text <- par("usr")[2]
}else if(( ! is.null(x.categ)) & x.log.scale == FALSE){
if(is.null(x.categ.pos)){
x.categ.pos <- 1:length(x.categ)
}else if(length(x.categ.pos) != length(x.categ)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": x.categ.pos MUST BE THE SAME LENGTH AS x.categ\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
par(xpd = TRUE)
if(isTRUE(all.equal(x.side, 1))){ #isTRUE(all.equal(x.side, 1)) is similar to x.side == 1 but deals with float
segments(x0 = x.left.plot.region, x1 = x.right.plot.region, y0 = y.bottom.plot.region, y1 = y.bottom.plot.region) # draw the line of the axis
text(x = x.categ.pos, y = y.mid.bottom.fig.region, labels = x.categ, srt = text.angle, cex = x.axis.magnific)
}else if(isTRUE(all.equal(x.side, 3))){ #isTRUE(all.equal(x.side, 1)) is similar to x.side == 3 but deals with float
segments(x0 = x.left.plot.region, x1 = x.right.plot.region, y0 = y.top.plot.region, y1 = y.top.plot.region) # draw the line of the axis
text(x = x.categ.pos, y = y.mid.top.fig.region, labels = x.categ, srt = text.angle, cex = x.axis.magnific)
}else{
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ARGUMENT x.side CAN ONLY BE 1 OR 3\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
par(xpd = FALSE)
x.text <- par("usr")[2]
}else{
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": PROBLEM WITH THE x.side (", x.side ,") OR x.log.scale (", x.log.scale,") ARGUMENTS\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
}else{
x.text <- par("usr")[2]
}
if(any(sapply(FUN = all.equal, c(2, 4), y.side) == TRUE)){
par(xpd=FALSE, yaxt="s")
if(is.null(y.categ) & y.log.scale == TRUE){
if(any(par()$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()$mgp[2] * tick.length) # back to main tick length
axis(side = y.side, at = c(1e-15, 1e-14, 1e-13, 1e-12, 1e-11, 1e-10, 1e-9, 1e-8, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10), labels = expression(10^-15, 10^-14, 10^-13, 10^-12, 10^-11, 10^-10, 10^-9, 10^-8, 10^-7, 10^-6, 10^-5, 10^-4, 10^-3, 10^-2, 10^-1, 10^0, 10^1, 10^2, 10^3, 10^4, 10^5, 10^6, 10^7, 10^8, 10^9, 10^10), lwd = 0, lwd.ticks = 1, cex.axis = y.axis.magnific)
y.text <- 10^(par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
mtext(side = y.side, text = y.lab, line = y.dist.legend / 0.2, las = 0, cex = y.label.magnific)
}else if(is.null(y.categ) & y.log.scale == FALSE){
axis(side=y.side, at=c(par()$usr[3], par()$usr[4]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
axis(side=y.side, at=round(seq(par()$yaxp[1], par()$yaxp[2], length.out=par()$yaxp[3]+1), 2), cex.axis = y.axis.magnific)
mtext(side = y.side, text = y.lab, line = y.dist.legend / 0.2, las = 0, cex = y.label.magnific)
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)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": y.categ.pos MUST BE THE SAME LENGTH AS y.categ\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
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
text(x = x.mid.left.fig.region, y = y.categ.pos, labels = y.categ, srt = text.angle, cex = y.axis.magnific)
}else if(isTRUE(all.equal(y.side, 4))){ # idem
text(x = x.mid.right.fig.region, y = y.categ.pos, labels = y.categ, srt = text.angle, cex = y.axis.magnific)
}else{
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ARGUMENT y.side CAN ONLY BE 2 OR 4\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
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{
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": PROBLEM WITH THE y.side (", y.side ,") OR y.log.scale (", y.log.scale,") ARGUMENTSn\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
}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)
text(x = x.mid.right.fig.region, y = y.text, corner.text, adj=c(1, 1.1), cex = magnific.corner.text) # text at the topright corner. Replace x.right.fig.region by x.text if text at the right edge of the plot region
if(just.label.add == TRUE & isTRUE(all.equal(x.side, 0)) & x.lab != ""){
text(x = x.mid.plot.region, y = y.mid.bottom.fig.region, x.lab, adj=c(0.5, 0.5), cex = x.label.magnific) # x label
}
if(just.label.add == TRUE & isTRUE(all.equal(y.side, 0)) & y.lab != ""){
text(x = y.mid.plot.region, y = x.mid.left.fig.region, y.lab, adj=c(0.5, 0.5), cex = y.label.magnific) # x label
}
par(xpd=FALSE)
if(par.reset == TRUE){
tempo.par <- fun_open(pdf.disp = FALSE, return.output = TRUE)
invisible(dev.off()) # close the new window
if( ! is.null(custom.par)){
if( ! names(custom.par) %in% names(tempo.par$ini.par)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": custom.par ARGUMENT SHOULD HAVE THE NAMES OF THE COMPARTMENT LIST COMING FROM THE par() LIST\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
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)
}