cute_little_R_functions.R 616 KB
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par(xpd=FALSE, xaxt="s")
if(is.null(x.categ) & x.log.scale == TRUE){
if(any(par()$xaxp[1:2] == 0)){
if(par()$xaxp[1] == 0){
par(xaxp = c(10^-30, par()$xaxp[2:3])) # because log10(par()$xaxp[1] == 0) == -Inf
}
if(par()$xaxp[2] == 0){
par(xaxp = c(par()$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()$mgp[2] * tick.length) # back to main ticks
}
x.text <- par("usr")[2]
}else if(( ! is.null(x.categ)) & x.log.scale == FALSE){
if(is.null(x.categ.pos)){
x.categ.pos <- 1:length(x.categ)
}else if(length(x.categ.pos) != length(x.categ)){
stop("\n\nPROBLEM: x.categ.pos MUST BE THE SAME LENGTH AS x.categ\n\n")
}
par(xpd = TRUE)
if(x.side == 1){
segments(x0 = x.left.plot.region, x1 = x.right.plot.region, y0 = y.bottom.plot.region, y1 = y.bottom.plot.region) # draw the line of the axis
text(x = x.categ.pos, y = y.mid.bottom.fig.region, labels = x.categ, srt = text.angle, cex = x.axis.magnific)
}else if(x.side == 3){
segments(x0 = x.left.plot.region, x1 = x.right.plot.region, y0 = y.top.plot.region, y1 = y.top.plot.region) # draw the line of the axis
text(x = x.categ.pos, y = y.mid.top.fig.region, labels = x.categ, srt = text.angle, cex = x.axis.magnific)
}else{
stop("\n\nARGUMENT x.side CAN ONLY BE 1 OR 3\n\n")
}
par(xpd = FALSE)
x.text <- par("usr")[2]
}else{
stop("\n\nPROBLEM WITH THE x.side (", x.side ,") OR x.log.scale (", x.log.scale,") ARGUMENTS\n\n")
}
}else{
x.text <- par("usr")[2]
}
if(y.side == 2 | y.side == 4){
par(xpd=FALSE, yaxt="s")
if(is.null(y.categ) & y.log.scale == TRUE){
if(any(par()$yaxp[1:2] == 0)){
if(par()$yaxp[1] == 0){
par(yaxp = c(10^-30, par()$yaxp[2:3])) # because log10(par()$yaxp[1] == 0) == -Inf
}
if(par()$yaxp[2] == 0){
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)){
stop("\n\nPROBLEM: y.categ.pos MUST BE THE SAME LENGTH AS y.categ\n\n")
}
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(y.side == 2){
text(x = x.mid.left.fig.region, y = y.categ.pos, labels = y.categ, srt = text.angle, cex = y.axis.magnific)
}else if(y.side == 4){
text(x = x.mid.right.fig.region, y = y.categ.pos, labels = y.categ, srt = text.angle, cex = y.axis.magnific)
}else{
stop("\n\nARGUMENT y.side CAN ONLY BE 2 OR 4\n\n")
}
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{
stop("\n\nPROBLEM WITH THE y.side (", y.side ,") OR y.log.scale (", y.log.scale,") ARGUMENTS\n\n")
}
}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 & 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 & 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_window(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$ini.par)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": custom.par ARGUMENT SHOULD HAVE THE NAMES OF THE COMPARTMENT LIST COMING FROM THE par() LIST\n\n================\n\n")
stop(tempo.cat)
}
par(custom.par)
text <- c(text, "\nGRAPH PARAMETERS SET TO VALUES DEFINED BY custom.par ARGUMENT\n")
}else{
par(tempo.par$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)
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}


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######## fun_close_specif_window() #### close specific graphic windows
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# Check OK: clear to go Apollo
fun_close_specif_window <- function(kind = "pdf", return.text = FALSE){
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# AIM
# close only specific graphic windows (devices)
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_param_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_specif_window(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(find("fun_param_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat)
}
# end required function checking
# argument checking
arg.check <- NULL # for function debbuging
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
tempo <- fun_param_check(data = kind, options = c("windows", "quartz", "x11", "X11", "pdf", "bmp", "png", "tiff"), fun.name = function.name) ; eval(ee)
tempo <- fun_param_check(data = return.text, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop() # nothing else because print = TRUE by default in fun_param_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_param_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_param_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)
}
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}


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


# Check OK: clear to go Apollo
fun_empty_graph <- function(text, title = NULL, text.size = 1){
# 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
# REQUIRED PACKAGES
# none
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_param_check()
# RETURN
# an empty plot
# EXAMPLES
# fun_empty_graph(text = "NO GRAPH", title = "GRAPH1")
# 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(find("fun_param_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat)
}
# end required function checking
# argument checking
arg.check <- NULL # for function debbuging
checked.arg.names <- NULL # for function debbuging
ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
tempo <- fun_param_check(data = text, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_param_check(data = text.size, class = "vector", mode = "numeric", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop() # nothing else because print = TRUE by default in fun_param_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_param_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_param_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]))
text(x = 1, y = 1, labels = text, cex = text.size)
text(x = x.left.dev.region, y = y.top.dev.region, labels = title, adj=c(0, 1), cex = text.size)
par(ini.par)
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}


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################ gg graphics
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######## fun_gg_palette() #### ggplot2 default color palette
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# Check OK: clear to go Apollo
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fun_gg_palette <- function(n){
# 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
# REQUIRED PACKAGES
# none
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_param_check()
# RETURN
# the vector of hexadecimal colors
# EXAMPLES
# fun_gg_palette(n = 2)
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# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7)) # the ggplot2 palette when 7 different colors
# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7)[5]) # selection of the 5th color of the ggplot2 palette when 7 different colors
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# DEBUGGING
# n = 0
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(find("fun_param_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat)
}
# end required function checking
# argument checking
arg.check <- NULL # for function debbuging
checked.arg.names <- NULL # for function debbuging
ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
tempo <- fun_param_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 & n == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": n ARGUMENT MUST BE A NON ZERO INTEGER. HERE IT IS: ", paste(n, collapse = " "), "\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}
if(any(arg.check) == TRUE){
stop() # nothing else because print = TRUE by default in fun_param_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_param_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_param_check()
# end argument checking
# main code
hues = seq(15, 375, length = n + 1)
hcl(h = hues, l = 65, c = 100)[1:n]
}


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


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# Check OK: clear to go Apollo
fun_gg_just <- function(angle, axis){
# AIM
# provide correct justification for axis labeling, depending on the chosen angle
# ARGUMENTS
# angle: integer value of the text angle for the axis labels. 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.
# axis: which axis for? Either "x" or "y"
# REQUIRED PACKAGES
# none
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_param_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)
# $hjust: the horizontal justification
# $vjust: the vertical justification
# EXAMPLES
# fun_gg_just(angle = 45, axis = "x")
# fun_gg_just(angle = (360*2 + 45), axis = "y")
# output <- fun_gg_just(angle = 45, axis = "x") ; obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10)) ; ggplot2::ggplot() + ggplot2::geom_bar(data = obs1, mapping = ggplot2::aes(x = group, y = time), stat = "identity") + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = output$angle, hjust = output$hjust, vjust = output$vjust))
# output <- fun_gg_just(angle = -45, axis = "y") ; obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10)) ; ggplot2::ggplot() + ggplot2::geom_bar(data = obs1, mapping = ggplot2::aes(x = group, y = time), stat = "identity") + ggplot2::theme(axis.text.y = ggplot2::element_text(angle = output$angle, hjust = output$hjust, vjust = output$vjust)) + ggplot2::coord_flip()
# output1 <- fun_gg_just(angle = 90, axis = "x") ; output2 <- fun_gg_just(angle = -45, axis = "y") ; obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10)) ; ggplot2::ggplot() + ggplot2::geom_bar(data = obs1, mapping = ggplot2::aes(x = group, y = time), stat = "identity") + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = output1$angle, hjust = output1$hjust, vjust = output1$vjust), axis.text.y = ggplot2::element_text(angle = output2$angle, hjust = output2$hjust, vjust = output2$vjust))
# DEBUGGING
# angle = 45 ; axis = "y"
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(find("fun_param_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat)
}
# end required function checking
# argument checking
arg.check <- NULL # for function debbuging
checked.arg.names <- NULL # for function debbuging
ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
tempo <- fun_param_check(data = angle, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_param_check(data = axis, options = c("x", "y"), length = 1, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop() # nothing else because print = TRUE by default in fun_param_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_param_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_param_check()
# end argument checking
# main code
# to get angle between -360 and 360
while(angle > 360){
angle <- angle - 360
}
while(angle < -360){
angle <- angle + 360
}
# end to get angle between -360 and 360
# justifications
if(axis == "x"){
if(angle == -360 | angle == -180 | angle == 0 | angle == 180 | angle == 360){
hjust <- 0.5
vjust <- 0.5
}else if(angle == -270 | angle == 90){
hjust <- 1
vjust <- 0.5
}else if(angle == -90 | angle == 270){
hjust <- 0
vjust <- 0.5
}else if((angle > -360 & angle < -270) | (angle > 0 & angle < 90)){
hjust <- 1
vjust <- 1
}else if((angle > -270 & angle < -180) | (angle > 90 & angle < 180)){
hjust <- 1
vjust <- 0
}else if((angle > -180 & angle < -90) | (angle > 180 & angle < 270)){
hjust <- 0
vjust <- 0
}else if((angle > -90 & angle < 0) | (angle > 270 & angle < 360)){
hjust <- 0
vjust <- 1
}
}else if(axis == "y"){
if(angle == -270 | angle == -90 | angle == 90 | angle == 270){
hjust <- 0.5
vjust <- 0.5
}else if(angle == -360 | angle == 0 | angle == 360){
hjust <- 1
vjust <- 0.5
}else if(angle == -180 | angle == 180){
hjust <- 0
vjust <- 0.5
}else if((angle > -360 & angle < -270) | (angle > 0 & angle < 90)){
hjust <- 1
vjust <- 0
}else if((angle > -270 & angle < -180) | (angle > 90 & angle < 180)){
hjust <- 0
vjust <- 0
}else if((angle > -180 & angle < -90) | (angle > 180 & angle < 270)){
hjust <- 0
vjust <- 1
}else if((angle > -90 & angle < 0) | (angle > 270 & angle < 360)){
hjust <- 1
vjust <- 1
}
}
# end justifications
output <- list(angle = angle, hjust = hjust, vjust = vjust)
return(output)
}


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######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer


# Check OK: clear to go Apollo
fun_gg_point_rast <- function(data = NULL, mapping = NULL, stat = "identity", position = "identity", ..., na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, raster.width = NULL, raster.height = NULL, raster.dpi = 300, inactivate = TRUE, path.lib = NULL){
# AIM
# equivalent to ggplot2::geom_point() but in raster mode
# use it like ggplot2::geom_point() with the main raster.dpi additional argument
# WARNINGS
# can be long to generate the plot
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# use a square plot region. Otherwise, the dots will have ellipsoid shape
# solve the transparency problems with some GUI
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# this function derives from the geom_point_rast() function, created by VPetukhov, and present in the ggrastr package (https://rdrr.io/github/VPetukhov/ggrastr/src/R/geom-point-rast.R). Has been placed here to minimize package dependencies
# ARGUMENTS
# classical arguments of geom_point(), shown here https://rdrr.io/github/VPetukhov/ggrastr/man/geom_point_rast.html
# raster.width : width of the result image (in inches). Default: deterined by the current device parameters
# raster.height: height of the result image (in inches). Default: deterined by the current device parameters
# raster.dpi: resolution of the result image
# inactivate: logical. Inactivate the fun.name argument of the fun_param_check() function? If TRUE, the name of the fun_param_check() function in error messages coming from this function. Use TRUE if fun_gg_point_rast() is used like this: eval(parse(text = "fun_gg_point_rast"))
# path.lib: absolute path of the required packages, if not in the default folders
# REQUIRED PACKAGES
# ggplot2
# grid
# Cairo
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_param_check()
# fun_pack_import()
# RETURN
# a raster scatter plot
# EXAMPLES
# Two pdf in the current directory
# set.seed(1) ; data1 = data.frame(x = rnorm(100000), y = rnorm(10000)) ; fun_open_window(pdf.name.file = "Raster") ; ggplot2::ggplot() + fun_gg_point_rast(data = data1, mapping = ggplot2::aes(x = x, y = y)) ; fun_open_window(pdf.name.file = "Vectorial") ; ggplot2::ggplot() + ggplot2::geom_point(data = data1, mapping = ggplot2::aes(x = x, y = y)) ; dev.off() ; dev.off()
# DEBUGGING
# 
# function name
if(all(inactivate == FALSE)){ # inactivate has to be used here but will be fully checked below
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
}else if(all(inactivate == TRUE)){
function.name <- NULL
}else{
tempo.cat <- (paste0("\n\n============\n\nERROR IN fun_gg_point_rast(): CODE INCONSISTENCY 1\n\n============\n\n"))
stop(tempo.cat)
}
# end function name
# required function checking
if(length(find("fun_param_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat)
}
if(length(find("fun_pack_import", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_pack_import() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat)
}
# end required function checking
# argument checking
arg.check <- NULL # for function debbuging
checked.arg.names <- NULL # for function debbuging
ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
if( ! is.null(data)){
tempo <- fun_param_check(data = data, class = "data.frame", fun.name = function.name) ; eval(ee)
}
if( ! is.null(mapping)){
tempo <- fun_param_check(data = mapping, class = "uneval", typeof = "list", fun.name = function.name) ; eval(ee) # aes() is tested
}
# stat and position not tested because too complicate
tempo <- fun_param_check(data = na.rm, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_param_check(data = show.legend, class = "vector", mode = "logical", length = 1, na.contain = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_param_check(data = inherit.aes, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(raster.width)){
tempo <- fun_param_check(data = raster.width, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
}
if( ! is.null(raster.height)){
tempo <- fun_param_check(data = raster.height, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
}
tempo <- fun_param_check(data = raster.dpi, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_param_check(data = inactivate, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(path.lib)){
tempo <- fun_param_check(data = path.lib, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE & ! all(dir.exists(path.lib))){
cat(paste0("\n\n============\n\nERROR IN ", function.name, ": \nDIRECTORY PATH INDICATED IN THE path.lib PARAMETER DOES NOT EXISTS: ", path.lib, "\n\n============\n\n"))
arg.check <- c(arg.check, TRUE)
}
}
if(any(arg.check) == TRUE){
stop() # nothing else because print = TRUE by default in fun_param_check()
}
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_param_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_param_check()
# end argument checking
# package checking
fun_pack_import(req.package = c("ggplot2"), path.lib = path.lib)
fun_pack_import(req.package = c("grid"), path.lib = path.lib)
fun_pack_import(req.package = c("Cairo"), path.lib = path.lib)
# end package checking
# additional functions
DrawGeomPointRast <- function(data, panel_params, coord, na.rm = FALSE, raster.width = NULL, raster.height= NULL, raster.dpi = 300){
if (is.null(raster.width)){
raster.width <- par('fin')[1]
}
if (is.null(raster.height)){
 raster.height <- par('fin')[2]
}
prev_dev_id <- dev.cur()
p <- ggplot2::GeomPoint$draw_panel(data, panel_params, coord)
dev_id <- Cairo::Cairo(type='raster', width = raster.width*raster.dpi, height = raster.height*raster.dpi, dpi = raster.dpi, units = 'px', bg = "transparent")[1]
grid::pushViewport(grid::viewport(width = 1, height = 1))
grid::grid.points(x = p$x, y = p$y, pch = p$pch, size = p$size,
name = p$name, gp = p$gp, vp = p$vp, draw = T)
grid::popViewport()
cap <- grid::grid.cap()
dev.off(dev_id)
dev.set(prev_dev_id)
grid::rasterGrob(cap, x = 0, y = 0, width = 1, height = 1, default.units = "native", just = c("left","bottom"))
}
# end additional functions
# main code
GeomPointRast <- ggplot2::ggproto("GeomPointRast", ggplot2::GeomPoint, draw_panel = DrawGeomPointRast)
ggplot2::layer(
data = data, 
mapping = mapping, 
stat = stat, 
geom = GeomPointRast, 
position = position, 
show.legend = show.legend, 
inherit.aes = inherit.aes, 
params = list(
na.rm = na.rm, 
raster.width = raster.width, 
raster.height = raster.height, 
raster.dpi = raster.dpi, 
...
)
)
# end main code
}


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######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally)


# Check OK: clear to go Apollo
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fun_gg_scatter <- function(data1, x, y, categ = NULL, legend.name = NULL, color = NULL, geom = "geom_point", alpha = 0.5, dot.size = 2, line.size = 0.5, xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = NULL, ylab = NULL, title = "", text.size = 12, classic = FALSE, grid = FALSE, raster = FALSE, vectorial.limit = NULL, return = FALSE, path.lib = NULL){
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# AIM
# ggplot2 scatterplot with the possibility to overlay dots from up to 3 different data frames and lines from up to 3 different data frames (up to 6 overlays totally)
# for ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
# WARNINGS
# rows containing NA in data1[, c(y, categ)] will be removed before processing, with a warning (see below)
# ARGUMENTS
# data1: a dataframe compatible with ggplot, or a list of data frames
# x: character string or list of character string (one compartment for each list compartment of data1) of the data1 column name for x-axis
# y: character string or list of character string (one compartment for each list compartment of data1) of the data1 column name for y-axis. Write NULL for hline or vline geom
# categ: character string or list of character string (one compartment for each list compartment of data1) of the data1 column name for categories. If categ = NULL, no categories (no legend). Some of the list compartments can be NULL, and other not
# legend.name: character string list of character string (one compartment for each list compartment of data1) of the legend title. If legend.name = NULL and categ != NULL, then legend.name <- categ. Some of the list compartments can be NULL, and other not
# color: vector of character string or list of character vectors (one compartment for each list compartment of data1) for the colors of categ arguments. If color = NULL, default colors of ggplot2. If non null, it can be either: (1) a single color string (all the dots of the corresponding data1 will have this color, whatever categ NULL or not), (2) if categ non null, a vector of string colors, one for each class of categ (each color will be associated according to the alphabetical order of categ classes), (3) if categ non null, a vector or factor of string colors, like if it was one of the column of data1 data frame (beware: a single color per class of categ and a single class of categ per color must be respected). Integers are also accepted instead of character strings, as long as above rules about length are respected. Integers will be processed by fun_gg_palette() using the max integer value among all the integers in color. If color is a list, some of the compartments can be NULL. In that case, a different grey color will be used for each NULL compartment
# geom: character string or list of character string (one compartment for each list compartment of data1) for the kind of plot. Either "geom_point" (scatterplot), "geom_line" (coordinates plotted then line connection from the lowest to highest coordinates), "geom_path" (line connection respecting the order in data1), "geom_hline" (horizontal line) or "geom_vline" (vertical line). BEWARE: for "geom_hline" or "geom_vline", (1) y argument must be NULL, (2) the function will draw n lines for n values in the x argument column name of the data1 data frame. If several colors required, the categ argument must be specified and the corresponding categ column name must exist in the data1 data frame
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# alpha: numeric value (from 0 to 1) of the transparency or list of numeric values (one compartment for each list compartment of data1)
# dot.size: numeric value of point size
# line.size: numeric value of line size
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# xlim: 2 numeric values for x-axis range. If NULL, range of x of all the data frames in data1 (excluding Inf, NA and NaN)
# ylim: 2 numeric values for y-axis range. If NULL, range of y of all the data frames in data1 (excluding Inf, NA and NaN)
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# extra.margin: single proportion (between 0 and 1) indicating if extra margins must be added to xlim and ylim. If different from 0, add the range of the axis * extra.margin (e.g., abs(xlim[2] - xlim[1]) * extra.margin) on each side of the axis
# xlab: a character string for x-axis legend. If NULL, x of the first data frame in data1. Warning message if the x are different between data frames in data1
# ylab: a character string y-axis legend. If NULL, y of the first data frame in data1. Warning message if the y are different between data frames in data1
# title: character string of the graph title
# text.size: numeric value of the text size (in points)
# classic: logical. Use the classic theme (article like)?
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# grid: logical. Draw horizontal and vertical lines in the background to better read the values? Not considered if classic = FALSE
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# raster: logical. Dots in raster mode? If FALSE, dots from each geom_point from geom argument are in vectorial mode (bigger pdf and long to display if millions of dots). If TRUE, dots from each geom_point from geom argument are in matricial mode (smaller pdf and easy display if millions of dots, but long to generate the layer). If TRUE, the region plot will be square to avoid a bug in fun_gg_point_rast(). If TRUE, solve the transparency problem with some GUI. Overriden by vectorial.limit if non NULL
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# vectorial.limit: positive integer value indicating the limit of the dot number above which geom_point from geom argument switch from vectorial mode to raster mode (see the raster argument). If any layer is raster, then the region plot will be square to avoid a bug in fun_gg_point_rast(). Inactive the raster argument if non NULL
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# return: logical. Return the graph parameters?
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# path.lib: absolute path of the required packages, if not in the default folders
# REQUIRED PACKAGES
# ggplot2
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# if raster plots are drawn (see the raster and vectorial.limit arguments):
# Cairo
# grid
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# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_gg_palette()
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# fun_gg_point_rast()
# fun_pack_import()
# fun_param_check()
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# RETURN
# a scatter plot
# a list of the graph info if return argument is TRUE:
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# $data: the graphic info coordinates
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# $removed.row.nb: a list of the removed rows numbers in data frames (because of NA). NULL if no row removed
# $removed.rows: a list of the removed rows in data frames (because of NA). NULL if no row removed
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# $warnings: the warning messages
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# EXAMPLES
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# simple scatter plot
# obs1 <- data.frame(km = 1:6, time = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")) ; obs1 ; fun_gg_scatter(data1 =obs1, x = "km", y = "time", categ = "group")
# the same but using the list writting (geom and alpha have to be included because the default value are not lists)
# obs1 <- data.frame(km = 1:6, time = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")) ; obs1 ; fun_gg_scatter(data1 = list(L1 = obs1), x = list(L1 = "km"), y = list(L1 = "time"), categ = list(L1 = "group"), geom = list(L1 = "geom_point"), alpha = list(L1 = 1))
# obs1 <- data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")) ; obs1 ; fun_gg_scatter(data1 = list(L1 = obs1), x = list(L1 = names(obs1)[1]), y = list(L1 = names(obs1)[2]), categ = NULL, legend.name = NULL, geom = list(L1 = "geom_point"), alpha = list(L1 = 1), xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = "test_x", ylab = "test_y", color = list(L1 = 5), dot.size = 2, line.size = 0.5, title = "GRAPH1", text.size = 15, classic = FALSE, return = TRUE)
# obs1 <- data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")) ; obs1 ; fun_gg_scatter(data1 = list(L1 = obs1), x = list(L1 = names(obs1)[1]), y = list(L1 = names(obs1)[2]), categ = NULL, legend.name = NULL, geom = list(L1 = "geom_path"), alpha = list(L1 = 1), xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = "test_x", ylab = "test_y", color = list(L1 = 5), dot.size = 2, line.size = 0.5, title = "GRAPH1", text.size = 15, classic = FALSE, return = TRUE)
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")), L2 = data.frame(a = (1:6)*2, b = ((1:6)^2)*2, group = c("A1", "A1", "A1", "B1", "B1", "B1"))) ; data1 ; fun_gg_scatter(data1 = data1, x = list(L1 = names(data1$L1)[1], L2 = names(data1$L2)[1]), y = list(L1 = names(data1$L1)[2], L2 = names(data1$L2)[2]), categ = list(L1 = names(data1$L1)[3], L2 = names(data1$L2)[3]), legend.name = list(L1 = "GROUP1", L2 = "GROUP2"), color = list(L1 = fun_gg_palette(4)[1:2], L2 = fun_gg_palette(4)[3:4]), geom = list(L1 = "geom_point", L2 = "geom_point"), alpha = list(L1 = 0.5, L2 = 0.5), xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = NULL, ylab = NULL, dot.size = 2, line.size = 0.5, title = "GRAPH1", text.size = 12, classic = FALSE, return = TRUE)
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")), L2 = data.frame(a = (1:6)*2, b = ((1:6)^2)*2, group = c("A1", "A1", "A1", "B1", "B1", "B1")), L3 = data.frame(a = (1:6)*3, b = ((1:6)^2)*3, group3 = c("A2", "A2", "A3", "A3", "B1", "B1"))) ; data1 ; fun_gg_scatter(data1 = data1, x = list(L1 = names(data1$L1)[1], L2 = names(data1$L2)[1], L3 = names(data1$L3)[1]), y = list(L1 = names(data1$L1)[2], L2 = names(data1$L2)[2], L3 = names(data1$L3)[2]), categ = list(L1 = names(data1$L1)[3], L2 = names(data1$L2)[3], L3 = names(data1$L3)[3]), legend.name = NULL, color = list(L1 = fun_gg_palette(7)[1:2], L2 = fun_gg_palette(7)[3:4], L3 = fun_gg_palette(7)[5:7]), geom = list(L1 = "geom_point", L2 = "geom_point", L3 = "geom_path"), , alpha = list(L1 = 0.5, L2 = 0.5, L3 = 0.5), xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = NULL, ylab = NULL, dot.size = 4, line.size = 0.5, title = "GRAPH1", text.size = 12, classic = FALSE, return = TRUE)
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")), L2 = data.frame(a = (1:6)*2, b = ((1:6)^2)*2, group = c("A1", "A1", "A1", "B1", "B1", "B1")), L3 = data.frame(a = (1:6)*3, b = ((1:6)^2)*3, group3 = c("A2", "A2", "A3", "A3", "B1", "B1"))) ; data1 ; fun_gg_scatter(data1 = data1, x = list(L1 = names(data1$L1)[1], L2 = names(data1$L2)[1], L3 = names(data1$L3)[1]), y = list(L1 = names(data1$L1)[2], L2 = names(data1$L2)[2], L3 = names(data1$L3)[2]), categ = list(L1 = names(data1$L1)[3], L2 = names(data1$L2)[3], NULL), legend.name = NULL, color = list(L1 = fun_gg_palette(7)[1:2], L2 = fun_gg_palette(7)[3:4], L3 = NULL), geom = list(L1 = "geom_point", L2 = "geom_point", L3 = "geom_path"), alpha = list(L1 = 0.5, L2 = 0.5, L3 = 0.5), xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = NULL, ylab = NULL, dot.size = 4, line.size = 0.5, title = "GRAPH1", text.size = 12, classic = FALSE, return = TRUE)
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")), L2 = data.frame(a = (1:6)*2, b = ((1:6)^2)*2, group = c("A1", "A1", "A1", "B1", "B1", "B1")), L3 = data.frame(a = (1:6)*3, b = ((1:6)^2)*3, group3 = c("A4", "A5", "A6", "A7", "B4", "B5"))) ; data1 ; fun_gg_scatter(data1 = data1, x = list(L1 = names(data1$L1)[1], L2 = names(data1$L2)[1], L3 = names(data1$L3)[1]), y = list(L1 = names(data1$L1)[2], L2 = names(data1$L2)[2], L3 = NULL), categ = list(L1 = names(data1$L1)[3], L2 = names(data1$L2)[3], L3 = names(data1$L3)[3]), legend.name = NULL, color = list(L1 = "red", L2 = "blue", L3 = "green"), geom = list(L1 = "geom_point", L2 = "geom_point", L3 = "geom_vline"),  alpha = list(L1 = 0.5, L2 = 0.5, L3 = 0.5), xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = NULL, ylab = NULL, dot.size = 4, line.size = 0.5, title = "GRAPH1", text.size = 12, classic = FALSE, return = TRUE)
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")), L2 = data.frame(a = (1:6)*2, b = ((1:6)^2)*2, group = c("A1", "A1", "A1", "B1", "B1", "B1")), L3 = data.frame(a = (1:6)*3, b = ((1:6)^2)*3, group3 = c("A4", "A5", "A6", "A7", "B4", "B5"))) ; data1$L1$a[3] <- NA ; data1$L1$group[5] <- NA ; data1$L3$group3[4] <- NA ; data1 ; fun_gg_scatter(data1 = data1, x = list(L1 = names(data1$L1)[1], L2 = names(data1$L2)[1], L3 = names(data1$L3)[1]), y = list(L1 = names(data1$L1)[2], L2 = names(data1$L2)[2], L3 = NULL), categ = list(L1 = names(data1$L1)[3], L2 = names(data1$L2)[3], L3 = names(data1$L3)[3]), legend.name = NULL, color = list(L1 = "red", L2 = "blue", L3 = "green"), geom = list(L1 = "geom_point", L2 = "geom_point", L3 = "geom_vline"),  alpha = list(L1 = 0.5, L2 = 0.5, L3 = 0.5), xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = NULL, ylab = NULL, dot.size = 4, line.size = 0.5, title = "GRAPH1", text.size = 12, classic = FALSE, return = TRUE)
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")), L2 = data.frame(a = (1:6)*2, b = ((1:6)^2)*2, group = c("A1", "A1", "A1", "B1", "B1", "B1")), L3 = data.frame(a = (1:6)*3, b = ((1:6)^2)*3, group3 = c("A2", "A2", "A3", "A3", "B1", "B1"))) ; data1 ; fun_gg_scatter(data1 = data1, x = list(L1 = names(data1$L1)[1], L2 = names(data1$L2)[1], L3 = names(data1$L3)[1]), y = list(L1 = names(data1$L1)[2], L2 = names(data1$L2)[2], L3 = names(data1$L3)[2]), categ = NULL, legend.name = list(L1 = "A", L2 = "B", L3 = "C"), color = list(L1 = "black", L2 = 2, L3 = "purple"), geom = list(L1 = "geom_point", L2 = "geom_point", L3 = "geom_point"),  alpha = list(L1 = 1, L2 = 1, L3 = 1), xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = NULL, ylab = NULL, dot.size = 1, line.size = 0.5, title = "GRAPH1", text.size = 20, classic = TRUE, return = TRUE)
# whole arguments
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A1", "A2", "A3", "B1", "B2", "B3"))) ; data1$L1$a[2:3] <- NA ; x = list(L1 = names(data1$L1)[1]) ; y = list(L1 = NULL) ; categ = list(L1 = names(data1$L1)[3]) ; data1 ; fun_gg_scatter(data1 = data1, x = list(L1 = names(data1$L1)[1]), y = list(L1 = NULL), categ = list(L1 = names(data1$L1)[3]), legend.name = list(L1 = "VALUE"), color = list(L1 = "red"), geom = list(L1 = "geom_hline"),  alpha = list(L1 = 0.5), xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = NULL, ylab = NULL, dot.size = 1, line.size = 0.5, title = "GRAPH1", text.size = 12, classic = TRUE, grid = TRUE, return = TRUE)
# whole arguments
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# set.seed(1) ; obs1 <- data.frame(km = rnorm(1000, 10, 3), time = rnorm(1000, 10, 3), group1 = rep(c("A1", "A2"), 500)) ; obs2 <-data.frame(km = rnorm(1000, 15, 3), time = rnorm(1000, 15, 3), group2 = rep(c("G1", "G2"), 500)) ; set.seed(NULL) ; obs1$L1$km[2:3] <- NA ; fun_gg_scatter(data1 = list(L1 = obs1, L2 = obs2), x = list(L1 = "km", L2 = "km"), y = list(L1 = "time", L2 = "time"), categ = list(L1 = "group1", L2 = "group2"), legend.name = NULL, color = list(L1 = 4:5, L2 = 7:8), geom = list(L1 = "geom_point", L2 = "geom_point"), alpha = list(L1 = 0.5, L2 = 0.5), dot.size = 3, line.size = 0.5, xlim = NULL, ylim = NULL, extra.margin = 0.05, xlab = NULL, ylab = NULL,  title = "GRAPH1", text.size = 12, classic = TRUE, grid = FALSE, raster = TRUE, vectorial.limit = NULL, return = FALSE, path.lib = NULL)
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# DEBUGGING
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# data1 <- data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")) ; x = names(data1)[1] ; y = names(data1)[2] ; categ = names(data1)[3] ; legend.name = NULL ; color = NULL ; geom = "geom_point" ; xlim = NULL ; ylim = NULL ; extra.margin = 0.05 ; xlab = NULL ; ylab = NULL ; dot.size = 1 ; line.size = 0.5 ; alpha = 0.5 ; title = "GRAPH1" ; text.size = 12 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; raster = FALSE ; vectorial.limit = NULL ; return = FALSE ; path.lib = NULL
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B"))) ; x = list(L1 = names(data1$L1)[1]) ; y = list(L1 = names(data1$L1)[2]) ; categ = list(L1 = names(data1$L1)[3]) ; legend.name = list(L1 = "VALUE") ; color = NULL ; geom = list(L1 = "geom_point") ; xlim = NULL ; ylim = NULL ; extra.margin = 0.05 ; xlab = NULL ; ylab = NULL ; dot.size = 1 ; line.size = 0.5 ; alpha = 0.5 ; title = "GRAPH1" ; text.size = 12 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; raster = FALSE ; vectorial.limit = NULL ; return = FALSE ; path.lib = NULL
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")), L2 = data.frame(a = (1:6)*2, b = ((1:6)^2)*2, group = c("A1", "A1", "A1", "B1", "B1", "B1"))) ; x = list(L1 = names(data1$L1)[1], L2 = names(data1$L2)[1]) ; y = list(L1 = names(data1$L1)[2], L2 = names(data1$L2)[2]) ; categ = list(L1 = names(data1$L1)[3], L2 = names(data1$L2)[3]) ; legend.name = list(L1 = "GROUP1", L2 = "GROUP2") ; color = NULL ; geom = list(L1 = "geom_point", L2 = "geom_path") ; xlim = NULL ; ylim = NULL ; extra.margin = 0.05 ; xlab = NULL ; ylab = NULL ; dot.size = 1 ; line.size = 0.5 ; alpha = 0.5 ; title = "GRAPH1" ; text.size = 12 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; raster = FALSE ; vectorial.limit = NULL ; return = FALSE ; path.lib = NULL
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group1 = c("A", "A", "A", "B", "B", "B")), L2 = data.frame(a = (1:6)*2, b = ((1:6)^2)*2, group2 = c("A1", "A1", "A1", "B1", "B1", "B1"))) ; x = list(L1 = names(data1$L1)[1], L2 = names(data1$L2)[1]) ; y = list(L1 = names(data1$L1)[2], L2 = names(data1$L2)[2]) ; categ = list(L1 = names(data1$L1)[3], L2 = names(data1$L2)[3]) ; legend.name = list(L1 = "GROUP1", L2 = "GROUP2") ; color = list(L1 = 1:2, L2 = 3:4) ; geom = list(L1 = "geom_point", L2 = "geom_line") ; xlim = NULL ; ylim = NULL ; extra.margin = 0.05 ; xlab = NULL ; ylab = NULL ; dot.size = 2 ; line.size = 0.5 ; alpha = 0.5 ; title = "GRAPH1" ; text.size = 12 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; raster = FALSE ; vectorial.limit = NULL ; return = FALSE ; path.lib = NULL
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B"))) ; x = list(L1 = names(data1$L1)[1]) ; y = list(L1 = names(data1$L1)[2]) ; categ = NULL ; legend.name = NULL ; color = list(L1 = 5) ; geom = list(L1 = "geom_point") ; xlim = NULL ; ylim = NULL ; extra.margin = 0.05 ; xlab = "x test" ; ylab = "y test" ; dot.size = 2 ; line.size = 0.5 ; alpha = 1 ; title = "GRAPH1" ; text.size = 15 ; classic = FALSE ; grid = FALSE ; raster = FALSE ; vectorial.limit = NULL ; return = FALSE ; path.lib = NULL
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A1", "A2", "A3", "B1", "B2", "B3"))) ; x = list(L1 = names(data1$L1)[1]) ; y = list(L1 = NULL) ; categ = list(L1 = names(data1$L1)[3]) ; legend.name = list(L1 = "VALUE") ; color = list(L1 = "red") ; geom = list(L1 = "geom_hline") ; xlim = NULL ; ylim = NULL ; extra.margin = 0.05 ; xlab = NULL ; ylab = NULL ; dot.size = 1 ; line.size = 0.5 ; alpha = 0.5 ; title = "GRAPH1" ; text.size = 12 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; raster = FALSE ; vectorial.limit = NULL ; return = FALSE ; path.lib = NULL
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A1", "A2", "A3", "B1", "B2", "B3"))) ; data1$L1$a[2:3] <- NA ; x = list(L1 = names(data1$L1)[1]) ; y = list(L1 = NULL) ; categ = list(L1 = names(data1$L1)[3]) ; legend.name = list(L1 = "VALUE") ; color = list(L1 = "red") ; geom = list(L1 = "geom_hline") ; xlim = NULL ; ylim = NULL ; extra.margin = 0.05 ; xlab = NULL ; ylab = NULL ; dot.size = 1 ; line.size = 0.5 ; alpha = 0.5 ; title = "GRAPH1" ; text.size = 12 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; raster = FALSE ; vectorial.limit = NULL ; return = FALSE ; path.lib = NULL
# data1 <- list(L1 = data.frame(a = 1:6, b = (1:6)^2, group = c("A", "A", "A", "B", "B", "B")), L2 = data.frame(a = (1:6)*2, b = ((1:6)^2)*2, group = c("A1", "A1", "A1", "B1", "B1", "B1")), L3 = data.frame(a = (1:6)*3, b = ((1:6)^2)*3, group3 = c("A4", "A5", "A6", "A7", "B4", "B5"))) ; data1$L1$a[3] <- NA ; data1$L1$group[5] <- NA ; data1$L3$group3[4] <- NA ; x = list(L1 = names(data1$L1)[1], L2 = names(data1$L2)[1], L3 = names(data1$L3)[1]) ; y = list(L1 = names(data1$L1)[2], L2 = names(data1$L2)[2], L3 = NULL) ; categ = list(L1 = names(data1$L1)[3], L2 = names(data1$L2)[3], L3 = names(data1$L3)[3]) ; legend.name = NULL ; color = list(L1 = "red", L2 = "blue", L3 = "green") ; geom = list(L1 = "geom_point", L2 = "geom_point", L3 = "geom_vline") ; xlim = NULL ; ylim = NULL ; extra.margin = 0.05 ; xlab = NULL ; ylab = NULL ; dot.size = 4 ; line.size = 0.5 ; alpha = list(L1 = 0.5, L2 =  0.5, L3 =  0.5) ; title = "GRAPH1" ; text.size = 12 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; raster = TRUE ; vectorial.limit = 5 ; return = FALSE ; path.lib = NULL
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# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
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if(length(find("fun_gg_palette", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_gg_palette() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
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stop(tempo.cat)
}
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if(length(find("fun_gg_point_rast", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_gg_point_rast() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
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stop(tempo.cat)
}
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if(length(find("fun_pack_import", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_pack_import() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
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stop(tempo.cat)
}
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if(length(find("fun_param_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
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stop(tempo.cat)
}
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# end required function checking
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# reserved words to avoid bugs (used in this function)
reserved.words <- c("fake_y", "fake_categ")
# end reserved words to avoid bugs (used in this function)
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# check list lengths (and names of data1 compartments if non name present)
warning <- NULL
if(all(class(data1) == "list")){
if(length(data1) > 6){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": data1 ARGUMENT MUST BE A LIST OF 6 DATA FRAMES MAXIMUM (6 OVERLAYS MAX)\n\n================\n\n")
stop(tempo.cat)
}
if(is.null(names(data1))){
names(data1) <- paste0("L", 1:length(data1))
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": NULL NAME COMPARTMENT OF data1 LIST -> NAMES RESPECTIVELY ATTRIBUTED TO EACH COMPARTMENT:\n", paste(names(data1), collapse = " "))
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}
if( ! (all(class(x) == "list") & length(data1) == length(x))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": x ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
stop(tempo.cat)
}
if( ! (all(class(y) == "list") & length(data1) == length(y))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": y ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
stop(tempo.cat)
}
if( ! is.null(categ)){
if( ! (all(class(categ) == "list") & length(data1) == length(categ))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": categ ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
stop(tempo.cat)
}
}
if( ! is.null(legend.name)){
if( ! (all(class(legend.name) == "list") & length(data1) == length(legend.name))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": legend.name ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
stop(tempo.cat)
}
}
if( ! is.null(color)){
if( ! (all(class(color) == "list") & length(data1) == length(color))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": color ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
stop(tempo.cat)
}
}
if( ! (all(class(geom) == "list") & length(data1) == length(geom))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": geom ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
stop(tempo.cat)
}
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if( ! (all(class(alpha) == "list") & length(data1) == length(alpha))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": alpha ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST\n\n================\n\n")
stop(tempo.cat)
}
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}
# end check list lengths (and names of data1 compartments if non name present)
# conversion into lists
if(all(is.data.frame(data1))){
data1 <- list(L1 = data1)
if(all(class(x) == "list")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": x ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
stop(tempo.cat)
}else{
x <- list(L1 = x)
}
if(all(class(y) == "list")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": y ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
stop(tempo.cat)
}else{
y <- list(L1 = y)
}
if( ! is.null(categ)){
if(all(class(categ) == "list")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": categ ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
stop(tempo.cat)
}else{
categ <- list(L1 = categ)
}
}
if( ! is.null(legend.name)){
if(all(class(legend.name) == "list")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": legend.name ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
stop(tempo.cat)
}else{
legend.name <- list(L1 = legend.name)
}
}
if( ! is.null(color)){
if(all(class(color) == "list")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": color ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
stop(tempo.cat)
}else{
color <- list(L1 = color)
}
}
if(all(class(geom) == "list")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": geom ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
stop(tempo.cat)
}else{
geom <- list(L1 = geom)
}
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if(all(class(alpha) == "list")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": alpha ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME\n\n================\n\n")
stop(tempo.cat)
}else{
alpha <- list(L1 = alpha)
}
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}
# end conversion into lists
# legend name filling
if(is.null(legend.name) & ! is.null(categ)){
legend.name <- categ
}else if(is.null(legend.name) & is.null(categ)){
legend.name <- vector("list", length(data1)) # null list
}
# end legend name filling
# integer colors into gg_palette
tempo.check.color <- NULL
for(i1 in 1:length(data1)){
if(any(is.na(color[[i1]]))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ": color ARGUMENT CANNOT CONTAIN NA\n\n================\n\n")
stop(tempo.cat)
}
tempo.check.color <- c(tempo.check.color, fun_param_check(data = color[[i1]], data.name = ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name, print = FALSE)$problem)
}
tempo.check.color <- ! tempo.check.color # invert TRUE and FALSE because if integer, then problem = FALSE
if(any(tempo.check.color == TRUE)){ # convert integers into colors
tempo.integer <- unlist(color[tempo.check.color])
tempo.color <- fun_gg_palette(max(tempo.integer, na.rm = TRUE))
for(i1 in 1:length(data1)){
if(tempo.check.color[i1] == TRUE){
color[[i1]] <-tempo.color[color[[i1]]]
}
}
}
# end integer colors into gg_palette
# argument checking
arg.check <- NULL # for function debbuging
checked.arg.names <- NULL # for function debbuging
ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
compart.null.color <- 0 # will be used to attribute a color when color is non NULL but a compatment of color is NULL
data1.ini <- data1 # to report NA removal
removed.row.nb <- vector("list", length = length(data1)) # to report NA removal
removed.rows <- vector("list", length = length(data1)) # to report NA removal
for(i1 in 1:length(data1)){
tempo <- fun_param_check(data = data1[[i1]], data.name = ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
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# reserved word checking
if(any(names(data1[[i1]]) %in% reserved.words)){ # I do not use fun_name_change() because cannot control y before creating "fake_y". But ok because reserved are not that common
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": COLUMN NAMES OF ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), " ARGUMENT CANNOT BE ONE OF THESE WORDS\n", paste(reserved.words, collapse = " "), "\nTHESE ARE RESERVED FOR THE ", function.name, " FUNCTION\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}
# end reserved word checking
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tempo <- fun_param_check(data = x[[i1]], data.name = ifelse(length(x) == 1, "x", paste0("x NUMBER ", i1)), class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
# check of geom now because required for y argument
tempo <- fun_param_check(data = geom[[i1]], data.name = ifelse(length(geom) == 1, "geom", paste0("geom NUMBER ", i1)), options = c("geom_point", "geom_line", "geom_path", "geom_hline", "geom_vline"), length = 1, fun.name = function.name) ; eval(ee)
# end check of geom now because required for y argument
if(is.null(y[[i1]])){
if(all(geom[[i1]] != "geom_hline") & all(geom[[i1]] != "geom_vline")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ": y ARGUMENT CANNOT BE NULL EXCEPT IF ", ifelse(length(geom) == 1, "y", paste0("geom NUMBER ", i1)), " ARGUMENT IS\"geom_hline\" OR \"geom_vline\"\nHERE geom ARGUMENT IS: ", paste(geom[[i1]], collapse = " "), "\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}else{
y[[i1]] <- "fake_y"
data1[[i1]] <- cbind(data1[[i1]], fake_y = NA)
data1[[i1]][, "fake_y"] <- as.numeric(data1[[i1]][, "fake_y"])
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": NULL ", ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), " ARGUMENT ASSOCIATED TO ", ifelse(length(geom) == 1, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT ", geom[[i1]], " -> FAKE COLUMN ADDED TO DATA FRAME ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", NAMED \"fake_y\" FOR FINAL DRAWING")
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}
}else{
if(all(geom[[i1]] == "geom_hline") | all(geom[[i1]] == "geom_vline")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ": y ARGUMENT CANNOT BE NON NULL IF ", ifelse(length(geom) == 1, "y", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_hline\" OR \"geom_vline\"\nHERE geom ARGUMENT IS: ", paste(geom[[i1]], collapse = " "), "\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}
tempo <- fun_param_check(data = y[[i1]], data.name = ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
}
if( ! (x[[i1]] %in% names(data1[[i1]]))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(x) == 1, "x", paste0("x NUMBER ", i1)), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), "\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}
if( ! (y[[i1]] %in% names(data1[[i1]]))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), "\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}
# na detection and removal (done now to be sure of the correct length of categ)
if(any(is.na(data1[[i1]][, c(x[[i1]], if(y[[i1]] == "fake_y"){NULL}else{y[[i1]]})]))){
tempo.removed.row.nb <- unlist(lapply(lapply(c(data1[[i1]][c(x[[i1]], if(y[[i1]] == "fake_y"){NULL}else{y[[i1]]})]), FUN = is.na), FUN = which))
removed.row.nb[[i1]] <- c(removed.row.nb[[i1]], tempo.removed.row.nb)
# report of removed rows will be performed at the very end
data1[[i1]] <- data1[[i1]][-tempo.removed.row.nb, ]
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": NA DETECTED IN COLUMN ", ifelse(length(x) == 1, "x", paste0("x NUMBER ", i1)), if(y[[i1]] == "fake_y"){""}else{paste0(" AND ", ifelse(length(y) == 1, "y", paste0("y NUMBER ", i1)))}, " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ". CORRESPONDING ROWS HAVE BEEN REMOVED (SEE $removed.row.nb AND $removed.rows)")
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}
# end na detection and removal (done now to be sure of the correct length of categ)
tempo <- fun_param_check(data = data1[[i1]][, x[[i1]]], data.name = ifelse(length(x) == 1, "x OF data1", paste0("x NUMBER ", i1, " OF data1 NUMBER ", i1)), class = "vector", mode = "numeric", na.contain = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_param_check(data = data1[[i1]][, y[[i1]]], data.name = ifelse(length(y) == 1, "y OF data1", paste0("y NUMBER ", i1, " OF data1 NUMBER ", i1)), class = "vector", mode = "numeric", na.contain = ifelse(y[[i1]] == "fake_y", TRUE, FALSE), fun.name = function.name) ; eval(ee)
if(( ! is.null(categ)) & ( ! is.null(categ[[i1]]))){ # if categ[[i1]] = NULL, fake_categ will be created later on
tempo <- fun_param_check(data = categ[[i1]], data.name = ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)),, class = "vector", mode = "character", length = 1, fun.name = function.name)
if( ! (categ[[i1]] %in% names(data1[[i1]]))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), "\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}
# na detection and removal (done now to be sure of the correct length of categ)
if(any(is.na(data1[[i1]][, categ[[i1]]]))){
tempo.removed.row.nb <- unlist(lapply(lapply(c(data1[[i1]][categ[[i1]]]), FUN = is.na), FUN = which))
removed.row.nb[[i1]] <- c(removed.row.nb[[i1]], tempo.removed.row.nb)
# report of removed rows will be performed at the very end
data1[[i1]] <- data1[[i1]][-tempo.removed.row.nb, ]
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": IN ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", THE CATEGORY COLUMN:\n", paste(categ[[i1]], collapse = " "), "\nCONTAINS NA")
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}
# end na detection and removal (done now to be sure of the correct length of categ)
tempo1 <- fun_param_check(data = data1[[i1]][, categ[[i1]]], data.name = ifelse(length(categ) == 1, "categ OF data1", paste0("categ NUMBER ", i1, " OF data1 NUMBER ", i1)), class = "vector", mode = "character", na.contain = FALSE, fun.name = function.name, print = FALSE)
tempo2 <- fun_param_check(data = data1[[i1]][, categ[[i1]]], data.name = ifelse(length(categ) == 1, "categ OF data1", paste0("categ NUMBER ", i1, " OF data1 NUMBER ", i1)), class = "factor", na.contain = FALSE, fun.name = function.name, print = FALSE)
if(tempo1$problem == TRUE & tempo2$problem == TRUE){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(categ) == 1, "categ OF data1", paste0("categ NUMBER ", i1, " OF data1 NUMBER ", i1)), " MUST BE A FACTOR OR CHARACTER VECTOR\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}else if(tempo1$problem == FALSE){
data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": IN ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", THE CHARACTER COLUMN HAS BEEN CONVERTED TO FACTOR")
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))

}
if(geom[[i1]] == "geom_vline" | geom[[i1]] == "geom_hline"){
if(length(unique(data1[[i1]][, categ[[i1]]])) != nrow(data1[[i1]])){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(geom) == 1, "geom OF data1", paste0("geom NUMBER ", i1, " OF data1 NUMBER ", i1)), " ARGUMENT IS ", geom[[i1]], ", MEANING THAT ", ifelse(length(categ) == 1, "categ OF data1", paste0("categ NUMBER ", i1, " OF data1 NUMBER ", i1)), " MUST HAVE A DIFFERENT CLASS PER LINE OF data1 (ONE x VALUE PER CLASS)\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}
}
}else if(( ! is.null(categ)) & is.null(categ[[i1]])){ # if categ[[i1]] = NULL, fake_categ will be created 
categ[[i1]] <- "fake_categ"
data1[[i1]] <- cbind(data1[[i1]], fake_categ = "")
data1[[i1]][, "fake_categ"] <- as.numeric(data1[[i1]][, "fake_categ"])
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": NULL ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " ARGUMENT -> FAKE COLUMN ADDED TO DATA FRAME ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", NAMED \"fake_categ\" FOR FINAL DRAWING")
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}
if( ! is.null(legend.name[[i1]])){
tempo <- fun_param_check(data = legend.name[[i1]], data.name = ifelse(length(legend.name) == 1, "legend.name", paste0("legend.name NUMBER ", i1)),, class = "vector", mode = "character", length = 1, fun.name = function.name)
}
if( ! is.null(color)){ # if color is NULL, will be filled later on
# check the nature of color
if(is.null(color[[i1]])){
compart.null.color <- compart.null.color + 1
color[[i1]] <- grey(compart.null.color / 8) # cannot be more than 7 overlays. Thus 7 different greys. 8/8 is excluded because white dots
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": NULL COLOR IN ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", SINGLE COLOR ", paste(color[[i1]], collapse = " "), " HAS BEEN ATTRIBUTED")
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}
tempo1 <- fun_param_check(data = color[[i1]], data.name = ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name, print = FALSE)
tempo2 <- fun_param_check(data = color[[i1]], data.name = ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), class = "factor", na.contain = TRUE, fun.name = function.name, print = FALSE)
if(tempo1$problem == TRUE & tempo2$problem == TRUE){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " MUST BE A FACTOR OR CHARACTER VECTOR OR INTEGER VECTOR\n\n================\n\n") # integer possible because dealt above
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arg.check <- c(arg.check, TRUE)
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}else if( ! (all(color[[i1]] %in% colors() | grepl(pattern = "^#", color[[i1]])))){ # check that all strings of low.color start by #
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors(): ", paste(unique(color[[i1]]), collapse = " "), "\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}
if(any(is.na(color[[i1]]))){
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": IN ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", THE COLORS:\n", paste(unique(color[[i1]]), collapse = " "), "\nCONTAINS NA")
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}
# end check the nature of color
# check the length of color
if(is.null(categ) & length(color[[i1]]) != 1){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT MUST BE A SINGLE COLOR IF categ IS NULL\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}else if( ! is.null(categ)){
# No problem of NA management by ggplot2 because already removed
if(length(color[[i1]]) == length(unique(data1[[i1]][, categ[[i1]]]))){ # here length(color) is equal to the different number of categ
data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": IN ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", THE FOLLOWING COLORS:\n", paste(color[[i1]], collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "))
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}else if(length(color[[i1]]) == length(data1[[i1]][, categ[[i1]]])){# here length(color) is equal to nrow(data1[[i1]]) -> Modif to have length(color) equal to the different number of categ (length(color) == length(levels(data1[[i1]][, categ[[i1]]])))
data1[[i1]] <- cbind(data1[[i1]], color = color[[i1]])
tempo.check <- unique(data1[[i1]][ , c(categ[[i1]], "color")])
if( ! (nrow(tempo.check) == length(color[[i1]]) & nrow(tempo.check) == length(unique(data1[[i1]][ , categ[[i1]]])))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT HAS THE LENGTH OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), " COLUMN VALUES\nBUT IS INCORRECTLY ASSOCIATED TO EACH CLASS OF THIS categ:\n", paste(unique(mapply(FUN = "paste", data1[[i1]][ ,categ[[i1]]], data1[[i1]][ ,"color"])), collapse = "\n"), "\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}else{
data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
color[[i1]] <- unique(color[[i1]][order(data1[[i1]][, categ[[i1]]])]) # Modif to have length(color) equal to the different number of categ (length(color) == length(levels(data1[[i1]][, categ[[i1]]])))
tempo.warning <- paste0(ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT HAS THE LENGTH OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), " COLUMN VALUES\nCOLORS HAVE BEEN RESPECTIVELY ASSOCIATED TO EACH CLASS OF categ AS:\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "), "\n", paste(color[[i1]], collapse = " "))
warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}
}else if(length(color[[i1]]) == 1){
data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
color[[i1]] <- rep(color[[i1]], length(levels(data1[[i1]][, categ[[i1]]])))
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": IN ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), ", COLOR HAS LENGTH 1 MEANING THAT ALL THE DIFFERENT CLASSES OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), "\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "), "\nWILL HAVE THE SAME COLOR\n", paste(color[[i1]], collapse = " "))
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}else{
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ", ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), " ARGUMENT MUST BE (1) LENGTH 1, OR (2) THE LENGTH OF ", ifelse(length(categ) == 1, "categ", paste0("categ NUMBER ", i1)), " IN ", ifelse(length(data1) == 1, "data1", paste0("data1 NUMBER ", i1)), " COLUMN VALUES, OR (3) THE LENGTH OF THE CLASSES IN THIS COLUMN. HERE IT IS COLOR LENGTH ", length(color[[i1]]), " VERSUS CATEG LENGTH ", length(data1[[i1]][, categ[[i1]]]), " AND CATEG CLASS LENGTH ", length(unique(data1[[i1]][, categ[[i1]]])), "\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}
}
}
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tempo <- fun_param_check(data = alpha[[i1]], , data.name = ifelse(length(color) == 1, "color", paste0("color NUMBER ", i1)), prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
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}
if(length(data1) > 1){
if(length(unique(unlist(x))) > 1){
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": THE x ARGUMENT DOES NOT CONTAIN IDENTICAL COLUMN NAMES:\n", paste(unlist(x), collapse = " "), "\nX-AXIS OVERLAYING DIFFERENT VARIABLES?")
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}
}
if(length(data1) > 1){
if(length(unique(unlist(y))) > 1){
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tempo.warning <- paste0("FROM FUNCTION ", function.name, ": THE y ARGUMENT DOES NOT CONTAIN IDENTICAL COLUMN NAMES:\n", paste(unlist(y), collapse = " "), "\nY-AXIS OVERLAYING DIFFERENT VARIABLES?")
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warning <- paste0(ifelse(is.null(warning), tempo.warning, paste0(warning, "\n\n", tempo.warning)))
}
}
if(sum(geom %in% "geom_point") > 3){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": geom ARGUMENT CANNOT HAVE MORE THAN FOUR \"geom_point\" ELEMENTS\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}else if(length(geom) - sum(geom %in% "geom_point") > 3){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": geom ARGUMENT CANNOT HAVE MORE THAN THREE LINE ELEMENTS\n\n================\n\n")
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arg.check <- c(arg.check, TRUE)
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}
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tempo <- fun_param_check(data = dot.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_param_check(data = line.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
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if( ! is.null(xlim)){
tempo <- fun_param_check(data = xlim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
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if(tempo$problem == FALSE & any(xlim %in% c(Inf, -Inf))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": xlim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES\n\n================\n\n")
arg.check <- c(arg.check, TRUE)
}
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}
if( ! is.null(ylim)){
tempo <- fun_param_check(data = ylim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
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if(tempo$problem == FALSE & any(ylim %in% c(Inf, -Inf))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ylim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES\n\n================\n\n")
arg.check <- c(arg.check, TRUE)
}
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}
tempo <- fun_param_check(data = extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(xlab)){
tempo <- fun_param_check(data = xlab, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
}
if( ! is.null(ylab)){
tempo <- fun_param_check(data = ylab, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)