cute_little_R_functions.R 721 KB
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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)
}


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


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


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


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


 


# Check OK: clear to go Apollo
fun_empty_graph <- function(text = NULL, text.size = 1, title = NULL, title.size = 1.5){
# AIM
# display an empty plot with a text in the middle of the window (for instance to specify that no plot can be drawn)
# ARGUMENTS
# text: character string of the message to display
# text.size: numeric value of the text size
# title: character string of the graph title
# title.size: numeric value of the title size (in points)
# REQUIRED PACKAGES
# none
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# RETURN
# an empty plot
# EXAMPLES
# simple example
# fun_empty_graph(text = "NO GRAPH")
# white page
# fun_empty_graph() # white page
# all the arguments
# fun_empty_graph(text = "NO GRAPH", text.size = 2, title = "GRAPH1", title.size = 1)
# DEBUGGING
# text = "NO GRAPH" ; title = "GRAPH1" ; text.size = 1
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
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))
if( ! is.null(text)){
tempo <- fun_check(data = text, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
}
tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(title)){
tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
}
tempo <- fun_check(data = title.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
par(ann=FALSE, xaxt="n", yaxt="n", mar = rep(1, 4), bty = "n", xpd = NA)
plot(1, 1, type = "n") # no display with type = "n"
x.left.dev.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1])
y.top.dev.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4]))
if( ! is.null(text)){
text(x = 1, y = 1, labels = text, cex = text.size)
}
if( ! is.null(title)){
text(x = x.left.dev.region, y = y.top.dev.region, labels = title, adj=c(0, 1), cex = title.size)
}
par(ini.par)
}


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


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


 


# Check OK: clear to go Apollo
fun_gg_palette <- function(n, kind = "std"){
# AIM
# provide colors used by ggplot2
# the interest is to use another single color that is not the red one used by default
# for ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
# ARGUMENTS
# n: number of groups on the graph
# kind: either "std" for standard gg colors, "dark" for darkened gg colors, or "light" for pastel gg colors
# REQUIRED PACKAGES
# none
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# RETURN
# the vector of hexadecimal colors
# EXAMPLES
# output of the function
# fun_gg_palette(n = 2)
# the ggplot2 palette when asking for 7 different colors
# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7))
# selection of the 5th color of the ggplot2 palette made of 7 different colors
# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7)[5])
# the ggplot2 palette made of 7 darkened colors
# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7, kind = "dark"))
# the ggplot2 palette made of 7 lighten colors
# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7, kind = "light"))
# DEBUGGING
# n = 0
# kind = "std"
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
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$fun.name))
tempo <- fun_check(data = n, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE & isTRUE(all.equal(n, 0))){ # isTRUE(all.equal(n, 0))) is similar to n == 0 but deals with float
tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT MUST BE A NON ZERO INTEGER. HERE IT IS: ", paste(n, collapse = " "))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
tempo <- fun_check(data = kind, options = c("std", "dark", "light"), length = 1, fun.name = function.name) ; eval(ee)
}
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
hues = seq(15, 375, length = n + 1)
hcl(h = hues, l = if(kind == "std"){65}else if(kind == "dark"){35}else if(kind == "light"){85}, c = 100)[1:n]
}


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


 


# Check OK: clear to go Apollo
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_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$vjust))
# DEBUGGING
# angle = 45 ; axis = "y"
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end required function checking
# argument checking
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = angle, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = axis, options = c("x", "y"), 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
# 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(any(sapply(FUN = all.equal, c(-360, -180, 0, 180, 360), angle) == TRUE)){ # equivalent of angle == -360 | angle == -180 | angle == 0 | angle == 180 | angle == 360 but deals with floats
hjust <- 0.5
vjust <- 0.5
}else if(any(sapply(FUN = all.equal, c(-270, 90), angle) == TRUE)){
hjust <- 1
vjust <- 0.5
}else if(any(sapply(FUN = all.equal, c(-90, 270), angle) == TRUE)){
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(any(sapply(FUN = all.equal, c(-270, -90, 90, 270), angle) == TRUE)){ # equivalent of angle == -270 | angle == -90 | angle == 90 | angle == 270 but deals with floats
hjust <- 0.5
vjust <- 0.5
}else if(any(sapply(FUN = all.equal, c(-360, 0, 360), angle) == TRUE)){
hjust <- 1
vjust <- 0.5
}else if(any(sapply(FUN = all.equal, c(-180, 180), angle) == TRUE)){
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)
}


######## 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, lib.path = 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
# 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 is derived from the geom_point_rast() function, created by Viktor Petukhov , and present in the ggrastr package (https://rdrr.io/github/VPetukhov/ggrastr/src/R/geom-point-rast.R, MIT License, Copyright (c) 2017 Viktor Petukhov). Has been placed here to minimize package dependencies
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# 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_check() function? If TRUE, the name of the fun_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"))
# lib.path: 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_check()
# fun_pack()
# 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(pdf.name.file = "Raster") ; ggplot2::ggplot() + fun_gg_point_rast(data = data1, mapping = ggplot2::aes(x = x, y = y)) ; fun_open(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, call. = FALSE)
}
# 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_pack", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_pack() 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$fun.name))
if( ! is.null(data)){
tempo <- fun_check(data = data, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
}
if( ! is.null(mapping)){
tempo <- fun_check(data = mapping, class = "uneval", typeof = "list", fun.name = function.name) ; eval(ee) # aes() is tested
}
# stat and position not tested because too complicate
tempo <- fun_check(data = na.rm, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = show.legend, class = "vector", mode = "logical", length = 1, na.contain = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = inherit.aes, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(raster.width)){
tempo <- fun_check(data = raster.width, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
}
if( ! is.null(raster.height)){
tempo <- fun_check(data = raster.height, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
}
tempo <- fun_check(data = raster.dpi, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = inactivate, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(lib.path)){
tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
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if(tempo$problem == FALSE){
if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
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text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
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}
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if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# package checking
fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
fun_pack(req.package = c("grid"), lib.path = lib.path)
fun_pack(req.package = c("Cairo"), lib.path = lib.path)
# end package checking
# additional functions
DrawGeomPointRast <- function(data, panel_params, coord, na.rm = FALSE, raster.width = NULL, raster.height= NULL, raster.dpi = 300){
if (is.null(raster.width)){
raster.width <- par('fin')[1]
}
if (is.null(raster.height)){
 raster.height <- par('fin')[2]
}
prev_dev_id <- dev.cur()
p <- ggplot2::GeomPoint$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
}


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


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######## fun_gg_bar() #### ggplot2 mean barplot + overlaid dots if required


 


# Check NOT DONE
fun_gg_bar <- function(data1, y, categ, categ.class.order = NULL, categ.legend.name = NULL, categ.color = NULL, bar.width = 0.5, error.disp = NULL, error.whisker.width = 0.5,  dot.color = "same", dot.tidy = FALSE, dot.bin.nb = 30, dot.jitter = 0.25, dot.size = 3, dot.border.size = 0.5, dot.alpha = 0.5, ylim = NULL, ylog = "no", y.tick.nb = NULL, y.inter.tick.nb = NULL, y.include.zero = FALSE, y.top.extra.margin = 0, y.bottom.extra.margin = 0, stat.disp = NULL, stat.size = 4, stat.dist = 2, xlab = NULL, ylab = NULL, vertical = TRUE, text.size = 12, title = "", title.text.size = 8, text.angle = 0, classic = FALSE, grid = FALSE, return = FALSE, plot = TRUE, add = NULL, warn.print = FALSE, lib.path = NULL){
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# AIM
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# ggplot2 vertical barplot representing mean values with the possibility to add error bars and to overlay dots
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# 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)
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# if ever bars disappear, see the end of https://github.com/tidyverse/ggplot2/issues/2887
# to have a single bar, create a factor column with a single class and specify the name of this column in categ argument as unique element (no categ2 in categ argument). For a single set of grouped bars, create a factor column with a single class and specify this column in categ argument as first element (categ1). See categ below
# with several single bars (categ argument with only one element), bar.width argument (i.e., width argument of ggplot2::geom_bar()) defines each bar width. The bar.width argument also defines the space between bars by using (1 - bar.width). In addition, xmin and xmax of the fun_gg_bar() output report the bar boundaries (around x-axis unit 1, 2, 3, etc., for each bar)
# with several sets of grouped bars (categ argument with two elements), bar.width argument defines each set of grouped bar width. The bar.width argument also defines the space between set of grouped bars by using (1 - bar.width). In addition, xmin and xmax of the fun_gg_bar() output report the bar boundaries (around x-axis unit 1, 2, 3, etc., for each set of grouped bar)
# to manually change the 0 base bar into this code, see https://stackoverflow.com/questions/35324892/ggplot2-setting-geom-bar-baseline-to-1-instead-of-zero
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# ARGUMENTS
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# data1: a dataframe containing one column of values (see y argument below) and one or two columns of categories (see categ argument below). Duplicated column names not allowed
# y: character string of the data1 column name for y-axis (containing numeric values). Numeric values will be averaged by categ to generate the bars and will also be used to plot the dots
# categ: vector of character strings of the data1 column name for categories (column of characters or factor). Must either be one or two column names. If a single column name (further refered to as categ1), then one bar per class of categ1. If two column names (further refered to as categ1 and categ2), then one bar per class of categ2, which form a group of bars in each class of categ1. BEWARE, categ1 (and categ2 if it exists) must have a single value of y per class of categ1 (and categ2). To have a single bar, create a factor column with a single class and specify the name of this column in categ argument as unique element (no categ2 in categ argument). For a single set of grouped bars, create a factor column with a single class and specify this column in categ argument as first element (categ1)
# categ.class.order: list indicating the order of the classes of categ1 and categ2 represented on the barplot (the first compartment for categ1 and and the second for categ2). If categ.class.order = NULL, classes are represented according to the alphabetical order. Some compartment can be NULL and other not
# categ.legend.name: character string of the legend title for categ2. If categ.legend.name = NULL, then categ.legend.name <- categ1 if only categ1 is present and categ.legend.name <- categ2 if categ1 and categ2 are present. Write "" if no legend required
# categ.color: vector of character color string for bar filling. If categ.color = NULL, default colors of ggplot2, whatever categ1 and categ2. If categ.color is non null and only categ1 in categ argument, categ.color can be either: (1) a single color string (all the bars will have this color, whatever the classes of categ1), (2) a vector of string colors, one for each class of categ1 (each color will be associated according to categ.class.order of categ1), (3) 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 categ1 and a single class of categ1 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 categ.color. If categ.color is non null and categ1 and categ2 specified, all the rules described above will apply to categ2 instead of categ1 (colors will be determined for bars inside a group of bars)
# bar.width: numeric value (from 0 to 1) of the bar or set of grouped bar width (see WARNINGS above)
# error.disp: either "SD", "SD.TOP", "SEM" or "SEM.TOP". If NULL, no error bars added
# error.whisker.width: numeric value (from 0 to 1) of the whisker (error bar extremities) width, with 0 meaning no whiskers and 1 meaning a width equal to the corresponding bar width
# dot.color: vector of character string. Idem as categ.color but for dots, except that in the possibility (3), the rule "a single color per class of categ1 and a single class of categ1", cannot be respected (each dot can have a different color). If NULL, no dots plotted
# dot.tidy: logical. Nice dot spreading? If TRUE, use the geom_dotplot() function for a nice representation. If FALSE, dots are randomly spread, using the dot.jitter argument (see below)
# dot.bin.nb: positive integer indicating the number of bins (i.e., nb of separations) of the ylim range. Each dot will then be put in one of the bin, with the size the width of the bin. Not considered if dot.tidy is FALSE
# dot.jitter: numeric value (from 0 to 1) of random dot horizontal dispersion, with 0 meaning no dispersion and 1 meaning a dispersion in the corresponding bar width interval. Not considered if dot.tidy is TRUE
# dot.size: numeric value of dot size. Not considered if dot.tidy is TRUE
# dot.border.size: numeric value of border dot size. Write zero for no dot border. If dot.tidy is TRUE, value 0 remove the border. Another one leave the border without size control (geom_doplot() feature)
# dot.alpha: numeric value (from 0 to 1) of dot transparency (full transparent to full opaque, respectively)
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# ylim: 2 numeric values for y-axis range. If NULL, range of y in data1. Order of the 2 values matters (for inverted axis). BEWARE: values of the ylim must be already in the corresponding log if ylog argument is not "no" (see below)
# ylog: Either "no" (values in the y argument column of the data1 data frame are not log), "log2" (values in the y argument column of the data1 data frame are log2 transformed) or "log10" (values in the y argument column of the data1 data frame are log10 transformed). BEWARE: do not tranform the data, but just display ticks in a log scale manner. Thus, negative or zero values allowed. BEWARE: not possible to have horizontal bars with a log axis, due to a bug in ggplot2 (see https://github.com/tidyverse/ggplot2/issues/881)
# y.tick.nb: approximate number of desired label values on the y-axis (n argument of the the fun_scale() function)
# y.inter.tick.nb: number of desired secondary ticks between main ticks. Not considered if ylog is other than "no". In that case, play with the ylim and y.tick.nb arguments
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# y.include.zero: logical. Does ylim range include 0? Ok even if ylog = TRUE because ylim must already be log transformed values
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# y.top.extra.margin: single proportion (between 0 and 1) indicating if extra margins must be added to ylim. If different from 0, add the range of the axis * y.top.extra.margin (e.g., abs(ylim[2] - ylim[1]) * y.top.extra.margin) to the top of y-axis
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# y.bottom.extra.margin: idem as y.top.extra.margin but to the bottom of y-axis
# stat.disp: add the mean number above the corresponding bar. Either NULL (no number shown), "top" (at the top of the figure region) or "above" (above each bar)
# stat.size: numeric value of the stat size (in points). Increase the value to increase text size
# stat.dist: numeric value of the stat distance. Increase the value to increase the distance
# xlab: a character string or expression for x-axis legend. If NULL, character string of categ1
# ylab: a character string or expression for y-axis legend. If NULL, character string of the y argument
# vertical: logical. Vertical bars? BEWARE: will be automatically set to TRUE if ylog argument is other than "no". Indeed, not possible to have horizontal bars with a log axis, due to a bug in ggplot2 (see https://github.com/tidyverse/ggplot2/issues/881)
# text.size: numeric value of the size of the (1) axis numbers and axis legends, (2) texts in the graphic legend, (3) stats above bars (in points)
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# title: character string of the graph title
# title.text.size: numeric value of the title size (in points)
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# text.angle: integer value of the text angle for the x-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.
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# classic: logical. Use the classic theme (article like)?
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# grid: logical. draw horizontal lines in the background to better read the bar values? Not considered if classic = FALSE
# return: logical. Return the graph parameters?
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# plot: logical. Plot the graphic? If FALSE and return argument is TRUE, graphical parameters and associated warnings are provided without plotting
# add: character string allowing to add more ggplot2 features (dots, lines, themes, etc.). BEWARE: (1) must start with "+" just after the simple or double opening quote (no space, end of line, carriage return, etc., allowed), (2) must finish with ")" just before the simple or double closing quote (no space, end of line, carriage return, etc., allowed) and (3) each function must be preceded by "ggplot2::" (for instance: "ggplot2::coord_flip()). If the character string contains the "ggplot2::theme" string, then internal ggplot2 theme() and theme_classic() functions will be inactivated to be reused by add. BEWARE: handle this argument with caution since added functions can create conflicts with the preexisting internal ggplot2 functions
# warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
# lib.path: absolute path of the required packages, if not in the default folders
# REQUIRED PACKAGES
# ggplot2
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# scales
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# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
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# fun_comp_2d()
# fun_gg_just()
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# fun_gg_palette()
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# fun_name_change()
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# fun_pack()
# fun_check()
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# fun_round()
# fun_scale()
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# RETURN
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# a barplot if plot argument is TRUE
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# a list of the graph info if return argument is TRUE:
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# $stat: the graphic statistics
# $removed.row.nb: which rows have been removed due to NA detection in y and categ columns (NULL if no row removed)
# $removed.rows: removed rows containing NA (NULL if no row removed)
# $data: the graphic bar and dot coordinates
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# $axes: the x-axis and y-axis info
# $warn: the warning messages. Use cat() for proper display. NULL if no warning
# EXAMPLES
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### nice representation (1)
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), categ.class.order = list(NULL, c("B", "A")), categ.legend.name = "LEGEND", categ.color = NULL, bar.width = 0.3, error.disp = "SD.TOP", error.whisker.width = 0.8, dot.color = "same", dot.jitter = 0.5, dot.size = 3.5, dot.border.size = 0.2, dot.alpha = 0.5, ylim = c(10, 25), y.include.zero = TRUE, stat.disp = "above", stat.size = 4, xlab = "GROUP", ylab = "VALUE", text.size = 12, title = "GRAPH1", title.text.size = 8, text.angle = 0, classic = TRUE, grid = TRUE)
### nice representation (2)
# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(24, 0), rnorm(24, -10), rnorm(24, 10), rnorm(24, 20)), Group1 = rep(c("CAT", "DOG"), times = 48), Group2 = rep(c("A", "B", "C", "D"), each = 24)) ; set.seed(NULL) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), categ.class.order = list(NULL, c("B", "A", "D", "C")), categ.legend.name = "LEGEND", categ.color = NULL, bar.width = 0.8, dot.color = "grey50", dot.tidy = TRUE, dot.bin.nb = 60, dot.size = 3.5, dot.border.size = 0.2, dot.alpha = 0.5, ylim= c(-20, 30), stat.disp = "above", stat.size = 4, stat.dist = 1, xlab = "GROUP", ylab = "VALUE", vertical = FALSE, text.size = 12, title = "GRAPH1", title.text.size = 8, text.angle = 45, classic = FALSE)
### simple example
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = "Group1")
### separate bars. Example (1) of modification of bar color using a single value
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = "Group1", categ.color = "white")
### separate bars. Example (2) of modification of bar color using one value par class of categ2
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = "Group1", categ.color = c("coral", "lightblue"))
### separate bars. Example (3) of modification of bar color using the bar.color data frame column, with respect of the correspondence between categ2 and bar.color columns
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), bar.color = rep(c("coral", "lightblue"), time = 10)) ; obs1 ; fun_gg_bar(data1 = obs1, y = "Time", categ = "Group1", categ.color = obs1$bar.color)
### separate bars. Example (1) of modification of dot color, using the same dot color as the corresponding bar
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = "Group1", dot.color = "same")
### separate bars. Example (2) of modification of dot color, using a single color for all the dots
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = "Group1", dot.color = "green")
### separate bars. Example (3) of modification of dot color, using one value par class of categ2
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = "Group1", dot.color = c("green", "brown"))
### separate bars. Example (4) of modification of dot color, using different colors for each dot
# obs1 <- data.frame(Time = 1:10, Group1 = rep(c("G", "H"), times = 5)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = "Group1", dot.color = hsv(h = (1:nrow(obs1)) / nrow(obs1)))
### grouped bars. Simple example
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"))
### grouped bars. More grouped bars
# obs1 <- data.frame(Time = 1:24, Group1 = rep(c("G", "H"), times = 12), Group2 = rep(c("A", "B", "C", "D"), each = 6)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"))
### grouped bars. Example (1) of modification of bar color, using a single value
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), categ.color = "white")
### grouped bars. Example (2) of modification of bar color, using one value par class of categ2
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), categ.color = c("coral", "lightblue"))
### grouped bars. Example (3) of modification of bar color, using one value per line of obs1, with respect of the correspondence between categ2 and bar.color columns
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10), bar.color = rep(c("coral", "lightblue"), each = 10)) ; obs1 ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), categ.color = obs1$bar.color)
### grouped bars. Example (1) of modification of dot color, using the same dot color as the corresponding bar
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = "same")
### grouped bars. Example (2) of modification of dot color, using a single color for all the dots
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = "green")
### grouped bars. Example (3) of modification of dot color, using one value par class of categ2
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = c("green", "brown"))
### grouped bars. Example (4) of modification of dot color, using different colors for each dot
# obs1 <- data.frame(Time = 1:10, Group1 = rep(c("G", "H"), times = 5), Group2 = rep(c("A", "B"), each = 5)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = hsv(h = (1:nrow(obs1)) / nrow(obs1)))
### no dots (y.include.zero set to TRUE to see the lowest bar):
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = NULL, y.include.zero = TRUE)
### bar width. Example (1) with bar.width = 0.25 -> three times more space between single bars than the bar width (y.include.zero set to TRUE to see the lowest bar)
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), each = 500)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = "Group1", dot.color = NULL, y.include.zero = TRUE, bar.width = 0.25)
### bar width. Example (2) with bar.width = 1, no space between single bars
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), each = 500)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = "Group1", dot.color = NULL, y.include.zero = TRUE, bar.width = 1)
### bar width. Example (3) with bar.width = 0.25 -> three times more space between sets of grouped bars than the set width
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), times = 500), Group2 = rep(LETTERS[1:5], each = 200)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = NULL, y.include.zero = TRUE, bar.width = 0.25)
### bar width. Example (4) with bar.width = 0 -> no space between sets of grouped bars
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), times = 500), Group2 = rep(LETTERS[1:5], each = 200)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = NULL, y.include.zero = TRUE, bar.width = 1)
### error bars
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), times = 500), Group2 = rep(LETTERS[1:5], each = 200)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = NULL, error.disp = "SD.TOP")
### whisker width. Example (1) with error.whisker.width = 1 -> whiskers have the width of the corresponding bar
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), times = 500), Group2 = rep(LETTERS[1:5], each = 200)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = NULL, error.disp = "SD", error.whisker.width = 1)
### whisker width. Example (2) error bars with no whiskers
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), times = 500), Group2 = rep(LETTERS[1:5], each = 200)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = NULL, error.disp = "SD", error.whisker.width = 0)
### tidy dot distribution. Example (1)
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), times = 500), Group2 = rep(LETTERS[1:5], each = 200)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = "same", dot.tidy = TRUE, dot.bin.nb = 100)
### tidy dot distribution. Example (2) reducing the dot size with dot.bin.nb
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), times = 500), Group2 = rep(LETTERS[1:5], each = 200)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = "same", dot.tidy = TRUE, dot.bin.nb = 150)
### dot jitter. Example (1)
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), times = 500), Group2 = rep(LETTERS[1:5], each = 200)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = "same", dot.tidy = FALSE, dot.jitter = 1, dot.size = 2)
### dot jitter. Example (2) with dot.jitter = 1 -> dispersion around the corresponding bar width
# obs1 <- data.frame(Time = 1:1000, Group1 = rep(c("G", "H"), times = 500), Group2 = rep(LETTERS[1:5], each = 200)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = "grey", dot.size = 3, dot.alpha = 1,  dot.jitter = 1)
### dot jitter. Example (3) with no dispersion
# obs1 <- data.frame(Time = 1:100, Group1 = rep(c("G", "H"), times = 50), Group2 = rep(LETTERS[1:5], each = 20)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = "grey", dot.size = 3, dot.alpha = 1,  dot.jitter = 0)
### dot size, dot border size and dot transparency
# obs1 <- data.frame(Time = 1:100, Group1 = rep(c("G", "H"), times = 50), Group2 = rep(LETTERS[1:5], each = 20)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), dot.color = "grey", dot.size = 4, dot.border.size = 0, dot.alpha = 0.6)
### y-axis limits. Example (1)
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), ylim = c(-1, 25))
### y-axis limits. Example (2) showing that order matters in ylim argument
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), ylim = c(25, -1))
### log scale. Example (1). BEWARE: y column must be log, otherwise incoherent scale (see below warning message with the return argument)
# obs1 <- data.frame(Time = log10((1:20) * 100), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), ylog = "log10")
### log scale. Example (2). BEWARE: values of the ylim must be in the corresponding log
# obs1 <- data.frame(Time = log10((1:20) * 100), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), ylog = "log10", ylim = c(1,4))
### tick number. Example (1)
# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), y.tick.nb = 10)
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### tick number. Example (2) using a log2 scale
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# obs1 <- data.frame(Time = log2((1:20) * 100), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), ylog = "log2", y.tick.nb = 10, ylim = c(1, 16))
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### tick number. Example (3) using a log10 scale
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# obs1 <- data.frame(Time = log10((1:20) * 100), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), ylog = "log10", y.tick.nb = 10)
### tick number. Example (4) using a log10 scale: the reverse y-axis correctly deal with log10 scale
# obs1 <- data.frame(Time = log10((1:20) * 100), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), ylog = "log10", y.tick.nb = 10, ylim = c(4, 1))
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### secondary tick number. Example (1)
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# obs1 <- data.frame(Time = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), y.inter.tick.nb = 2)
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### secondary ticks. Example (2) not for log2 and log10 scales (see below warning message with the return argument)
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# obs1 <- data.frame(Time = log10((1:20) * 100), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), ylog = "log10", y.inter.tick.nb = 2)
### include zero in the y-axis
# obs1 <- data.frame(Time = (1:20), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), y.include.zero = TRUE)
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### extra margins. To avoid dot cuts
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# obs1 <- data.frame(Time = (1:20), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), y.top.extra.margin = 0.25, y.bottom.extra.margin = 0.25)
### mean diplay. Example (1) at the top of the plot region
# obs1 <- data.frame(Time = (1:20), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), y.top.extra.margin = 0.1, stat.disp = "top", stat.size = 4, stat.dist = 2)
### mean diplay. Example (2) above bars
# obs1 <- data.frame(Time = (1:20), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), y.top.extra.margin = 0.1, stat.disp = "above", stat.size = 4, stat.dist = 2)
### bar orientation.  Example (1) without log scale, showing that the other arguments are still operational
# obs1 <- data.frame(Time = (1:20), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), y.tick.nb = 10, y.inter.tick.nb = 2, y.include.zero = TRUE, vertical = FALSE)
### bar orientation. Example (2) with log scale. Horizontal orientation is blocked with log2 and log10 scales because of a bug in ggplot2 (https://github.com/tidyverse/ggplot2/issues/881)
# obs1 <- data.frame(Time = log10((1:20) * 100), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), ylog = "log10", vertical = FALSE)
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### classic representation (use grid = TRUE to display the background lines of the y axis ticks)
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# obs1 <- data.frame(Time = (1:20), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), classic = TRUE, grid = FALSE)
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### graphic info. Example (1)
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# obs1 <- data.frame(Time = log10((1:20) * 100), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), return = TRUE)
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### graphic info. Example (2) of assignation and warning message display
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# obs1 <- data.frame(Time = log10((1:20) * 100), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; warn <- fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), ylog = "log10", return = TRUE) ; cat(warn$warn)
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### add ggplot2 functions
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# obs1 <- data.frame(Time = log10((1:20) * 100), Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "Time", categ = c("Group1", "Group2"), add = "+ggplot2::theme_classic()")
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### all the arguments
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# obs1 <- data.frame(x = 1:20, Group1 = rep(c("G", "H"), times = 10), Group2 = rep(c("A", "B"), each = 10)) ; fun_gg_bar(data1 = obs1, y = "x", categ = c("Group1", "Group2"), categ.class.order = list(NULL, c("B", "A")), categ.legend.name = "", categ.color = c("red", "blue"), bar.width = 0.25, error.disp = "SD", error.whisker.width = 0.8, dot.color = "grey", dot.tidy = FALSE, dot.bin.nb = 30, dot.jitter = 1, dot.size = 4, dot.border.size = 0, dot.alpha = 1, ylim = c(0, 25), ylog = "no", y.tick.nb = NULL, y.inter.tick.nb = NULL, y.include.zero = FALSE, y.top.extra.margin = 0.05, y.bottom.extra.margin = 0, stat.disp = "above", stat.size = 4, stat.dist = 2, xlab = "GROUP", ylab = "VALUE", vertical = FALSE, text.size = 12, title = "", title.text.size = 8, text.angle = 45, classic = TRUE, grid = TRUE, return = TRUE, plot = TRUE, add = NULL, warn.print = TRUE, lib.path = NULL)
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# DEBUGGING
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# data1 <- data.frame(a = 1:20, group1 = rep(c("G", "H"), times = 10), group2 = rep(c("A", "B"), each = 10), bar.color = rep(c("brown", "orange"), each = 10)) ; data1[2:3, 1] <- NA ; data1[7:8, 2] <- NA ; y = names(data1)[1] ; categ = c(names(data1)[2], names(data1)[3]) ; categ.class.order = list(L1 = NULL, L2 = c("B", "A")) ; categ.legend.name = NULL ; categ.color = na.omit(data1)$bar.color ; bar.width = 0.5 ; error.disp = "SD" ; error.whisker.width = 0.5 ; dot.color = "same" ; dot.tidy = FALSE ; dot.bin.nb = 30 ; dot.jitter = 0.25 ; dot.size = 3 ; dot.border.size = 0.5 ; dot.alpha = 1 ; ylim = NULL ; ylog = "no" ; y.tick.nb = NULL ; y.inter.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0 ; stat.disp = NULL ; stat.size = 4 ; stat.dist = 2 ; xlab = NULL ; ylab = NULL ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; return = FALSE ; plot = TRUE ; add = NULL ; warn.print = TRUE ; lib.path = NULL
# data1 <-data.frame(a = rep(1:20, 5), group1 = rep(c("G", "H"), times = 50), group2 = rep(LETTERS[1:5], each = 20)) ; y = names(data1)[1] ; categ = c(names(data1)[2], names(data1)[3]) ; categ.class.order = list(L1 = NULL, L2 = c("B", "A", "E", "D", "C")) ; categ.legend.name = NULL ; categ.color = NULL ; bar.width = 0.5 ; error.disp = "SD" ; error.whisker.width = 0.5 ; dot.color = "same" ; dot.tidy = TRUE ; dot.bin.nb = 30 ; dot.jitter = 0.25 ; dot.size = 3 ; dot.border.size = 0.5 ; dot.alpha = 1 ; ylim = NULL ; ylog = "no" ; y.tick.nb = NULL ; y.inter.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0 ; stat.disp = NULL ; stat.size = 4 ; stat.dist = 2 ; xlab = NULL ; ylab = NULL ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; return = FALSE; plot = TRUE ; add = NULL ; warn.print = TRUE ; lib.path = NULL
# data1 <- data.frame(a = 1:20, group1 = rep(c("G", "H"), times = 10), group2 = rep(c("A", "B"), each = 10), bar.color = rep(c("brown", "orange"), each = 10)) ; data1[2:3, 1] <- NA ; data1[7:8, 2] <- NA ; y = names(data1)[1] ; categ = c(names(data1)[2], names(data1)[3]) ; categ.class.order = list(L1 = NULL, L2 = c("B", "A")) ; categ.legend.name = NULL ; categ.color = na.omit(data1)$bar.color ; bar.width = 0.5 ; error.disp = "SD" ; error.whisker.width = 0.5 ; dot.color = "same" ; dot.tidy = TRUE ; dot.bin.nb = 30 ; dot.jitter = 0.25 ; dot.size = 3 ; dot.border.size = 0.5 ; dot.alpha = 1 ; ylim = NULL ; ylog = "no" ; y.tick.nb = NULL ; y.inter.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0 ; stat.disp = "above" ; stat.size = 4 ; stat.dist = 2 ; xlab = NULL ; ylab = NULL ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; text.angle = 0 ; classic = FALSE ; grid = FALSE ; return = FALSE; plot = TRUE ; add = NULL ; warn.print = TRUE ; lib.path = NULL
# set.seed(1) ; data1 <- data.frame(a = c(rnorm(25, 0), rnorm(25, -10), rnorm(25, 10), rnorm(25, 20)), group1 = rep(c("G", "H"), times = 50), group2 = rep(c("A", "B", "C", "D"), each = 25)) ; set.seed(NULL) ; y = "Time" ; categ = c("group1", "group2") ; categ.class.order = list(NULL, c("B", "A", "D", "C")) ; categ.legend.name = "LEGEND" ; categ.color = NULL ; bar.width = 0.8 ; error.disp = "SD" ; error.whisker.width = 0.5 ; dot.color = "same" ; dot.tidy = TRUE ; dot.bin.nb = 60 ; dot.jitter = 0.25 ; dot.size = 3.5 ; dot.border.size = 0 ; dot.alpha = 1 ; ylim= c(-15, 25) ; ylog = "no" ; y.tick.nb = NULL ; y.inter.tick.nb = NULL ; y.include.zero = "no" ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0 ; stat.disp = "above" ; stat.size = 4 ; stat.dist = 2 ; xlab = "GROUP" ; ylab = "VALUE" ; vertical = FALSE ; text.size = 12 ; title = "" ; title.text.size = 8 ; text.angle = -200 ; classic = FALSE ; grid = FALSE ; return = FALSE; plot = TRUE ; add = NULL ; warn.print = TRUE ; lib.path = NULL
# set.seed(1) ; data1 <- data.frame(x = 1:1000, group1 = rep(c("G", "H"), times = 500), group2 = rep(LETTERS[1:5], each = 200)) ; set.seed(NULL) ; y = "x" ; categ <- c("group1", "group2") ; categ.class.order = list(NULL, c("B", "A", "D", "C", "E")) ; categ.legend.name = "LEGEND" ; categ.color = NULL ; bar.width = 0.8 ; error.disp = "SD" ; error.whisker.width = 1 ; dot.color = NULL ; dot.tidy = FALSE ; dot.bin.nb = 60 ; dot.jitter = 0.25 ; dot.size = 3.5 ; dot.border.size = 0.2 ; dot.alpha = 1 ; ylim= c(1, 4) ; ylog = "log10" ; y.tick.nb = NULL ; y.inter.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0 ; y.bottom.extra.margin = 0 ; stat.disp = "above" ; stat.size = 4 ; stat.dist = 1 ; xlab = "GROUP" ; ylab = "VALUE" ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; text.angle = -200 ; classic = FALSE ; grid = FALSE ; return = FALSE; plot = TRUE ; add = NULL ; warn.print = TRUE ; lib.path = 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(utils::find("fun_comp_2d", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_comp_2d() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(length(utils::find("fun_gg_just", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_gg_just() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
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if(length(utils::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")
stop(tempo.cat, call. = FALSE)
}
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if(length(utils::find("fun_name_change", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_name_change() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
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stop(tempo.cat, call. = FALSE)
}
if(length(utils::find("fun_pack", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
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)
}
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if(length(utils::find("fun_round", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_round() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(length(utils::find("fun_scale", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_scale() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
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# end required function checking
# reserved words to avoid bugs (used in this function)
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reserved.words <- c("categ.check", "categ.color", "dot.color", "dot.max", "dot.min", "ERROR.INF", "ERROR.SUP", "group", "group.check", "max.dot.error", "MEAN", "min.dot.error", "SD", "SEM", "tempo.categ1", "tempo.categ2", "text.max.pos", "text.min.pos", "x", "x.y", "y", "y.check", "y_from.dot.max", "ymax")
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# end reserved words to avoid bugs (used in this function)
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# argument checking (and modification for proper color management)
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warn <- NULL
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warn.count <- 0
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arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = data1, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE & any(duplicated(names(data1)))){
tempo.cat <- paste0("ERROR IN ", function.name, ": DUPLICATED COLUMN NAMES OF data1 ARGUMENT NOT ALLOWED:\n", paste(names(data1)[duplicated(names(data1))], collapse = " "))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
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}
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tempo <- fun_check(data = y, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE & ! (y %in% names(data1))){
tempo.cat <- paste0("ERROR IN ", function.name, ": y ARGUMENT MUST BE A COLUMN NAME OF data1")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}else if(tempo$problem == FALSE){
tempo <- fun_check(data = data1[, y], data.name = "y COLUMN OF data1", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
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}
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tempo <- fun_check(data = categ, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE & length(categ) > 2){
tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT CANNOT HAVE MORE THAN 2 COLUMN NAMES OF data1\n\n================\n\n")
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text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
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}else if(tempo$problem == FALSE & ! all(categ %in% names(data1))){
tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT MUST BE COLUMN NAMES OF data1. HERE IT IS:\n", paste(categ, collapse = " "))
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text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
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# reserved word checking
if(any(names(data1) %in% reserved.words)){
if(any(duplicated(names(data1)))){
tempo.cat <- paste0("ERROR IN ", function.name, ": DUPLICATED COLUMN NAMES OF data1 ARGUMENT NOT ALLOWED:\n", paste(names(data1)[duplicated(names(data1))], collapse = " "))
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text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
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tempo.output <- fun_name_change(names(data1), reserved.words)
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for(i2 in 1:length(tempo.output$ini)){ # a loop to be sure to take the good ones
names(data1)[names(data1) == tempo.output$ini[i2]] <- tempo.output$post[i2]
if(any(y == tempo.output$ini[i2])){
y[y == tempo.output$ini[i2]] <- tempo.output$post[i2]
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warn.count <- warn.count + 1
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tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": IN y ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i2], " HAS BEEN REPLACED BY ", tempo.output$post[i2], "\nBECAUSE RISK OF BUG AS SOME NAMES IN y ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
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warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
}
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if(any(categ == tempo.output$ini[i2])){
categ[categ == tempo.output$ini[i2]] <- tempo.output$post[i2]
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warn.count <- warn.count + 1
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tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": IN categ ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i2], " HAS BEEN REPLACED BY ", tempo.output$post[i2], "\nBECAUSE RISK OF BUG AS SOME NAMES IN categ ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
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warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
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}
}
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warn.count <- warn.count + 1
tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": REGARDING COLUMN NAMES REPLACEMENT, THE NAMES\n", paste(tempo.output$ini, collapse = " "), "\nHAVE BEEN REPLACED BY\n", paste(tempo.output$post, collapse = " "))
warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
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}
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# end reserved word checking
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# na detection and removal (done now to be sure of the correct length of categ)
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if(any(is.na(data1[, c(y, categ)]))){
removed.row.nb <- unlist(lapply(lapply(c(data1[c(y, categ)]), FUN = is.na), FUN = which))
removed.rows <- data1[removed.row.nb, ]
data1 <- data1[-removed.row.nb, ]
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warn.count <- warn.count + 1
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tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": NA DETECTED IN COLUMN ", paste(c(y, categ), collapse = " "), " OF data1 AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
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warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
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}else{
removed.row.nb <- NULL
removed.rows <- NULL
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}
# end na detection and removal (done now to be sure of the correct length of categ)
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for(i1 in 1:length(categ)){
if(any(is.na(data1[, categ[i1]]))){
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warn.count <- warn.count + 1
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tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": IN categ NUMBER ", i1, " IN data1, THE CATEGORY COLUMN ", categ[i1], " CONTAINS NA")
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warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
}
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tempo1 <- fun_check(data = data1[, categ[i1]], data.name = paste0("categ NUMBER ", i1, " OF data1"), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name, print = FALSE)
tempo2 <- fun_check(data = data1[, categ[i1]], data.name = paste0("categ NUMBER ", i1, " OF data1"), class = "factor", na.contain = TRUE, fun.name = function.name, print = FALSE)
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if(tempo1$problem == TRUE & tempo2$problem == TRUE){
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tempo.cat <- paste0("ERROR IN ", function.name, ": ", paste0("categ NUMBER ", i1, " OF data1"), " MUST BE A FACTOR OR CHARACTER VECTOR\n\n================\n\n")
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text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}else if(tempo1$problem == FALSE){
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warn.count <- warn.count + 1
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tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": IN categ NUMBER ", i1, " IN data1, THE CHARACTER COLUMN HAS BEEN CONVERTED TO FACTOR")
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warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
}
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data1[, categ[i1]] <- factor(data1[, categ[i1]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
}
if( ! is.null(categ.class.order)){
tempo <- fun_check(data = categ.class.order, class = "list", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE & length(categ.class.order) > 2){
tempo.cat <- paste0("ERROR IN ", function.name, ": categ.class.order ARGUMENT MUST BE A LIST OF MAX LENGTH 2\n\n================\n\n")
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text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
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}else if(tempo$problem == FALSE){
for(i3 in 1:length(categ.class.order)){
if(is.null(categ.class.order[[i3]])){
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warn.count <- warn.count + 1
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tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": THE categ.class.order COMPARTMENT ", i3, " IS NULL. ALPHABETICAL ORDER WILL BE APPLIED")
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warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
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data1[, categ[i3]] <- factor(as.character(data1[, categ[i3]])) # if already a factor, change nothing, if characters, levels according to alphabetical order
}else if(any(duplicated(categ.class.order[[i3]]))){
tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i3, " OF categ.class.order ARGUMENT CANNOT HAVE DUPLICATED CLASSES: ", paste(categ.class.order[[i3]], collapse = " "))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}else if( ! (all(categ.class.order[[i3]] %in% unique(data1[, categ[i3]])) & all(unique(data1[, categ[i3]]) %in% categ.class.order[[i3]]))){
tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i3, " OF categ.class.order ARGUMENT MUST BE CLASSES OF ELEMENT ", i3, " OF categ\nHERE IT IS:\nCOMPARTMENT ", i3, " OF categ.class.order:", paste(categ.class.order[[i3]], collapse = " "), "\nCOLUMN ", categ[i3], " OF data1: ", paste( unique(data1[, categ[i3]]), collapse = " "))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}else{
data1[, categ[i3]] <- factor(data1[, categ[i3]], levels = categ.class.order[[i3]]) # reorder the factor

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}
}
}
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}
if( ! is.null(categ.legend.name)){
tempo <- fun_check(data = categ.legend.name, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
}else{
categ.legend.name <- categ[length(categ)] # if only categ1, then legend name of categ1, if length(categ) == 2, then legend name of categ2
}
if( ! is.null(categ.color)){
# check the nature of color
tempo1 <- fun_check(data = categ.color, class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name, print = FALSE)
tempo2 <- fun_check(data = categ.color, class = "factor", na.contain = TRUE, fun.name = function.name, print = FALSE)
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if(tempo1$problem == TRUE & tempo2$problem == TRUE){
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# integer colors into gg_palette
tempo.check.color <- fun_check(data = categ.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name, print = FALSE)$problem
if(tempo.check.color == TRUE){
tempo.cat <- paste0("ERROR IN ", function.name, ": categ.color MUST BE A FACTOR OR CHARACTER VECTOR OR INTEGER VECTOR\n\n================\n\n") # integer possible because dealt above
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text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
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}else{ # convert integers into colors
categ.color <- fun_gg_palette(max(categ.color, na.rm = TRUE))
}
# end integer colors into gg_palette
}
if( ! (all(categ.color %in% colors() | grepl(pattern = "^#", categ.color)))){ # check that all strings of low.color start by #
tempo.cat <- paste0("ERROR IN ", function.name, ": categ.color ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors(): ", paste(unique(categ.color), collapse = " "))
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text.check <- c(text.check, tempo.cat)