diff --git a/README.md b/README.md
index b3f333728f0ff27e7c303a2ad1737ddf6147c747..a4b0094d17b9ec67c1f985d48570bf773d6fcea7 100644
--- a/README.md
+++ b/README.md
@@ -48,6 +48,13 @@ Check for updated versions (more recent release tags) at https://gitlab.pasteur.
#### WHAT'S NEW IN
+## v4.5.0
+
+1) fun_open_window() improved to deal with Linux systems
+
+2) fun_graph_param_prior_plot() improved to deal with Linux systems
+
+
## v4.4.0
1) fun_dataframe_remodeling() now add a ini_rowname column in the output data frame when it is coherent and when initial row names are available (not NULL)
diff --git a/cute_little_R_functions.R b/cute_little_R_functions.R
index 58e4691b76ea3ea69d73a09bd958b6979ef8f813..5fde59f2598887bf9b379f0f0a409e58ef75238b 100644
--- a/cute_little_R_functions.R
+++ b/cute_little_R_functions.R
@@ -1,6 +1,6 @@
################################################################
## ##
-## CUTE LITTLE R FUNCTIONS v4.4.0 ##
+## CUTE LITTLE R FUNCTIONS v4.5.0 ##
## ##
## Gael A. Millot ##
## ##
@@ -1527,7 +1527,7 @@ fun_open_window <- function(pdf.disp = TRUE, path.fun = "working.dir", pdf.name.
# fun_param_check()
# ARGUMENTS:
# pdf.disp: use pdf or not
-# path.fun: where the pdf is saved. Must not finish by a path separator. Write "working.dir" if working directory is required (default)
+# path.fun: where the pdf is saved. Write "working.dir" if working directory is required (default)
# pdf.name.file: name of the pdf file containing the graphs (the .pdf extension is added by the function)
# width.fun: width of the windows (in inches)
# height.fun: height of the windows (in inches)
@@ -1543,6 +1543,7 @@ fun_open_window <- function(pdf.disp = TRUE, path.fun = "working.dir", pdf.name.
# fun_open_window(pdf.disp = FALSE, path.fun = "C:/Users/Gael/Desktop", pdf.name.file = "graph", width.fun = 7, height.fun = 7, paper = "special", no.pdf.overwrite = TRUE, return.output = TRUE)
# DEBUGGING
# pdf.disp = TRUE ; path.fun = "C:/Users/Gael/Desktop" ; pdf.name.file = "graphs" ; width.fun = 7 ; height.fun = 7 ; paper = "special" ; no.pdf.overwrite = TRUE ; return.output = TRUE # for function debugging
+# pdf.disp = TRUE ; path.fun = "/pasteur/homes/gmillot/" ; pdf.name.file = "graphs" ; width.fun = 7 ; height.fun = 7 ; paper = "special" ; no.pdf.overwrite = TRUE ; return.output = TRUE # for function debugging
# required function checking
if(length(find("fun_param_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN fun_open_window(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
@@ -1570,29 +1571,51 @@ stop()
if(path.fun == "working.dir"){
path.fun <- getwd()
}else{
+if(grepl(x = path.fun, pattern = ".+/$")){
+path.fun <- substr(path.fun, 1, nchar(path.fun) - 1) # remove the last /
+}
if(dir.exists(path.fun) == FALSE){
tempo.cat <- paste0("\n\n================\n\nERROR IN fun_open_window(): path.fun ARGUMENT DOES NOT CORRESPOND TO EXISTING DIRECTORY\n\n================\n\n")
stop(tempo.cat)
}
}
if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
-tempo <- NULL
+open.fail <- NULL
windows()
-ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset)
+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 bacause always a tempo window opened
invisible(dev.off()) # close the new window
}else if(Sys.info()["sysname"] == "Linux"){
-if( ! file.exists(paste0(getwd(), "/Rplots.pdf"))){
-tempo <- suppressWarnings(try(X11(), silent = TRUE))[] # open a X11 window or a pdf. So no need to use again X11(). tempo == NULL if no problem, meaning that the X11 window is opened. If tempo != NULL, a pdf is open here paste0(getwd(), "/Rplots.pdf")
-ini.par <- par(no.readonly = TRUE) # recover the initial graphical parameters. Works even if X11 is not working as R opens a pdf
-invisible(dev.off()) # can be used here to close the pdf windows if tempo != NULL and to close the X11 window if tempo == NULL
+if(pdf.disp == TRUE){
+if(file.exists(paste0(path.fun, "/recover_ini_par.pdf"))){
+tempo.cat <- paste0("\n\n================\n\nPROBLEM IN fun_open_window(): THIS FUNCTION CANNOT BE USED ON LINUX IF A recover_ini_par.pdf FILE ALREADY EXISTS HERE: ", paste(path.fun, collapse = " "), "\n\n================\n\n")
+stop(tempo.cat)
+}else{
+pdf(width = width.fun, height = height.fun, file=paste0(path.fun, "/recover_ini_par.pdf"), paper = paper)
+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 bacause always a tempo window opened
+invisible(dev.off()) # close the pdf windows
+file.remove(paste0(path.fun, "/recover_ini_par.pdf")) # remove the pdf file
+}
}else{
-tempo.cat <- paste0("\n\n================\n\nPROBLEM IN fun_open_window(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET.\nTO OVERCOME THIS, PLEASE SET pdf.disp ARGUMENT TO TRUE AND RERUN\n\n================\n\n")
+# test if X11 can be opened
+if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
+tempo.cat <- paste0("\n\n================\n\nERROR IN fun_open_window(): THIS FUNCTION CANNOT BE USED ON LINUX IF A Rplots.pdf FILE ALREADY EXISTS HERE: ", getwd(), "\n\n================\n\n")
stop(tempo.cat)
+}else{
+open.fail <- suppressWarnings(try(X11(), silent = TRUE))[] # try to open a X11 window. If open.fail == NULL, no problem, meaning that the X11 window is opened. If open.fail != NULL, a pdf can be opened here paste0(getwd(), "/Rplots.pdf")
+if(is.null(open.fail)){
+ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code bacause always a tempo window opened
+invisible(dev.off()) # close the new window
+}else if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
+file.remove(paste0(getwd(), "/Rplots.pdf")) # remove the pdf file
+tempo.cat <- ("\n\n================\n\nPROBLEM IN fun_open_window(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET).\nTO OVERCOME THIS, PLEASE SET pdf.disp ARGUMENT TO TRUE AND RERUN\n\n================\n\n")
+stop(tempo.cat)
+}
+}
}
}else{
-tempo <- NULL
+open.fail <- NULL
quartz()
-ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset)
+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 bacause always a tempo window opened
invisible(dev.off()) # close the new window
}
zone.ini <- matrix(1, ncol=1) # to recover the initial parameters for next figure region when device region split into several figure regions
@@ -1609,8 +1632,8 @@ pdf.loc <- NULL
if(Sys.info()["sysname"] == "Windows"){ # .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
windows(width = width.fun, height = height.fun, rescale="fixed")
}else if(Sys.info()["sysname"] == "Linux"){
-if( ! is.null(tempo)){
-stop("PROBLEM IN fun_open_window(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET.\nTO OVERCOME THIS, PLEASE SET pdf.disp ARGUMENT TO TRUE AND RERUN")
+if( ! is.null(open.fail)){
+stop("\n\n================\n\nPROBLEM IN fun_open_window(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET).\nTO OVERCOME THIS, PLEASE SET pdf.disp ARGUMENT TO TRUE AND RERUN\n\n================\n\n")
}else{
X11(width = width.fun, height = height.fun)
}
@@ -1633,6 +1656,7 @@ fun_graph_param_prior_plot <- function(param.reinitial = FALSE, xlog.scale = FAL
# AIM:
# very convenient to erase the axes for post plot axis redrawing using fun_feature_post_plot()
# reinitialize and set the graphic parameters before plotting
+# CANNOT be used if no graphic device already opened
# REQUIRED FUNCTIONS
# fun_param_check()
# ARGUMENTS
@@ -1659,9 +1683,9 @@ fun_graph_param_prior_plot <- function(param.reinitial = FALSE, xlog.scale = FAL
# RETURN
# return graphic parameter modification
# EXAMPLES
-# fun_graph_param_prior_plot(param.reinitial = FALSE, xlog.scale = FALSE, ylog.scale = FALSE, remove.label = TRUE, remove.x.axis = TRUE, remove.y.axis = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 4.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = FALSE)
+# fun_graph_param_prior_plot(param.reinitial = FALSE, xlog.scale = FALSE, ylog.scale = FALSE, remove.label = TRUE, remove.x.axis = TRUE, remove.y.axis = TRUE, std.x.range = TRUE, std.y.range = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 4.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = FALSE)
# DEBUGGING
-# param.reinitial = FALSE ; xlog.scale = FALSE ; ylog.scale = FALSE ; remove.label = TRUE ; remove.x.axis = TRUE ; remove.y.axis = TRUE ; down.space = 1 ; left.space = 1 ; up.space = 1 ; right.space = 1 ; orient = 1 ; dist.legend = 4.5 ; tick.length = 0.5 ; box.type = "n" ; amplif.label = 1 ; amplif.axis = 1 ; display.extend = FALSE ; return.par = FALSE # for function debugging
+# param.reinitial = FALSE ; xlog.scale = FALSE ; ylog.scale = FALSE ; remove.label = TRUE ; remove.x.axis = TRUE ; remove.y.axis = TRUE ; std.x.range = TRUE ; std.y.range = TRUE ; down.space = 1 ; left.space = 1 ; up.space = 1 ; right.space = 1 ; orient = 1 ; dist.legend = 4.5 ; tick.length = 0.5 ; box.type = "n" ; amplif.label = 1 ; amplif.axis = 1 ; display.extend = FALSE ; return.par = FALSE # for function debugging
# required function checking
if(length(find("fun_param_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN fun_graph_param_prior_plot(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
@@ -1697,6 +1721,10 @@ stop()
}
# 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 to check arguments status and if they have been checked using fun_param_check()
# end argument checking
+if(is.null(dev.list())){
+tempo.cat <- paste0("\n\n================\n\nERROR IN fun_graph_param_prior_plot(): THIS FUNCTION CANNOT BE USED IF NO GRAPHIC DEVICE ALREADY OPENED (dev.list() IS CURRENTLY NULL)\n\n================\n\n")
+stop(tempo.cat)
+}
if(param.reinitial == TRUE){
if( ! all(names(dev.cur()) == "null device")){
active.wind.nb <- dev.cur()
@@ -1705,18 +1733,31 @@ active.wind.nb <- 0
}
if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
windows()
+ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code bacause always a tempo window opened
+invisible(dev.off()) # close the new window
}else if(Sys.info()["sysname"] == "Linux"){
-if( ! file.exists(paste0(getwd(), "/Rplots.pdf"))){
-tempo <- suppressWarnings(try(X11(), silent = TRUE))[] # open a X11 window or a pdf. So no need to use again X11(). tempo == NULL if no problem, meaning that the X11 window is opened. If tempo != NULL, a pdf is open here paste0(getwd(), "/Rplots.pdf")
+if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
+tempo.cat <- paste0("\n\n================\n\nERROR IN fun_graph_param_prior_plot(): THIS FUNCTION CANNOT BE USED ON LINUX WITH param.reinitial SET TO TRUE IF A Rplots.pdf FILE ALREADY EXISTS HERE: ", getwd(), "\n\n================\n\n")
+stop(tempo.cat)
+}else{
+open.fail <- suppressWarnings(try(X11(), silent = TRUE))[] # try to open a X11 window. If open.fail == NULL, no problem, meaning that the X11 window is opened. If open.fail != NULL, a pdf can be opened here paste0(getwd(), "/Rplots.pdf")
+if(is.null(open.fail)){
+ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code bacause always a tempo window opened
+invisible(dev.off()) # close the new window
+}else if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
+ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code bacause always a tempo window opened
+invisible(dev.off()) # close the new window
+file.remove(paste0(getwd(), "/Rplots.pdf")) # remove the pdf file
}else{
-tempo.cat <- paste0("\n\n================\n\nPROBLEM IN fun_graph_param_prior_plot(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET.\nTO OVERCOME THIS, PLEASE SET pdf.disp ARGUMENT TO TRUE AND RERUN\n\n================\n\n")
+tempo.cat <- ("\n\n================\n\nPROBLEM IN fun_graph_param_prior_plot(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET).\nTO OVERCOME THIS, PLEASE USE PDF GRAPHIC INTERFACES AND RERUN\n\n================\n\n")
stop(tempo.cat)
}
+}
}else{ # macOS
quartz()
-}
-ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset)
+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 bacause always a tempo window opened)
invisible(dev.off()) # close the new window
+}
if( ! all(names(dev.cur()) == "null device")){
dev.set(active.wind.nb) # go back to the active windows if exists
par(ini.par) # apply the initial par to current window
@@ -1997,7 +2038,7 @@ axis(side = x.side, at = c(1e-15, 1e-14, 1e-13, 1e-12, 1e-11, 1e-10, 1e-9, 1e-8,
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), 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]
diff --git a/cute_little_R_functions.docx b/cute_little_R_functions.docx
index c6a9b06541c16e312961050e80db54ef5e49e093..10e28ba95260d7b40540f598354510e5d991e189 100644
Binary files a/cute_little_R_functions.docx and b/cute_little_R_functions.docx differ
diff --git a/examples_alone.txt b/examples_alone.txt
index 856d4245c843aeda8941f3982a38e0ae12887b65..cd76c860a1188c728ddb6803ab4e245b4e452b79 100644
--- a/examples_alone.txt
+++ b/examples_alone.txt
@@ -51,8 +51,7 @@ fun_window_width_resizing(class.nb = 10, inches.per.class.nb = 0.2, ini.window.w
fun_open_window(pdf.disp = FALSE, path.fun = "C:/Users/Gael/Desktop", pdf.name.file = "graph", width.fun = 7, height.fun = 7, paper = "special", no.pdf.overwrite = TRUE, return.output = TRUE)
-fun_graph_param_prior_plot(param.reinitial = FALSE, xlog.scale = FALSE, ylog.scale = FALSE, remove.label = TRUE, remove.x.axis = TRUE, remove.y.axis = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 4.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = FALSE)
-
+fun_graph_param_prior_plot(param.reinitial = FALSE, xlog.scale = FALSE, ylog.scale = FALSE, remove.label = TRUE, remove.x.axis = TRUE, remove.y.axis = TRUE, std.x.range = TRUE, std.y.range = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 4.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = FALSE)
# Example of log axis with log y-axis and unmodified x-axis:
prior.par <- fun_graph_param_prior_plot(param.reinitial = TRUE, xlog.scale = FALSE, ylog.scale = TRUE, remove.label = TRUE, remove.x.axis = FALSE, remove.y.axis = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 0.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = TRUE) ; plot(1:100, log = "y") ; fun_feature_post_plot(y.side = 2, y.log.scale = prior.par$ylog, x.lab = "Values", y.lab = "TEST", y.axis.magnific = 1.25, y.label.magnific = 1.5, y.dist.legend = 0.7, just.label.add = ! prior.par$ann)
# Example of log axis with redrawn x-axis and y-axis: