v4.0.0 release

README.md

 #### DESCRIPTION
 
-Cute Little R Functions contains 16 functions for R/RStudio that facilitate basic procedures in 1) object analysis, 2) object modification, 3) graphic handling and 4) log file management.
+Cute Little R Functions contains 17 functions for R/RStudio that facilitate basic procedures in 1) object analysis, 2) object modification, 3) graphic handling and 4) log file management.
 The function names are:
-fun_param_check()
-fun_object_info()
-fun_1D_comp()
-fun_2D_comp()
-fun_list_comp()
-fun_dataframe_flipping()
-fun_refactorization()
-fun_rounding()
-fun_90clock_matrix_rot()
-fun_hexa_hsv_color_matrix()
-fun_window_width_resizing()
-fun_open_window()
-fun_graph_param_prior_plot()
-fun_feature_post_plot()
-fun_close_specif_window()
-fun_export_data()
+fun_param_check()	Check the class, type, mode and length, prop, neg values, na.contains, etc., of an object
+fun_object_info()	provide a full description of the object
+fun_1D_comp()	compare two 1D datasets (vector of factor or 1D table) of the same class or not
+fun_2D_comp()	compare two 2D datasets of the same class or not
+fun_list_comp()	compare two lists
+fun_dataframe_remodeling()	remodel data frames
+fun_refactorization()	refactorize a factor or the factor columns of a data frame, such as only the class present are in the levels (no empty levels). The class order in levels is kept
+fun_rounding()	round a vector of values, if decimal, with the desired number of decimal digits after the decimal leading zeros
+fun_90clock_matrix_rot()	90° clockwise matrix rotation
+fun_hexa_hsv_color_matrix()	convert a matrix made of numbers into a hexadecimal matrix for rgb colorization
+fun_window_width_resizing()	rescale the width of a window to open depending on the number of classes to plot
+fun_open_window()	open a pdf or screen (GUI) graphic window
+fun_graph_param_prior_plot()	very convenient to erase the axes for post plot axis redrawing using fun_feature_post_plot()
+fun_feature_post_plot()	redesign axis and provide convenients coordinates for adding elements on the drawn graph
+fun_close_specif_window()	close only specific graphic windows (devices)
+fun_var_trim_display()	trim and display values from a numeric vector or matrix
+fun_export_data()	log file function: print a character string or a data object into a same output file
 
 
 #### HOW TO USE IT
@@ -47,6 +48,17 @@ Check for updated versions (more recent release tags) at https://gitlab.pasteur.
 
 #### WHAT'S NEW IN
 
+## v4.0.0
+
+1) fun_var_trim_display() function added
+
+2) fun_feature_post_plot() function now provides additional coordinates when there are margins between the figure region and the device region
+
+3) fun_2D_comp() function now provide the common row and column names, and a bug fixed in the detection of identical row or column content
+
+4) error messages now mention the function that generates this message 
+
+
 ## v3.1.0
 
 1) fun_export_data() function modified: argument data cannot be NULL

examples_alone.txt

@@ -16,7 +16,10 @@ obs1 = 1:5 ; obs2 = 1.1:6.1 ; fun_1D_comp(obs1, obs2)
 obs1 = as.table(1:5); obs2 = as.table(1:5) ; fun_1D_comp(obs1, obs2)
 obs1 = as.table(1:5); obs2 = 1:5 ; fun_1D_comp(obs1, obs2)
 
-obs1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = as.data.frame(matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5]))) ; fun_2D_comp(obs1, obs2)
+obs1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = as.data.frame(matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5]))) ; obs1 ; obs2 ; fun_2D_comp(obs1, obs2)
+obs1 = matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("a", "z", "b"), c(LETTERS[1:2], "k", LETTERS[5:4]))) ; obs1 ; obs2 ; fun_2D_comp(obs1, obs2)
+obs1 = t(matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5]))) ; obs2 = t(matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("a", "z", "b"), c(LETTERS[1:2], "k", LETTERS[5:4])))) ; obs1 ; obs2 ; fun_2D_comp(obs1, obs2)
+
 
 obs1 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; obs2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; fun_list_comp(obs1, obs2)
 obs1 = list(1:5, LETTERS[1:2]) ; obs2 = list(a = 1:5, b = LETTERS[1:2]) ; fun_list_comp(obs1, obs2)
@@ -50,9 +53,13 @@ fun_graph_param_prior_plot(param.reinitial = FALSE, xlog.scale = FALSE, ylog.sca
 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:
 prior.par <- fun_graph_param_prior_plot(param.reinitial = TRUE) ; plot(1:100) ; fun_feature_post_plot(x.side = 1, x.lab = "Values", y.side = 2, y.lab = "TEST", y.axis.magnific = 1, y.label.magnific = 2, y.dist.legend = 0.6)
-
+# example with margins in the device region:
+windows(5,5) ; par(mai=c(0.5,0.5,0.5,0.5), omi = c(0.25,0.25,1,0.25), xaxs = "i", yaxs = "i") ; plot(0:10) ; a <- fun_feature_post_plot(x.side = 0, y.side = 0) ; x <- c(a$x.mid.left.dev.region, a$x.left.dev.region, a$x.mid.right.dev.region, a$x.right.dev.region, a$x.mid.left.fig.region, a$x.left.fig.region, a$x.mid.right.fig.region, a$x.right.fig.region, a$x.right.plot.region, a$x.left.plot.region, a$x.mid.plot.region) ; y <- c(a$y.mid.bottom.dev.region, a$y.bottom.dev.region, a$y.mid.top.dev.region, a$y.top.dev.region, a$y.mid.bottom.fig.region, a$y.bottom.fig.region, a$y.mid.top.fig.region, a$y.top.fig.region, a$y.top.plot.region, a$y.bottom.plot.region, a$y.mid.plot.region) ; par(xpd = NA) ; points(x = rep(5, length(y)), y = y, pch = 16, col = "red") ; text(x = rep(5, length(y)), y = y, c("y.mid.bottom.dev.region", "y.bottom.dev.region", "y.mid.top.dev.region", "y.top.dev.region", "y.mid.bottom.fig.region", "y.bottom.fig.region", "y.mid.top.fig.region", "y.top.fig.region", "y.top.plot.region", "y.bottom.plot.region", "y.mid.plot.region"), cex = 0.65, col = grey(0.25)) ; points(y = rep(5, length(x)), x = x, pch = 16, col = "blue") ; text(y = rep(5, length(x)), x = x, c("x.mid.left.dev.region", "x.left.dev.region", "x.mid.right.dev.region", "x.right.dev.region", "x.mid.left.fig.region", "x.left.fig.region", "x.mid.right.fig.region", "x.right.fig.region", "x.right.plot.region", "x.left.plot.region", "x.mid.plot.region"), cex = 0.65, srt = 90, col = grey(0.25))
+ 
 windows() ; windows() ; pdf() ; dev.list() ; fun_close_specif_window(kind = c("pdf", "x11"), return.text = TRUE) ; dev.list()
 
+fun_var_trim_display(data = c(1:100, 1:10), displayed.nb = NULL, single.value.display = FALSE, trim.method = "mean.sd", trim.cutoffs = c(0.05, 0.975), interval.scale.disp = TRUE, down.space = 0.75, left.space = 0.75, up.space = 0.3, right.space = 0.25, orient = 1, dist.legend = 0.37, box.type = "l", amplif.label = 1.25, amplif.axis = 1.25, std.x.range = TRUE, std.y.range = TRUE, cex.pt = 0.2, col.box = hsv(0.55, 0.8, 0.8), x.nb.inter.tick = 4, y.nb.inter.tick = 0, tick.length = 0.5, sec.tick.length = 0.3, text.corner = "", amplif.legend = 1, magnific.text.corner = 0.75, trim.return = TRUE)
+
 fun_export_data()
 fun_export_data(data = 1:3, output = "results.txt", path = "C:/Users/Gael/Desktop", no.overwrite = TRUE, rownames.kept = FALSE, vector.cat = FALSE, sep = 2)