#in fact, using log10 and log2 -> convert the values. It is more logical because we want the y-axis modified but not the values in fact
#For heatmap: see https://bioinfo-fr.net/creer-des-heatmaps-a-partir-de-grosses-matrices-en-r
# double legends with suppressMessages(suppressWarnings(gridExtra::grid.arrange(fin.plot, legend.final, ncol=2, widths=c(1, legend.width))))
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@@ -7901,7 +7900,7 @@ lib.path = NULL
# article: logical. If TRUE, use a article theme (article like). If FALSE, use a classic related ggplot theme. Use the add argument (add = "+ggplot2::theme_classic()" for the exact classic ggplot theme
# grid: logical. Draw horizontal lines in the background to better read the box values? Not considered if article == FALSE
# return: logical. Return the graph parameters?
# return.ggplot: logical. Return the ggplot object in the output list? Ignored if return is FALSE. See $ggplot in the RETURN section below for more details
# return.ggplot: logical. Return the ggplot object in the output list? Ignored if return argument is FALSE. WARNING: always assign the fun_gg_boxplot() function (e.g., a <- fun_gg_boxplot()) if return.ggplot argument is TRUE, otherwise, double plotting is performed. See $ggplot in the RETURN section below for more details
# 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, facet, etc.). Ignored if NULL
# BEWARE: (1) the string must start with "+", (2) the string must finish with ")" and (3) each function must be preceded by "ggplot2::". Example: "+ ggplot2::coord_flip() + ggplot2::theme_bw()"
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@@ -7926,7 +7925,7 @@ lib.path = NULL
# RETURN
# a boxplot if plot argument is TRUE
# a list of the graph info if return argument is TRUE:
# $data: the initial data
# $data: the initial data with graphic information added. WARNING: if the y.log argument is not "no", y values are log2 or log10 converted in $data
# $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)
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@@ -7946,7 +7945,7 @@ lib.path = NULL
# $panel: the variable names used for the panels (NULL if no panels). BEWARE: NA can be present according to ggplot2 upgrade to v3.3.0
# $axes: the x-axis and y-axis info
# $warn: the warning messages. Use cat() for proper display. NULL if no warning. BEWARE: some of the warning messages (those delivered by the internal ggplot2 functions) are not apparent when using the argument plot = FALSE
# $ggplot: ggplot object that can be used for reprint (use print($ggplot) or update (use $ggplot + ggplot2::...). NULL if return.ggplot argument is FALSE. Indeed, a non NULL $ggplot in the output list is sometimes annoying as the manipulation of the list print the plot
# $ggplot: ggplot object that can be used for reprint (use print($ggplot) or update (use $ggplot + ggplot2::...). NULL if return.ggplot argument is FALSE. Of note, a non NULL $ggplot in the output list is sometimes annoying as the manipulation of this list prints the plot
# reactivate the 4 next lines to incorporate legend.width
# if(is.null(legend.width)){
# if( ! (return == TRUE & return.ggplot == TRUE)){ # because return() plots when return.ggplot is TRUE # finally not used -> see return.ggplot description