cute_little_R_functions.R 873 KB
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if(y.log != "no"){
tempo <- fun_inter_ticks(lim = y.lim, log = y.log)
y.second.tick.values <- tempo$values
y.second.tick.pos <- tempo$coordinates
# if(vertical == TRUE){ # do not remove in case the bug is fixed
assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
geom = "segment", 
y = y.second.tick.pos, 
yend = y.second.tick.pos, 
x = if(diff(x.lim) > 0){tempo.coord$x.range[1]}else{tempo.coord$x.range[2]}, 
xend = if(diff(x.lim) > 0){tempo.coord$x.range[1] + abs(diff(tempo.coord$x.range)) / 80}else{tempo.coord$x.range[2] - abs(diff(tempo.coord$x.range)) / 80}
))
# }else{ # not working because of the ggplot2 bug
# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", x = y.second.tick.pos, xend = y.second.tick.pos, y = tempo.coord$y.range[1], yend = tempo.coord$y.range[1] + diff(tempo.coord$y.range) / 80))
# }
coord.names <- c(coord.names, "y.second.tick.positions")
}else if(( ! is.null(y.second.tick.nb)) & y.log == "no"){
# if(y.second.tick.nb > 0){ #inactivated because already checked before
tempo <- fun_inter_ticks(lim = y.lim, log = y.log, breaks = tempo.scale, n = y.second.tick.nb)
y.second.tick.values <- tempo$values
y.second.tick.pos <- tempo$coordinates
assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
geom = "segment", 
y = y.second.tick.pos, 
yend = y.second.tick.pos, 
x = if(diff(x.lim) > 0){tempo.coord$x.range[1]}else{tempo.coord$x.range[2]}, 
xend = if(diff(x.lim) > 0){tempo.coord$x.range[1] + abs(diff(tempo.coord$x.range)) / 80}else{tempo.coord$x.range[2] - abs(diff(tempo.coord$x.range)) / 80}
))
coord.names <- c(coord.names, "y.second.tick.positions")
}
# for the ggplot2 bug with y.log, this does not work: eval(parse(text = ifelse(vertical == FALSE & y.log == "log10", "ggplot2::scale_x_continuous", "ggplot2::scale_y_continuous")))
assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_y_continuous(
breaks = tempo.scale, 
minor_breaks = y.second.tick.pos, 
labels = if(y.log == "log10"){scales::trans_format("identity", scales::math_format(10^.x))}else if(y.log == "log2"){scales::trans_format("identity", scales::math_format(2^.x))}else if(y.log == "no"){ggplot2::waiver()}else{tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 10") ; stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)}, 
expand = c(0, 0), # remove space after axis limits
limits = sort(y.lim), # NA indicate that limits must correspond to data limits but ylim() already used
oob = scales::rescale_none, 
trans = ifelse(diff(y.lim) < 0, "reverse", "identity") # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
))
# end y.second.tick.positions
assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_cartesian(xlim = x.lim, ylim = y.lim)) # clip = "off" to have secondary ticks outside plot region. The problem is that points out of bounds are also drawn outside the plot region. Thus, I cannot use it # at that stage, x.lim and y.lim not NULL anymore
# end scale management




# drawing
fin.plot <- eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + ")))
grob.save <- NULL
if(plot == TRUE){
if( ! is.null(legend.width)){ # any(unlist(legend.disp)) == TRUE removed to have empty legend space # not & any(unlist(fin.lg.disp)) == TRUE here because converted to FALSE
grob.save <- suppressMessages(suppressWarnings(gridExtra::grid.arrange(fin.plot, legend.final, ncol=2, widths=c(1, legend.width))))
}else{
grob.save <- suppressMessages(suppressWarnings(print(fin.plot)))
}
}else{
warn.count <- warn.count + 1
tempo.warn <- paste0("(", warn.count,") PLOT NOT SHOWN AS REQUESTED")
warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
}
# end drawing



# outputs
if(warn.print == TRUE & ! is.null(warn)){
warning(paste0("FROM ", function.name, " FUNCTION:\n\n", warn), call. = FALSE) # to recover the warning messages, use return = TRUE
}
if(return == TRUE){
output <- suppressMessages(ggplot2::ggplot_build(fin.plot))
# output$data <- output$data[-1] # yes for boxplot but not for scatter # remove the first data because corresponds to the initial empty boxplot
if(length(output$data) != length(coord.names)){
tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, ": length(output$data) AND length(coord.names) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
}else{
names(output$data) <- coord.names
}
if(is.null(unlist(removed.row.nb))){
removed.row.nb <- NULL
removed.rows <- NULL
}else{
for(i3 in 1:length(data1)){
if( ! is.null(removed.row.nb[[i3]])){
removed.row.nb[[i3]] <- sort(removed.row.nb[[i3]])
removed.rows[[i3]] <- data1.ini[[i3]][removed.row.nb[[i3]], ]
}
}
}
tempo <- output$layout$panel_params[[1]]
output <- list(
data = data1, 
removed.row.nb = removed.row.nb, 
removed.rows = removed.rows, 
plot = c(output$data, x.second.tick.values = list(x.second.tick.values), y.second.tick.values = list(y.second.tick.values)), 
panel = facet.categ, 
axes = list(
x.range = tempo$x.range, 
x.labels = if(is.null(attributes(tempo$x$breaks))){tempo$x$breaks}else{tempo$x$scale$get_labels()}, # is.null(attributes(tempo$x$breaks)) test if it is number (TRUE) or character (FALSE)
x.positions = if(is.null(attributes(tempo$x$breaks))){tempo$x$breaks}else{unlist(attributes(tempo$x$breaks))}, 
y.range = tempo$y.range, 
y.labels = if(is.null(attributes(tempo$y$breaks))){tempo$y$breaks}else{tempo$y$scale$get_labels()}, 
y.positions = if(is.null(attributes(tempo$y$breaks))){tempo$y$breaks}else{unlist(attributes(tempo$y$breaks))}
), 
warn = paste0("\n", warn, "\n\n"), 
ggplot = if(return.ggplot == TRUE){fin.plot}else{NULL}, # fin.plot plots the graph if return == TRUE
gtable = if(return.gtable == TRUE){grob.save}else{NULL} #
)
return(output) # this plots the graph if return.ggplot is TRUE and if no assignment
}
# end outputs
# end main code
}


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