#' @export plotDesign
#' @title Plot of the design matrix
#'
#' @description
#' Provides a graphical representation of the experimental design for up to 4 factors. It allows to visualize factors levels and check the balancing of the design.
#'
#' @param design A nxk "free encoded" experimental design data frame.
#' @param x By default: the first column of `design`. If not `NULL`, a character string giving the column name of `design` to be used for the x axis.
#' @param y By default: the second column of `design`. If not `NULL`, a character string giving the column name of `design` to be used for the y axis.
#' @param cols By default: the third column of `design` if present. If not `NULL`, a character vector with one or several column name(s) of `design` to be used for faceting along the columns.
#' @param rows By default: the fourth column of `design` if present. If not `NULL`, a character vector with one or several column name(s) of `design` to be used for faceting along the rows.
#' @param title Plot title.
#' @param theme ggplot theme, see `?ggtheme` for more info.
#'
#' @return A plot of the design (ggplot).
#'
#' @examples
#'
#' ### mtcars
#' data(mtcars)
#' library(tidyverse)
#' df <-  mtcars %>%
#'   dplyr::select(cyl, vs, am, gear, carb) %>%
#'   as.data.frame() %>%
#'   dplyr::mutate(across(everything(), as.factor))
#'
#' # 2 factors
#' plotDesign(design = df, x = "cyl", y = "vs",
#'           cols = NULL, rows = NULL)
#' # 3 factors
#' plotDesign(design = df, x = "cyl", y = "vs",
#'           cols = NULL, rows = c("am"))
#' # 4 factors
#' plotDesign(design = df, x = "cyl", y = "vs",
#'           cols = c("gear"), rows = c("am"))
#' # 5 factors
#' plotDesign(design = df, x = "cyl", y = "vs",
#'           cols = c("gear"), rows = c("am","carb"))
#'
#' plotDesign(design = df, x = "cyl", y = "vs",
#'           cols = c("vs"), rows = c("am","carb"))
#'
#' ### UCH
#' data("UCH")
#' plotDesign(design = UCH$design, x = "Hippurate", y = "Citrate", rows = "Day")
#'
#' @import ggplot2
#' @import dplyr
#' @import tidyverse

plotDesign <- function(design, x = NULL, y = NULL, rows = NULL, cols = NULL,
                       title = "Plot of the design", theme = theme_bw())
{
  
  # Create checkArg function
  
  #' @importFrom plyr is.formula
  
  checkArg = function(arg, checks, can.be.null = FALSE){
    check.list <- list(bool = c(is.logical, "a boolean"),
                       int = c(function(x) identical(as.numeric(x),round(as.numeric(x))), "an integer"),
                       num = c(is.numeric, "a numeric"),
                       str = c(is.character, "a character string"),
                       pos = c(function(x) {min(x)>0}, "positive"),
                       pos0 = c(function(x) {min(x) >= 0}, "positive or zero"),
                       formula = c(plyr::is.formula,"a formula"),
                       data.frame = c(is.data.frame,"a dataframe"),
                       matrix = c(is.matrix,"a matrix"),
                       list = c(is.list,"a list"),
                       length1 = c(function(x) {length(x) == 1}, "of length 1"))
    
    if (is.null(arg))  {
      if (!can.be.null)  {
        stop(deparse(substitute(arg)), " is null.")
      }
    } else  {
      for (c in checks) {
        if (!check.list[[c]][[1]](arg)) {
          stop(deparse(substitute(arg)), " is not ", check.list[[c]][[2]],".")
        }
      }
    }
  }
  # checks arguments ===================
  
  checkArg(design,"data.frame",can.be.null = FALSE)
  checkArg(x,c("str","length1"),can.be.null = TRUE)
  checkArg(y,c("str","length1"),can.be.null = TRUE)
  checkArg(rows,c("str"),can.be.null = TRUE)
  checkArg(cols,c("str"),can.be.null = TRUE)
  checkArg(title,c("str","length1"),can.be.null = TRUE)
  
  # initialize x, y, rows, cols
  
  if (is.null(x)&is.null(y)) xynull=TRUE else xynull=FALSE
  
  if(length(colnames(design))==1)  design=cbind(design,count="n")
  
  if (!is.null(x)){
    x <- match.arg(x, choices = colnames(design))
  } else{
    x <- colnames(design)[1]
  }
  
  if (!is.null(y)){
    y <- match.arg(y, choices = colnames(design))
  } else{
    y <- colnames(design)[2]
  }
  
  if (!is.null(cols)){
    if (!all(cols %in% colnames(design))){
      stop(paste0("cols (",paste0(cols, collapse = ", "),
                  ") is not matching column names of design: ",
                  paste0(colnames(design), collapse = ", ")))
    }
  } else{
    cn <- colnames(design)[3]
    if(xynull &ncol(design)>2 & ! cn %in% c(rows,x,y)){cols = colnames(design)[3]}
  }
  
  if (!is.null(rows)){
    if (!all(rows %in% colnames(design))){
      stop(paste0("rows (",paste0(rows, collapse = ", "),
                  ") is not matching column names of design: ",
                  paste0(colnames(design), collapse = ", ")))
    }
  } else{
    cn <- colnames(design)[4]
    if(xynull & ncol(design)>3& ! cn %in% c(cols,x,y)){rows = colnames(design)[4]}
  }
  
  # Calculate replicates by design point ===================
  
  df_count <- design %>%
    dplyr::count(dplyr::across(dplyr::all_of(c(x,y,rows,cols))))
  
  # prepare plot ===================
  
  p <- ggplot2::ggplot(df_count, ggplot2::aes_string(x = x, y = y)) 
  
  if (is.null(rows)){
    rows="."
  } else{rows = paste0(rows, collapse = "+")}
  
  if (is.null(cols)){
    cols="."
  } else{cols = paste0(cols, collapse = "+")}
  
  form <- paste0(rows,"~",cols)
  
  p <- p +  ggplot2::geom_text(aes_string(label = "n"))
  
  if(is.numeric(df_count[,y]))
  {cat("\n y numeric")
    maxy=max(df_count[,y])
    miny=min(df_count[,y])
    delta=(maxy-miny)/10
    p <- p + ylim(miny-delta,maxy+delta)} 
  
  if (!is.null(rows) | !is.null(cols)){
    p <- p + ggplot2::facet_grid(as.formula(form),
                                 labeller = label_both)}
  
  p <- p + ggplot2::ggtitle(title) + theme
  
  return(p)
  
}