R/hello.R
In agricolaeplotr: Visualization of Design of Experiments from the 'agricolae' Package

Documented in plot_alpha plot_bib plot_cyclic plot_dau plot_design_crd plot_design.factorial_crd plot_design.factorial_lsd plot_design.factorial_rcbd plot_graeco plot_latin_square plot_lattice_simple plot_lattice_triple plot_rcdb plot_split_crd plot_split_lsd plot_split_rcbd plot_strip plot_youden test_input_height test_input_ncols test_input_nrows test_input_reverse_x test_input_reverse_y test_input_width test_name_in_column test_names_design test_string theme_poster theme_pres

#' checks matrix column input
#'
#' checks if input is suitable for matrix column indication
#' @param x input to be tested
#'
#' @return error
#' @export
#' @examples
#' library(agricolaeplotr)
#' test_input_ncols(9)
test_input_ncols <- function(x) {
  if ((length(x)) > 1) {
    stop("The length of one integer value needs to be exact 1.")
  }
  if (is.numeric(x) == FALSE) {
    stop(paste0("Value is not an integer. It is from class ",
                class(x), "."))
  } else {
    if (round(x) != x) {
      stop("It is numeric value, but not an integer")
    }
    if (x <= 0) {
      stop("Integer value is smaller or equal than zero.
           The value needs to be greater than zero.")
    }
  }
}

#' checks matrix rows input
#'
#' checks if input is suitable for matrix row indication
#' @param x input to be tested
#'
#' @return error
#' @export
#' @examples
#' library(agricolaeplotr)
#' test_input_nrows(10)
test_input_nrows <- function(x) {
  if ((length(x)) > 1) {
    stop("The length of one integer value needs to be exact 1.")
  }
  if (is.numeric(x) == FALSE) {
    stop(paste0("Value is not an integer. It is from class ",
                class(x), "."))
  } else {
    if (round(x) != x) {
      stop("It is numeric value, but not an integer")
    }
    if (x <= 0) {
      stop("Integer value is smaller or equal than zero.
           The value needs to be greater than zero.")
    }
  }
}


#' Test if input for width is numeric
#'
#' Test if input is numeric for field width
#' @param x input to be tested
#'
#' @return error
#' @export
#' @examples
#' library(agricolaeplotr)
#' test_input_width(3)
test_input_width <- function(x) {

  if (is.numeric(x) == FALSE) {
    stop(paste0("Value is not numeric. It is from class ",
                class(x), "."))
  } else {
    if (x <= 0) {
      stop("Integer value is smaller or equal than zero.
           The value needs to be greater than zero.")
    }
  }
}

#' Test if input for height is numeric
#'
#' Test if input is numeric for field height
#' @param x input to be tested
#' @export
#' @return error
#' @examples
#' library(agricolaeplotr)
#' test_input_height(5)
test_input_height <- function(x) {

  if (is.numeric(x) == FALSE) {
    stop(paste0("Value is not numeric. It is from class ",
                class(x), "."))
  } else {
    if (x <= 0) {
      stop("Integer value is smaller or equal than zero.
           The value needs to be greater than zero.")
    }
  }
}



#' Test if input is a logical
#'
#' Test if input is a logical
#' @param x input to be tested
#'
#' @return error
#' @export
#' @examples
#' library(agricolaeplotr)
#' test_input_reverse_x(TRUE)
test_input_reverse_x <- function(x) {
  if ((length(x)) > 1) {
    stop("The length of one boolean value needs to be exact 1.")
  }
  if (is.logical(x) == FALSE) {
    stop(paste0("Value is not logical. Only TRUE and FALSE are allowed.
                Your value is from class ",
                class(x), "."))
  }
}
#' Test if input is a logical
#'
#' Test if input is a logical
#' @param x input to be tested
#'
#' @return error
#' @export
#' @examples
#' library(agricolaeplotr)
#' test_input_reverse_y(TRUE)
test_input_reverse_y <- function(x) {
  if ((length(x)) > 1) {
    stop("The length of one boolean value needs to be exact 1.")
  }
  if (is.logical(x) == FALSE) {
    stop(paste0("Value is not logical. Only TRUE and FALSE are allowed.
                Your value is from class ",
                class(x), "."))
  }
}

#' Test if input is a string
#'
#' Test if input is a string
#' @param x input to be tested
#'
#' @return error
#' @export
#' @examples
#' library(agricolaeplotr)
#' test_string('smallstring')
test_string <- function(x) {
  if (is.character(x) == FALSE) {
    stop(paste0("Input parameter needs to be a string. ",
                "Your value is from class ", class(x),
                "."))
  }
}


#' Test if input column names
#'
#' Test if input is in column names of a table
#' @param design design from \code{agricolae} package
#' @param x string input
#'
#' @return error
#' @export
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' trt<-c(2,4)
#' k=6
#' outdesign<-design.ab(trt, r=k, serie=3,design='rcbd')
#' test_name_in_column('B',outdesign)
test_name_in_column <- function(x, design) {
  test_string(x)
  if (x %in% colnames(design$book) == FALSE) {
    stop(paste0("Your string is not one of the column
                names the table of the design."))
  }
}


#' Test of experimental design
#'
#' Test if the outdesign file contains book and parameter list
#' @param design design from \code{agricolae} package
#'
#' @return error
#' @export
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' trt<-c(2,4)
#' k=6
#' outdesign<-design.ab(trt, r=k, serie=3,design='rcbd')
#' test_names_design(outdesign)
test_names_design <- function(design) {
  if (sum(c("parameters", "book") %in% names(design)) <
      2) {
    stop("The function expects a list of at least two following names:
         parameters , book ")

  }
}

#### plot factorial_rcbd ####
#' Plot Factorial Designs with rcbd Design
#'
#' Plot a design of a factorial  experiment with randomized complete block design (rcbd) from design.ab
#' @param design outdesign from \code{agricolae} package
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#' @import ggplot2
#' @import agricolae
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' trt<-c(2,4)
#' k=6
#' outdesign<-design.ab(trt, r=k, serie=3,design='rcbd')
#' plot_design.factorial_rcbd(design=outdesign,factor_name = 'B')
#' plot_design.factorial_rcbd(outdesign,reverse_y = TRUE,reverse_x = TRUE)
#'
plot_design.factorial_rcbd <- function(design,
                                       y = "row",
                                       factor_name = "A",
                                       width = 1,
                                       height = 1,
                                       space_width = 0.95,
                                       space_height = 0.85,
                                       reverse_x = FALSE,
                                       reverse_y = FALSE){
  if (design$parameters$design == "factorial" &&
      design$parameters$applied == "rcbd") {

    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    plots <- as.numeric(design$book[, 1])
    mat <- matrix(plots, byrow = TRUE,
                  ncol = max(as.numeric(design$book$block)))
    dims <- dim(mat)
    table <- as.table(mat)
    rownames(table) <- 1:dims[1]
    colnames(table) <- 1:dims[2]
    table <- as.data.frame(table)
    colnames(table) <- c("row", "col", "plots")
    table[, y] <- as.numeric(table[, y])
    table$col <- as.numeric(table$col)

    table <- merge(table, design$book, by.x = "plots",
                   by.y = "plots")

    table$col <- rep(1:(length(table$plots)/max(as.numeric(table[, y]))),
                        times = max(as.numeric(table[, y])))

    # no space, 0 == only space no space, 0
    # == only space

    table$col <- table$col * width
    table$row <- as.numeric(table[, y]) * height
    if (reverse_y == TRUE) {
      table$row <- abs(table$row - max(table$row)) +
        min(table$row)
    }

    if (reverse_x == TRUE) {
      table$col <- abs(table$col - max(table$col)) +
        min(table$col)
    }

    plt <- ggplot(table, aes_string(x = "col", y = y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = "plots"),
                colour = "black")

    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from a factorial design with a
                random complete block design (rcbd) is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }
}

#### plot design crd ####
#' Plot Complete Randomized Design
#'
#' Plot a design of a factorial experiment with randomized complete block design from \code{agricolae} design.ab
#' @param design outdesign from \code{agricolae} package
#' @param ncols integer value, choose the number of columns to which the experiment should be plotted
#' @param nrows integer value, choose the number of rows to which the experiment should be plotted
#' @param y Describes the y coordinates of a experiment design, default is row
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' trt = c(2,3,4,5,6)
#' outdesign1 <-design.crd(trt,r=5,serie=2,2543,'Mersenne-Twister')
#' plot_design_crd(outdesign1,ncols = 13,nrows = 3)

plot_design_crd <- function(design,
                            ncols,
                            nrows,
                            y = "row",
                            factor_name = "trt",
                            labels = "plots",
                            width = 1,
                            height = 1,
                            space_width = 0.95,
                            space_height = 0.85,
                            reverse_y = FALSE,
                            reverse_x = FALSE) {
  if (design$parameters$design == "crd") {

    plots <- as.numeric(design$book[, 1])
    if (ncols * nrows >= length(plots)) {
    nas <- rep(NaN, ncols * nrows - length(plots))
    plots <- c(plots, nas)

    mat <- matrix(plots, byrow = TRUE, ncol = ncols)
    dims <- dim(mat)
    table <- as.table(mat)
    rownames(table) <- 1:dims[1]
    colnames(table) <- 1:dims[2]
    table <- as.data.frame(table)
    colnames(table) <- c("row", "col", "plots")
    table$row <- as.numeric(table$row)
    table$col <- as.numeric(table$col)

    table <- merge(table, design$book, by.x = "plots",
                   by.y = "plots")

    table$row <- as.numeric(table$row) * height
    table$col <- as.numeric(table$col) *
      width

    if (reverse_y == TRUE) {
      table$row <- abs(table$row - max(table$row)) +
        min(table$row)
    }
    if (reverse_x == TRUE) {
      table$col <- abs(table$col - max(table$col)) +
        min(table$col)
    }
    plt <- ggplot(table, aes_string(x = "col", y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = labels), colour = "black")

    plt

    return(plt)
    } else {
      stop(paste("You have in multiplication of ncols:",
                 ncols, "and nrows:", nrows, "Elements.",
                 "You need at minimum a product of both higher than",
                 length(plots)))
    }
  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from a factorial design with a
                complete random design (crd) is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }
}


#### plot alpha design ####
#' Plot Alpha design Experiments
#'
#' Plot a design of an experiment with an alpha design from \code{agricolae} design.alpha
#'
#' @param design outdesign from \code{agricolae} package
#' @param x Describes the x coordinates of a experiment design
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)
#' trt<-1:30
#' t <- length(trt)
#' # size block k
#' k<-3
#' # Blocks s
#' s<-t/k
#' # replications r
#' r <- 2
#' outdesign<- design.alpha(trt,k,r,serie=2)
#' plot_alpha(outdesign)
plot_alpha <- function(design, x = "cols", y = "block",
                       factor_name = "trt", labels = "plots", width = 1,
                       height = 1, space_width = 0.95,
                       space_height = 0.85,
                       reverse_y = FALSE, reverse_x = FALSE) {
  if (design$parameters$design == "alpha") {
    test_string(x)
    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(labels, design)
    test_name_in_column(factor_name, design)

    table <- as.data.frame(design$book)
    table[, y] <- as.numeric(table[, y]) * height
    table[, x]  <- as.numeric(table[, x] ) * width


    if (reverse_x == TRUE) {
      table[, x]  <- abs(table[, x]  - max(table[, x] )) +
        min(table[, x] )
    }

    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }
    plt <- ggplot(table, aes_string(x, y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank())+
      geom_text(aes_string(label = labels), colour = "black")

    plt

    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from an alpha design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}



####### plot lattice design triple######

#' Plot Triple Lattice Design
#'
#' Plot a design of a factorial  experiment with a latin square design from \code{agricolae} design.lattice with r=3
#' @param design outdesign from \code{agricolae} package
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' trt<-LETTERS[1:9]
#' outdesign<-design.lattice(trt,r=3,serie=2)
#' plot_lattice_triple(design=outdesign,reverse_x=TRUE)
#'
plot_lattice_triple <- function(design,
                                y = "block", factor_name = "trt",
                                labels = "plots",
                                width = 1,
                                height = 1,
                                space_width = 0.95,
                                space_height = 0.85,
                                reverse_y = FALSE,
                                reverse_x = FALSE) {
  if (design$parameters$design == "lattice" && design$parameters$type ==
      "triple") {


    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    test_name_in_column(labels, design)

    table <- design$book
    max_b <- max(table(table[, y]))

    table$part <- rep(1:max_b,
                      times = length(table[, y])/max_b)
    table[, y] <- as.numeric(table[, y]) * height
    table$part <- table$part * width

    if (reverse_y == TRUE) {
      table$part <- abs(table$part - max(table$part)) +
        min(table$part)
    }

    if (reverse_x == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }

    plt <- ggplot(table, aes_string(x = "part", y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank())+
      geom_text(aes_string(label = labels), colour = "black")

    plt

    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from an lattice design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and a type of ", design$parameters$type,
                "."))
  }

}



####### plot lattice design simple #####
#' Plot Simple Lattice Design
#'
#' Plot a design of a factorial  experiment with a lattice design from \code{agricolae} design.lattice with r=2
#' @param design outdesign from \code{agricolae} package
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' trt<-1:100
#' outdesign<-design.lattice(trt,r=2,serie=3) # simple lattice design, 10x10
#' plot_lattice_simple(outdesign,width = 2, height = 1)

plot_lattice_simple <- function(design,
                                y = "block",
                                factor_name = "trt",
                                labels = "plots",
                                width = 1,
                                height = 1,
                                space_width = 0.95,
                                space_height = 0.85,
                                reverse_y = FALSE,
                                reverse_x = FALSE) {
  if (design$parameters$design == "lattice" && design$parameters$type ==
      "simple") {


    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    test_name_in_column(labels, design)

    table <- design$book
    table[, y] <- as.numeric(table[, y])
    table$part <- rep(1:sqrt(length(unique(table[, factor_name]))),
                      times = max(table[, y]))
    table[, y] <- table[, y] * height
    table$part <- table$part * width
    if (reverse_y == TRUE) {
      table$part <- abs(table$part - max(table$part)) +
        min(table$part)
    }

    if (reverse_x == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }

    plt <- ggplot(table, aes_string(x = "part", y)) +
      geom_tile(aes_string(fill = factor_name),
          width = width * space_width, height = height *
          space_height) +
      theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = labels), colour = "black")

    plt

    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from an lattice design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}



######## latin square design ######

#' Plot Latin Square Design
#'
#' Plot a design of a factorial  experiment with a latin square design from \code{agricolae} design.lsd
#' @param design outdesign from \code{agricolae} package
#' @param x Describes the x coordinates of a experiment design
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' trt<-LETTERS[1:9]
#' outdesign<- design.lsd(trt,serie=2)
#' plot_latin_square(outdesign, reverse_y = TRUE)

plot_latin_square <- function(design,
                              x = "col",
                              y = "row",
                              factor_name = "trt",
                              labels = "plots",
                              width = 1,
                              height = 1,
                              space_width = 0.95,
                              space_height = 0.85,
                              reverse_y = FALSE,
                              reverse_x = FALSE) {
  if (design$parameters$design == "lsd") {

    test_string(x)
    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    test_name_in_column(labels, design)
    table <- as.data.frame(design$book)
    table[, x]  <- as.numeric(table[, x] ) * width
    table[, y] <- as.numeric(table[, y]) * height
    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }
    if (reverse_x == TRUE) {
      table[, x]  <- abs(table[, x]  - max(table[, x] )) +
        min(table[, x] )
    }
    plt <- ggplot(table, aes_string(x = x, y = y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = labels), colour = "black")

    plt

    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from an latin_square design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}
#### graeco latin square #######

#' Plot Graeco Latin Square Design
#'
#' Plot a design of an experiment with an Graeco - latin square design from \code{agricolae} design.graeco
#' @param design outdesign from \code{agricolae} package
#' @param x Describes the x coordinates of a experiment design
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)
#' T1<-c('a','b','c','d')
#' T2<-c('v','w','x','y','z','zz')
#' outdesign <- design.graeco(trt1=T1, trt2=T2, serie = 2,
#'  seed = 0, kinds = 'Super-Duper',randomization=TRUE)
#' plot_graeco(outdesign, factor_name = 'T2',reverse_y = TRUE)
#' plot_graeco(outdesign, factor_name = 'T2',reverse_x = TRUE)

plot_graeco <- function(design,
                        x = "col",
                        y = "row",
                        factor_name = "T1",
                        labels = "plots",
                        width = 1,
                        height = 1,
                        space_width = 0.95,
                        space_height = 0.85,
                        reverse_y = FALSE,
                        reverse_x = FALSE) {
  if (design$parameters$design == "graeco") {


    test_string(x)
    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    test_name_in_column(labels, design)

    table <- as.data.frame(design$book)
    table[, x]  <- as.numeric(table[, x] ) * width
    table[, y] <- as.numeric(table[, y]) * height


    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }
    if (reverse_x == TRUE) {
      table[, x]  <- abs(table[, x]  - max(table[, x] )) +
        min(table[, x] )
    }
    plt <- ggplot(table, aes_string(x, y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width,
                height = height *space_height) +
      theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = labels), colour = "black")


    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from an graeco design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}



#### plot strip design ####
#' Plot Strip Design
#'
#' Plot a design of an experiment with an Strip Plot design from \code{agricolae} design.strip
#' @param design outdesign from \code{agricolae} package
#' @param x Describes the x coordinates of a experiment design
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name_1 Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param factor_name_2 Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)
#' T1<-c('a','b','c','d')
#' T2<-c('v','w','x','y','z')
#' r = 3
#' outdesign <- design.strip(trt1=T1, trt2=T2, r=r,serie = 2,
#'  seed = 0, kinds = 'Super-Duper',randomization=TRUE)
#' plot_strip(outdesign,factor_name_1 = "T1",factor_name_2="T2")
#' plot_strip(outdesign,factor_name_1 = "T1",factor_name_2="T2",reverse_x = TRUE)
plot_strip <- function(design,
                       x = "col",
                       y = "row",
                       factor_name_1 = "T1",
                       factor_name_2 = "T2",
                       labels = "plots",
                       width = 1,
                       height = 1,
                       space_width = 0.95,
                       space_height = 0.85,
                       reverse_y = FALSE,
                       reverse_x = FALSE) {
  if (design$parameters$design == "strip") {


    test_string(x)
    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name_1, design)
    test_name_in_column(factor_name_2, design)
    test_name_in_column(labels, design)

    table <- as.data.frame(design$book)
     #########
    # if blocks are horizontal:
    table[, x] <- as.numeric(table[, factor_name_1]) +
      (max(as.numeric(table[, factor_name_1]))*as.numeric(table$block)-1) -
      (max(as.numeric(table[, factor_name_1])))+1

    table[, x]  <- table[, x] * width
    table[, y] <- as.numeric(table[, factor_name_2]) * height
        #########

  # if block are not horizontal
  # table[, y]  <- as.numeric(table[, factor_name_2]) +
  #    (max(as.numeric(table[, factor_name_2]))*as.numeric(table$block)-1) -
  #    (max(as.numeric(table[, factor_name_2])))+1
  # table[, y] <- table[,y] * height
  # table[, x] <- as.numeric(table[, factor_name_1]) * width




    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }
    if (reverse_x == TRUE) {
      table[, x]  <- abs(table[, x]  - max(table[, x] )) +
        min(table[, x] )
    }
    plt <- ggplot(table, aes_string(x = x, y = y)) +
      geom_tile(aes_string(fill = factor_name_1),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = labels), colour = "black")


    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from an strip design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}




#### plot bib design #######

#' Plot Randomized Balanced Incomplete Block Designs
#'
#' Plot a design of an experiment with an Randomized Balanced Incomplete Block Designs (BIB) from design.bib
#' @param design outdesign from \code{agricolae} package
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)
#' trt<-c('A','B','C','D')
#' k<-3
#' outdesign<-design.bib(trt,k,serie=2,seed =41,kinds ='Super-Duper') # seed = 41
#' plot_bib(outdesign)
#' #now let us change position of the columns
#' plot_bib(outdesign,reverse_x = TRUE)
plot_bib <- function(design,
                     y = "block",
                     factor_name = "trt",
                     labels = "plots",
                     width = 1,
                     height = 1,
                     space_width = 0.95,
                     space_height = 0.85,
                     reverse_y = FALSE,
                     reverse_x = FALSE) {
  if (design$parameters$design == "bib") {



    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    test_name_in_column(labels, design)

    table <- as.data.frame(design$book)
    table$col <- rep(1:max(table(table[, y])),
                     times = max(as.numeric(table[, y])))
    table$col <- table$col * width
    table[, y] <- as.numeric(table[, y]) * height
    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }
    if (reverse_x == TRUE) {
      table$col <- abs(table$col - max(table$col)) +
        min(table$col)
    }
    plt <- ggplot(table, aes_string(x = "col", y = y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = labels), colour = "black")


    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from an bib design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}



####### plot cyclic design #######

#' Plot Cyclic Design
#'
#' Plot a design of an experiment with an cyclic design from \code{agricolae} design.cyclic
#' @param design outdesign from \code{agricolae} package
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' k <- 2
#' r <- 6
#' trt <-c('CIP-101','CIP-201','CIP-301','CIP-401','CIP-501',LETTERS[1:2])
#' outdesign<- design.cyclic(trt,k=k, r=r, serie=3, rowcol=TRUE)
#' plot_cyclic(outdesign, factor_name = 'trt')
plot_cyclic <- function(design,
                        y = "block",
                        factor_name = "trt",
                        labels = "plots",
                        width = 1,
                        height = 1,
                        space_width = 0.95,
                        space_height = 0.85,
                        reverse_y = FALSE,
                        reverse_x = FALSE) {
  if (design$parameters$design == "cyclic") {



    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(labels, design)

    table <- design$book
    table$part <- rep(1:max(table(table[, y])),
                  times = length(table[, factor_name])/max(table(table[, y])))

    table[, y] <- as.numeric(table[, y]) * height
    table$part <- table$part * width
    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }

    if (reverse_x == TRUE) {
      table$part <- abs(table$part - max(table$part)) +
        min(table$part)
    }
    plt <- ggplot(table, aes_string(x = "part", y = y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = labels), colour = "black")


    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from an cyclic design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}




####### plot dau design #######

#' Plot Design of Augmented Blocks (dau)
#'
#' Plot a design of an experiment with an augmented block design from \code{agricolae} design.dau
#' @param design outdesign from \code{agricolae} package
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' T1<-c('A','B','C','D','E','F')
#' T2<-letters[19:26]
#' outdesign <-design.dau(T1,T2, r=5,serie=2)
#' plot_dau(outdesign)
#' plot_dau(outdesign,reverse_y = TRUE)
plot_dau <- function(design,
                     y = "block",
                     factor_name = "trt",
                     labels = "plots",
                     width = 1,
                     height = 1,
                     space_width = 0.95,
                     space_height = 0.85,
                     reverse_y = FALSE,
                     reverse_x = FALSE) {
  if (design$parameters$design == "dau") {


    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    test_name_in_column(labels, design)
    table <- design$book
    freq <- table(design$book$block)
    freq <- as.vector(freq)
    seqx <- function(x) {
      return(1:x)
    }
    col <- sapply(freq, seqx)
    table$col <- unlist(col)


    table$col <- table$col * width
    table[, y] <- as.numeric(table[, y]) * height

    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }
    if (reverse_x == TRUE) {
      table$col <- abs(table$col - max(table$col)) +
        min(table$col)
    }
    plt <- ggplot(table, aes_string(x = "col", y = y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = labels), colour = "black")


    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from an cyclic design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}




###### plot rcdb ######

#' Plot randomized complete block designs
#'
#' Plot a design of an experiment with randomized complete block design (rcbd) design from \code{agricolae} design.rcbd
#' @param design outdesign from \code{agricolae} package
#' @param y Describes the y coordinates of a experiment design
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels Describes the column from that the plots are taken to display them
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' # 5 treatments and 6 blocks
#' trt<-c('A','B','C','D','E')
#' outdesign <-design.rcbd(trt,6,serie=2,986,'Wichmann-Hill') # seed = 986
#' plot_rcdb(outdesign)
#' plot_rcdb(outdesign,reverse_y = TRUE,reverse_x = TRUE)
#'
plot_rcdb <- function(design,
                      y = "block",
                      factor_name = "trt",
                      labels = "plots",
                      width = 1,
                      height = 1,
                      space_width = 0.95,
                      space_height = 0.85,
                      reverse_y = FALSE,
                      reverse_x = FALSE) {
  if (design$parameters$design == "rcbd") {


    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    test_name_in_column(labels, design)

    table <- as.data.frame(design$book)

    table$col <- rep(1:length(unique(table[, factor_name])),
                     length(unique(table[, y])))
    table[, y] <- as.numeric(table[, y])
    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }
    if (reverse_x == TRUE) {
      table$col <- abs(table$col - max(table$col)) +
        min(table$col)
    }
    table$col <- table$col * width
    table[, y] <- as.numeric(table[, y]) * height

    plt <- ggplot(table, aes_string(x = "col", y = y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = labels), colour = "black")


    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from a Randomized Complete Block Design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}





##### plot factorial crd ########

#' Plot Factorial Complete Randomized Designs (crd)
#'
#' Plot a design of a factorial experiment with completely randomized design (crd) from design.ab
#'
#' @param design outdesign from \code{agricolae} package
#' @param ncols integer value, choose the number of columns to which the experiment should be plotted
#' @param nrows integer value, choose the number of rows to which the experiment should be plotted
#' @param y Describes the y coordinates of a experiment design, default is row
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param labels string indicates the column of which the labels should be displayed
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#' @import ggplot2
#' @import agricolae
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' trt<-c(3,2) # factorial 3x2
#' outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
#' plot_design.factorial_crd(outdesign,ncols = 8,nrows = 6)
#' plot_design.factorial_crd(outdesign,reverse_y = TRUE,ncols = 8,nrows = 6)
#' plot_design.factorial_crd(outdesign,reverse_y = TRUE,reverse_x = TRUE,ncols = 8,nrows = 6)

plot_design.factorial_crd <- function(design,
                                      ncols,
                                      nrows,
                                      y = "row",
                                      factor_name = "A",
                                      labels="plots",
                                      width = 1,
                                      height = 1,
                                      space_width = 0.95,
                                      space_height = 0.85,
                                      reverse_y = FALSE,
                                      reverse_x = FALSE) {
  if (design$parameters$design == "factorial" &&
      design$parameters$applied == "crd") {


    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    test_name_in_column(labels, design)

    plots <- as.numeric(design$book[, 1])
    if (ncols * nrows >= length(plots)) {
    nas <- rep(NaN, ncols * nrows - length(plots))
    plots <- c(plots, nas)

    mat <- matrix(plots, byrow = TRUE, ncol = ncols)
    dims <- dim(mat)
    table <- as.table(mat)
    rownames(table) <- 1:dims[1]
    colnames(table) <- 1:dims[2]
    table <- as.data.frame(table)
    colnames(table) <- c("row", "col", "plots")
    table[, y] <- as.numeric(table[, y])
    table$col <- as.numeric(table$col)

    table <- merge(table, design$book, by.x = "plots",
                   by.y = "plots")
    table$col <- table$col * width
    table[, y] <- table[, y] * height
    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }
    if (reverse_x == TRUE) {
      table$col <- abs(table$col - max(table$col)) +
        min(table$col)
    }
    plt <- ggplot(table, aes_string(x = "col", y = y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() +
      theme(line = element_blank()) +
      geom_text(aes_string(label = labels),
                colour = "black")

    return(plt)
    } else {
      stop(paste("You have in multiplication of ncols:",
                 ncols, "and nrows:", nrows, "Elements.",
                 "You need at minimum a product of both higher than",
                 length(plots)))
    }
  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from a factorial design with
         a random complete block design (rcbd) is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }
}


##### plot factorial lsd ########

#' Plot Factorial Latin Square Designs (lsd)
#'
#' Plot a design of a factorial  experiment with latin square design (lsd) design from \code{agricolae} design.ab
#'
#' @param design outdesign from \code{agricolae} package
#' @param x Describes the x coordinates of a experiment design
#' @param y Describes the y coordinates of a experiment design
#' @param labels Describes the column from that the plots are taken to display them
#' @param factor_name Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#' @import ggplot2
#' @import agricolae
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)

#' trt<-c(3,2) # factorial 3x2
#' outdesign <-design.ab(trt, r=3, serie=2,design = 'lsd')
#' plot_design.factorial_lsd(outdesign,factor_name = 'B',reverse_x = TRUE)
#'
plot_design.factorial_lsd <- function(design,
                                      x = "col",
                                      y = "row",
                                      factor_name = "A",
                                      labels = "plots",
                                      width = 1,
                                      height = 1,
                                      space_width = 0.95,
                                      space_height = 0.85,
                                      reverse_y = FALSE,
                                      reverse_x = FALSE) {
  if (design$parameters$design == "factorial" &&
      design$parameters$applied == "lsd") {
    test_string(x)
    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    test_name_in_column(labels, design)
    table <- as.data.frame(design$book)
    table[, x]  <- as.numeric(table[, x]) * width
    table[, y] <- as.numeric(table[, y]) * height
    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }
    if (reverse_x == TRUE) {
      table[, x]  <- abs(table[, x]  - max(table[, x] )) +
        min(table[, x] )
    }
    plt <- ggplot(table, aes_string(x = x,
                                                      y = y)) +
      geom_tile(aes_string(fill = factor_name),
                  width = width * space_width, height = height *
              space_height) + theme_bw() +
      theme(line = element_blank()) +
      geom_text(aes_string(label = labels),
                         colour = "black")

    plt

    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from an latin square design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}

########## plot split plot design rcbd
########## #############

#' Plot Split Plot Designs with rcbd
#'
#' Plot a design of a split plot experiment with randomized complete blocks design (rcbd) from design.split
#' @param design outdesign from \code{agricolae} package
#' @param y string defines the block
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#' @param factor_name_1 string Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param factor_name_2 string Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels string Describes the column from that the plots are taken to display them
#' @param subplots should the plot function return the subplots (default) or main plots?
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#' @import ggplot2
#' @import agricolae
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)
#' T1<-c('a','b','c','d','e')
#' T2<-c('v','w','x','y','z','zz')
#' r = 3
#' outdesign2 <- design.split(trt1=T1, trt2=T2, r=r,serie = 2,
#'  seed = 0, kinds = 'Super-Duper',randomization=TRUE,
#'  first=TRUE,design = 'rcbd')
#' plot_split_rcbd(outdesign2,width = 1,height = 1)
#' plot_split_rcbd(outdesign2,width = 1,height = 1,reverse_y = TRUE)
#' plot_split_rcbd(outdesign2,width = 1,height = 1,reverse_x = TRUE,reverse_y = TRUE)

plot_split_rcbd <- function(design,
                            y = "block",
                            factor_name_1 = "T1",
                            factor_name_2 = "T2",
                            subplots=TRUE,
                            labels = "plots",
                            width = 1,
                            height = 1,
                            space_width = 0.95,
                            space_height = 0.85,
                            reverse_y = FALSE,
                            reverse_x = FALSE) {
  if (design$parameters$design == "split" &&
      design$parameters$applied == "rcbd") {

    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name_1, design)
    test_name_in_column(factor_name_2, design)

    test_name_in_column(labels, design)

    table <- design$book

    table$row <- rep(rep(1:length(unique(table[, factor_name_1])),
                         each=length(unique(table[, factor_name_2]))),
                     times=max(as.numeric(table[, y])))
    table$row <- table$row * width

    table$sequence <- rep(1:(length(unique(table[, factor_name_1])) *
                               length(unique(table[, factor_name_2]))),
                          times = max(as.numeric(table[, y])))

    table$sequence <- table$sequence * width
    table[, y] <- as.numeric(table[, y]) * height

    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }

    if (reverse_x == TRUE) {

      table$row <- abs(table$row - max(table$row)) +
        min(table$row)

      table$sequence <- abs(table$sequence - max(table$sequence)) +
        min(table$sequence)
    }


    if(subplots == TRUE){

      divider <- length(unique(table[, factor_name_1]))
      table$sequence <- table$sequence/divider

      plt2 <- ggplot(table, aes_string("sequence", y)) +
        geom_tile(aes_string(fill = factor_name_2),
                  width = width/divider * space_width,
                  height = height * space_height) + theme_bw() +
        theme(line = element_blank()) + geom_text(aes_string(label = labels),
                                                  colour = "black")


      return(plt2)

    } else{

      plt <- ggplot(table, aes_string("row", y)) +
        geom_tile(aes_string(fill = factor_name_1),
        width = width * space_width, height = height * space_height) +
        theme_bw() + theme(line = element_blank()) +
        geom_text(aes_string(label = labels), colour = "black")
      return(plt)
    }

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from a split plot design with a
                random complete block design (rcbd) is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }
}






########## plot split plot design lsd
########## #############

#' Plot Split Plot Design lsd
#'
#' Plot a design of a split plot experiment with latin squared design (lsd) from design.split
#' @param design outdesign from \code{agricolae} package
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#' @param factor_name_1 string Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param factor_name_2 string Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels string Describes the column from that the plots are taken to display them
#' @param subplots should the plot function return the subplots (default) or main plots?
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#' @import ggplot2
#' @import agricolae
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)
#' T1<-c('a','b','c','d','e')
#' T2<-c('v','w','x','y')
#' outdesign2 <- design.split(trt1=T1, trt2=T2, r=r,serie = 2,
#'                            seed = 0, kinds = 'Super-Duper',
#'                            randomization=TRUE,first=TRUE,design = 'lsd')
#' plot_split_lsd(outdesign2,width = 4,height = 4)

plot_split_lsd <- function(design,
                           factor_name_1 = "T1",
                           factor_name_2 = "T2",
                           labels = "plots",
                           subplots=TRUE,
                           width = 1,
                           height = 1,
                           space_width = 0.95,
                           space_height = 0.85,
                           reverse_y = FALSE,
                           reverse_x = FALSE) {
  if (design$parameters$design == "split" && design$parameters$applied ==
      "lsd") {

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name_1, design)
    test_name_in_column(factor_name_2, design)
    test_name_in_column(labels, design)

    table <- design$book

    table$sequence <- rep(1:(length(unique(table[, factor_name_1])) *
                             length(unique(table[, factor_name_2]))),
                        times = max(as.numeric(table$row)))

    table$sequence <- table$sequence * width

    table$col <- as.numeric(table$col) * width
    table$row <- as.numeric(table$row) * height

    # plot subplots

    if (reverse_y == TRUE) {
      table$row <- abs(table$row - max(table$row)) +
        min(table$row)
    }

    if (reverse_x == TRUE) {
      table$col <- abs(table$col - max(table$col)) +
        min(table$col)

      table$sequence <- abs(table$sequence -
                              max(table$sequence)) + min(table$sequence)
    }

    if(subplots == TRUE){

    divider <- length(unique(table[, factor_name_1]))
    table$sequence <- table$sequence/divider

    plt2 <- ggplot(table, aes_string("sequence", "row")) +
      geom_tile(aes_string(fill = factor_name_2),
                width = width/divider * space_width,
                height = height * space_height) + theme_bw() +
      theme(line = element_blank()) +
      geom_text(aes_string(label = labels),colour = "black")


    return(plt2)
    } else {
      plt <- ggplot(table, aes_string("col", "row")) +
        geom_tile(aes_string(fill = factor_name_1),
                  width = width * space_width, height = height *
                    space_height) + theme_bw() +
        theme(line = element_blank()) +
        geom_text(aes_string(label = labels),
                  colour = "black")

      return(plt)

    }

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from a split plot design with a
                random complete block design (lsd) is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }
}

########## plot split plot design crd
########## #############

#' Plot Split Plot Designs (crd)
#'
#' Plot a design of a split plot experiment with a complete randomized design (crd) from design.split
#'
#' @param design outdesign from \code{agricolae} package
#' @param ncols Number of columns for the design
#' @param nrows Number of rows for the design
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#' @param factor_name_1 string Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param factor_name_2 string Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels string Describes the column from that the plots are taken to display them
#' @param subplots should the plot function return the subplots (default) or main plots?
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#' @import ggplot2
#' @import agricolae
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)
#' T1<-c('a','b','c','d','e','f','g')
#' T2<-c('v','w','x','y','zzz')
#' r <- 4
#' outdesign2 <- design.split(trt1=T1, trt2=T2, r=r,
#' serie = 2, seed = 0, kinds = 'Super-Duper',
#' randomization=TRUE,first=TRUE,design = 'crd')
#' plot_split_crd(outdesign2,ncols = 6,nrows=5)
#'
#' outdesign2 <- design.split(trt1=T1, trt2=T2, r=r,
#' serie = 2, seed = 0, kinds = 'Super-Duper',
#' randomization=FALSE,first=TRUE,design = 'crd')
#' plot_split_crd(outdesign2,ncols = 6,nrows=5)

plot_split_crd <- function(design, nrows, ncols,
                           factor_name_1 = "T1",
                           factor_name_2 = "T2",
                           labels = "plots",
                           subplots = TRUE,
                           width = 1,
                           height = 1,
                           space_width = 0.95,
                           space_height = 0.85,
                           reverse_y = FALSE,
                           reverse_x = FALSE) {

  if (design$parameters$design == "split" && design$parameters$applied ==
      "crd") {
    column <- NULL
    test_input_ncols(ncols)
    test_input_nrows(nrows)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)
    test_input_height(height)
    test_input_width(width)
    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name_1, design)
    test_name_in_column(factor_name_2, design)
    test_name_in_column(labels, design)

    plots <- as.numeric(unique(design$book[, 1]))
    if (ncols * nrows >= length(plots)) {
      nas <- rep(NaN, (ncols * nrows) - length(plots))
      plots <- c(plots, nas)

      mat <- matrix(plots, byrow = TRUE, ncol = ncols)
      dims <- dim(mat)
      table <- as.table(mat)
      rownames(table) <- 1:dims[1]
      colnames(table) <- 1:dims[2]
      table <- as.data.frame(table)
      colnames(table) <- c("row", "col", "plots")
      table$row <- as.numeric(table$row)
      table$col <- as.numeric(table$col)

      table <- merge(table, design$book, by.x = "plots",
                     by.y = "plots")
      table$plots <- as.factor(table$plots)


      table$col <- table$col * width
      table$row <- table$row * height

      table <- table[with(table, order(plots,
                                       splots)), ]

      freq <- table(table$row)
      freq <- as.vector(freq)
      seqx <- function(x) {
        return(1:x)
      }
      sequence_numbers <- sapply(freq, seqx)

      table$sequence <- unlist(sequence_numbers)

      table$sequence <- table$sequence * width





      if (reverse_y == TRUE) {
        table$row <- abs(table$row - max(table$row)) +
          min(table$row)
      }

      if (reverse_x == TRUE) {
        table$col <- abs(table$col -
                              max(table$col)) + min(table$col)
        table$sequence <- abs(table$sequence -
                                max(table$sequence)) + min(table$sequence)
      }



      if(subplots == TRUE){

      divider <- length(unique(table[, factor_name_1]))
      table$sequence <- table$sequence/divider

      plt2 <- ggplot(table, aes_string("sequence", "row")) +
        geom_tile(aes_string(fill = factor_name_2),
                  width = width * space_width/divider,
                  height = height * space_height) +
        theme_bw() + theme(line = element_blank()) +
        geom_text(aes_string(label = labels),
                  colour = "black")

      return(plt2)
      } else {
        plt <- ggplot(table, aes_string("col", "row")) +
          geom_tile(aes_string(fill = factor_name_1),
                    width = width * space_width, height = height *
                      space_height) + theme_bw() +
          theme(line = element_blank()) +
          geom_text(aes_string(label = labels),
                    colour = "black")

        return(plt)

      }

    } else {
      stop(paste("You have in multiplication of ncols:",
                 ncols, "and nrows:", nrows, "Elements.",
                 "You need at minimum a product of both higher than",
                 length(plots)))
    }
  } else {
    stop(paste0("This is not the correct function for your experiment design.,
          A design from a split plot design with a
                random complete block design (crd) is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }
}


#' ggplot2 theme for outdoor presentation
#'
#' This theme is designed to increase font size to ensure readability on outdoor used devices
#' @return ggplot2 theme
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)
#' T1<-c('a','b','c','d','e','f','g')
#' T2<-c('v','w','x','y','z')
#' r <- 4
#' outdesign2 <- design.split(trt1=T1, trt2=T2, r=r,
#' serie = 2, seed = 0, kinds = 'Super-Duper',
#' randomization=FALSE,first=TRUE,design = 'crd')
#' plot_split_crd(outdesign2,ncols = 6,nrows=5)+
#' theme_pres()
theme_pres <- function() {
  theme(text = element_text(size = 16, colour = "black"),
        axis.text = element_text(size = 18, colour = "black"),
        axis.title = element_text(size = 18, colour = "black"),
        axis.line = element_line(colour = "black",
                                 size = 1, linetype = "solid"),
        axis.ticks = element_line(colour = "black")) +
    theme(plot.background = element_rect(fill = "white",
                                         color = NA),
          panel.background = element_rect(fill = "white",color = NA))
}


#' ggplot2 theme for poster presentation
#'
#' This theme is designed to increase font size to ensure readability on poster presentations
#' @return ggplot2 theme
#' @export
#'
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)
#' T1<-c('a','b','c','d','e','f','g')
#' T2<-c('v','w','x','y','z')
#' r <- 4
#' outdesign2 <- design.split(trt1=T1, trt2=T2, r=r,
#' serie = 2, seed = 0, kinds = 'Super-Duper',
#' randomization=FALSE,first=TRUE,design = 'crd')
#' plot_split_crd(outdesign2,ncols = 6,nrows=5)+
#' theme_poster()
theme_poster <- function() {
  theme(text = element_text(size = 24, colour = "black"),
        axis.text = element_text(size = 28, colour = "black"),
        axis.title = element_text(size = 28, colour = "black"),
        axis.line = element_line(colour = "black",
                                 size = 1, linetype = "solid"),
        axis.ticks = element_line(colour = "black")) +
    theme(plot.background = element_rect(fill = "white",
                                         color = NA),
          panel.background = element_rect(fill = "white", color = NA))
}


#' Plot Youden Design
#'
#' Plot a Youden experiment design from \code{agricolae} design.youden
#'
#' @param design outdesign from \code{agricolae} package
#' @param x Describes the x coordinates of a experiment design
#' @param y Describes the y coordinates of a experiment design
#' @param width numeric value, describes the width of a plot in an experiment
#' @param height numeric value, describes the height of a plot in an experiment
#' @param space_width numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of width
#' @param space_height numeric value, describes the share of the space of the plots. 0=only space, 1=no space between plots in term of height
#' @param reverse_y boolean, should the plots of the experiment be changed in reverse order in Row direction? use reverse_y=TRUE to have same sketch as in agricolae. default:reverse_y=FALSE
#' @param reverse_x boolean, should the plots of the experiment be changed in reverse order in column direction? default:reverse_x=FALSE
#' @param factor_name string Which factor should be used for plotting, needs to be a column in outdesign$book
#' @param labels string Describes the column from that the plots are taken to display them
#'
#' @return \code{ggplot} graphic that can be modified, if wished
#' @export
#' @import ggplot2
#' @import agricolae
#' @examples
#' library(agricolaeplotr)
#' library(agricolae)
#' varieties<-c('perricholi','yungay','maria bonita','tomasa')
#' outdesign <-design.youden(varieties,r=2,serie=2,seed=23)
#' plot_youden(outdesign, labels = 'varieties')
plot_youden <- function(design, x = "col", y = "row",
                        factor_name = "varieties", labels = "plots", width = 1,
                        height = 1, space_width = 0.95, space_height = 0.85,
                        reverse_y = FALSE, reverse_x = FALSE) {
  if (design$parameters$design == "youden") {

    test_string(x)
    test_string(y)

    test_input_reverse_x(reverse_x)
    test_input_reverse_y(reverse_y)

    test_input_height(height)
    test_input_width(width)

    test_input_height(space_height)
    test_input_width(space_width)

    test_name_in_column(factor_name, design)
    test_name_in_column(labels, design)

    table <- as.data.frame(design$book)

    table[, x]  <- as.numeric(table[, x] ) * width
    table[, y] <- as.numeric(table[, y]) * height

    if (reverse_y == TRUE) {
      table[, y] <- abs(table[, y] - max(table[, y])) +
        min(table[, y])
    }
    if (reverse_x == TRUE) {
      table[, x]  <- abs(table[, x]  - max(table[, x] )) +
        min(table[, x] )
    }


    plt <- ggplot(table, aes_string(x = x, y = y)) +
      geom_tile(aes_string(fill = factor_name),
                width = width * space_width, height = height *
                  space_height) + theme_bw() + theme(line = element_blank()) +
      geom_text(aes_string(label = labels), colour = "black")


    return(plt)

  } else {
    stop(paste0("This is not the correct function for your experiment design.
          A design from a Youden Design is needed here.",
                "you have a design of type ", design$parameters$design,
                " and an applied type of ", design$parameters$applied,
                "."))
  }

}

# example("plot_split_lsd")
# table$t1 und table$t2 mit  factor_name_1 und factor_name_2 austauschen
# table$trt durch factor_name
# table$TRT
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