R/ggprisma.R

In awconway/ggprisma: What the Package Does (One Line, Title Case)

#' Returns ggplot prisma diagram agreement
#' 
#'  @name ggprisma
#'  
#' @param retrieved number of search results from databases
#' @param duplicates number of duplicates removed
#' @param full_text number of full text articles screened
#' @param included number of articles included
#' @param wrong_intervention number of articles excluded due to intervention
#' @param wrong_design number of articles excluded due to researcg design
#' @param wrong_comparator number of articles excluded due to comparator
#' @param awaiting_classification number of citations awaiting classification

#' @rdname ggprisma

#' @export


ggprisma <- function(retrieved, duplicates, included, full_text,
                     wrong_intervention, wrong_comparator, wrong_design, 
                     awaiting_classification,
         line_size = 0.50, box_type = "round", box_lines = 0.5, 
         box_colour = "#ff4f14", box_fill = "white", text_colour = "#ff4f14",
         arrow_colour = "#ff4f14"){

# Based on user input
  screened = {{ retrieved }}-{{ duplicates }} 
  screen_excluded = screened-{{ full_text }} - {{ awaiting_classification }}
  full_text_excluded = {{ full_text }} -{{ included }} 
  

# Main flow y coordinates  
import_y_max <- 100
import_y_min <- 90
screen_y_max <- 80
screen_y_min <- 70
full_y_max <- 60
full_y_min <- 50
included_y_max <- 40
included_y_min <- 30

# Scondary flow y coordinates  
duplicates_y_max <- 90
duplicates_y_min <- 80

full_excluded_y_min <- 25
full_excluded_y_max <- 45

screen_excluded_y_min <- 65
screen_excluded_y_max <- 75

awaiting_classification_y_min <- 50
awaiting_classification_y_max <- 60

# x coordinates  
main_x_min <- 20
main_x_max <- 70

second_x_min <- 75
second_x_max <- 95

arrow_x <- 45

###Plot space set-up####
ggplot2::ggplot(data=NULL, ggplot2::aes()) +

  ########## Main box flow ###########

# import box

ggplot2::annotation_custom(grob = grid::roundrectGrob(gp = grid::gpar(col = box_colour, fill = box_fill)),
                  xmin = main_x_min, xmax=main_x_max, ymin=import_y_min, ymax=import_y_max)+
  ggfittext::geom_fit_text(ggplot2::aes(xmin = main_x_min, xmax=main_x_max, ymin=import_y_min, ymax=100),
                label= glue::glue({{ retrieved }} , ' references identified'), 
                reflow = TRUE, colour = text_colour, data = data.frame()) +
  
  # screen box
  ggplot2::annotation_custom(grob = grid::roundrectGrob(gp = 
                                                 grid::gpar(col = box_colour, fill = box_fill)),
                    xmin = main_x_min, xmax=main_x_max, ymin=screen_y_min, 
                    ymax=screen_y_max) +
  ggfittext::geom_fit_text(ggplot2::aes(xmin = main_x_min, xmax=main_x_max, ymin=screen_y_min, ymax=screen_y_max),
                label= glue::glue(screened, ' titles and abstracts screened'), 
                reflow = TRUE, colour = text_colour, data = data.frame()) +
  
  # full text box
  ggplot2::annotation_custom(grob = grid::roundrectGrob(gp = 
                                                 grid::gpar(col = box_colour, fill = box_fill)),
                    xmin = main_x_min, xmax=main_x_max, ymin=full_y_min, ymax=full_y_max) +
  ggfittext::geom_fit_text(ggplot2::aes( xmin = main_x_min, xmax=main_x_max, ymin=full_y_min, ymax=full_y_max),
                 label= glue::glue({{ full_text }} , ' full-text articles assessed'), 
                 reflow = TRUE, colour = text_colour, data = data.frame()) +
  
  # included box 
  ggplot2::annotation_custom(grob = grid::roundrectGrob(gp = 
                                                 grid::gpar(col = box_colour, fill = box_fill)),
                    xmin = main_x_min, xmax=main_x_max, 
                    ymin=included_y_min, ymax=included_y_max) +
  ggfittext::geom_fit_text(ggplot2::aes(xmin = main_x_min, xmax=main_x_max, 
                ymin=included_y_min, ymax=included_y_max),
                label= glue::glue({{ included }} , ' studies included'), 
                reflow = TRUE, colour = text_colour, data = data.frame()) +
  
  ######### Secondary flow boxes ############


ggplot2::annotation_custom(grob = grid::roundrectGrob(gp = 
                                               grid::gpar(col = box_colour, fill = box_fill)),
                  xmin = second_x_min, xmax=second_x_max, 
                  ymin=duplicates_y_min, ymax=duplicates_y_max) +
  ggfittext::geom_fit_text(ggplot2::aes(xmin = second_x_min, xmax=second_x_max, 
                ymin=duplicates_y_min, ymax=duplicates_y_max),
                label= glue::glue({{ duplicates }} , ' duplicates removed'),
                reflow = TRUE, colour = text_colour, data = data.frame()) +
  
  
  # excluded box 
  ggplot2::annotation_custom(grob = 
                      grid::roundrectGrob(gp = 
                                            grid::gpar(col = box_colour, fill = box_fill)),
                    xmin = second_x_min, xmax=second_x_max, 
                    ymin=screen_excluded_y_min, ymax=screen_excluded_y_max) +
  ggfittext::geom_fit_text(ggplot2::aes(xmin = second_x_min, xmax=second_x_max, 
                ymin=screen_excluded_y_min, ymax=screen_excluded_y_max),
                label= glue::glue(screen_excluded, ' studies excluded'),
                reflow = TRUE, colour = text_colour, data = data.frame()) +
  
  # awaiting classifications box 
  ggplot2::annotation_custom(grob = 
                      grid::roundrectGrob(gp = 
                                            grid::gpar(col = box_colour, fill = box_fill)),
                    xmin = second_x_min, xmax=second_x_max, 
                    ymin=awaiting_classification_y_min, ymax=awaiting_classification_y_max) +
  ggfittext::geom_fit_text(ggplot2::aes(xmin = second_x_min, xmax=second_x_max, 
                ymin=awaiting_classification_y_min, ymax=awaiting_classification_y_max),
                label= glue::glue({{ awaiting_classification}} , ' studies awaiting classification'),
                reflow = TRUE, colour = text_colour, data = data.frame()) +
  
  # full text excluded box 
  ggplot2::annotation_custom(grob = 
                      grid::roundrectGrob(gp = 
                                            grid::gpar(col = box_colour, fill = box_fill)),
                    xmin = second_x_min, xmax=second_x_max, 
                    ymin=full_excluded_y_min, ymax=full_excluded_y_max) +
  ggfittext::geom_fit_text(ggplot2::aes(xmin = second_x_min, xmax=second_x_max,
                ymin=full_excluded_y_max-7, ymax=full_excluded_y_max),
                label= glue::glue(full_text_excluded, ' studies excluded'),
                reflow = TRUE, colour = text_colour, data = data.frame()) +
  ggfittext::geom_fit_text(ggplot2::aes(xmin = second_x_min, xmax=second_x_max,
                ymin=full_excluded_y_max-17, ymax=full_excluded_y_max-7),
                label= glue::glue({{ wrong_intervention }} , ' wrong intervention','\n',
                                  {{ wrong_comparator }} , ' wrong comparator','\n',
                                  {{ wrong_design }} , ' wrong design'),
                colour = text_colour, data = data.frame()) +
  
  
  ####### Main flow arrows#######

# Import - screen
ggplot2::geom_segment(ggplot2::aes(
  x=arrow_x, xend = arrow_x, y = import_y_min, yend = screen_y_max+0.25), 
  size = line_size,  colour = arrow_colour,
  arrow = ggplot2::arrow(length = ggplot2::unit(2, "mm"), type= "closed")) +
  
  # Screen - full text
  ggplot2::geom_segment(ggplot2::aes(
    x=arrow_x, xend=arrow_x, y=screen_y_min, yend=full_y_max+0.25), 
    size = line_size,  colour = arrow_colour,
    arrow = ggplot2::arrow(length = ggplot2::unit(2, "mm"), type= "closed")) +
  
  # Full text - included
  
  ggplot2::geom_segment(ggplot2::aes(
    x=arrow_x, xend=arrow_x, y=full_y_min, yend=included_y_max+0.25), 
    size = line_size,  colour = arrow_colour,
    arrow = ggplot2::arrow(length = ggplot2::unit(2, "mm"), type= "closed")) +
  
  ####Secondary flow arrows########    

# Import - duplicates  

ggplot2::geom_curve(ggplot2::aes(
  x = arrow_x, xend = second_x_min, 
  y = duplicates_y_max,  yend = duplicates_y_max-5), linetype = "dashed",
  curvature = 0.1, colour = arrow_colour) +
  
  # Screen - excluded  
  
  ggplot2::geom_curve(ggplot2::aes(
    x = arrow_x, xend = second_x_min, 
    y = screen_y_min,  yend = screen_excluded_y_max-5), linetype = "dashed",
    curvature = 0.1, colour = arrow_colour) +
  
  # Screen - awaiting  
  
  ggplot2::geom_curve(ggplot2::aes(
    x = arrow_x, xend = second_x_min, 
    y = screen_y_min,  yend = awaiting_classification_y_max-4), linetype = "dashed",
    curvature = -0.15, colour = arrow_colour) +
  
  # Full text - excluded  
  
  ggplot2::geom_curve(ggplot2::aes(
    x = arrow_x, xend = second_x_min, 
    y = full_y_min, yend = full_excluded_y_max-8), linetype = "dashed",
    curvature = -0.15, colour = arrow_colour) +
  
  ggplot2::theme_void()

}