#############################
# Barplots: ggplot
# stats +/-
# violin +/-
# barplot +/
# beeswarm
#############################

lf_bp <- function(lf_df = lf_duet
                  , p_title = "DUET-DDG"
                  , colour_categ = "outcome"
                  , x_grp = "mutation_info_labels"
                  , y_var = "param_value"
                  , facet_var = "param_type"
                  , n_facet_row = 1
                  , y_scales = "free_y"
                  , colour_bp_strip = "khaki2"
                  , dot_size = 3
                  , dot_transparency = 0.3
                  , violin_quantiles = c(0.25, 0.5, 0.75) # can be NULL
                  , my_ats = 11 # axis text size
                  , my_als = 10 # axis label size
                  , my_fls = 10 # facet label size
                  , my_pts = 11 # plot title size)
                  , make_boxplot = FALSE
                  , bp_width = c("auto", 0.5)
                  , add_stats = TRUE
                  , stat_grp_comp = c("R", "S")
                  , stat_method = "wilcox.test"
                  , my_paired = FALSE
                  , stat_label = c("p.format", "p.signif")
                  ) {
  
  fwv = as.formula(paste0("~", facet_var))
  #fwv = reformulate(facet_var)
  
  p1 <- ggplot(lf_df, aes_string(x = x_grp, y = y_var))  + 
    
    facet_wrap( fwv
               , nrow = n_facet_row
               , scales = y_scales) +
    
    geom_violin(trim = T
                , scale = "width"
                #, position = position_dodge(width = 0.9)
                , draw_quantiles = violin_quantiles)
    
    if (make_boxplot){
      
      if (bp_width == "auto"){
        bp_width = 0.5/length(unique(lf_df[[x_grp]]))
        cat("\nAutomatically calculated boxplot width, using bp_width:\n", bp_width, "\n")
      }else{
        cat("\nBoxplot width value provided, using:",  bp_width, "\n")
        bp_width = bp_width} 
    
    p2 = p1 + geom_boxplot(fill = "white"
                  , outlier.colour = NA
                  #, position = position_dodge(width = 0.9)
                  , width = bp_width) + 
      geom_quasirandom(#priority = "density"
                    #, shape = 21
                    size = dot_size
                    , alpha = dot_transparency
                    , show.legend = FALSE
                    , cex = 0.8
                    , aes(
                      colour = factor(
                        eval(
                          parse(
                            text = colour_categ
                            )
                          )
                        )
                      )
                    ) + ggplot2::scale_color_manual(values = consurf_colours)  
      
    } else {
    #Legend=factor(eval(parse(text = colour_categ)))
    # ggbeeswarm (better than geom_point)
    p2 = p1 +
      #theme(legend.title=element_text('XXX')) + # Legend doesn't need a title)
      
      geom_quasirandom(#priority = "density"
                    #, shape = 21
                    size = dot_size
                    , alpha = dot_transparency
                    , show.legend = FALSE
                    # , fast = FALSE
                    , cex = 0.8
                    , aes(
                      colour = factor(
                        eval(
                          parse(
                            text = colour_categ
                            )
                          )
                        )
                      )
                    #, aes(colour = Legend)
                    ) +
      ggplot2::scale_color_manual(values = consurf_colours)


    }

   # Add foramtting to graph
   OutPlot = p2 + theme(axis.text.x = element_text(size = my_ats)
                   , axis.text.y = element_text(size = my_ats
                                       , angle = 0
                                       , hjust = 1
                                       , vjust = 0)
                   , axis.title.x = element_text(size = my_ats)
                   , axis.title.y = element_text(size = my_ats)
                   , plot.title = element_text(size = my_pts
                                      , hjust = 0.5
                                      , colour = "black"
                                      , face = "bold")
                   , strip.background = element_rect(fill = colour_bp_strip)
                   , strip.text.x = element_text(size = my_fls
                                                  , colour = "black")
                   , legend.title = element_text(color = "black"
                                                  , size = my_als)
                   , legend.text = element_text(size = my_ats)
                   , legend.direction = "vertical") +
    
    labs(title = p_title
         , x = ""
         , y = "") 
   
    if (add_stats){
      my_comparisonsL <- list( stat_grp_comp )
      
    OutPlot = OutPlot + stat_compare_means(comparisons = my_comparisonsL
                       , method = stat_method
                       , paired = my_paired
                       , label = stat_label[2])
      
    return(OutPlot)
    }
   
   return(OutPlot)
}