library(ggpubr)
###################################################################

####################################
lf_bp_with_stats <- function(lf_df
                        , x_grp = "mutation_info"
                        , y_var = "param_value"
                        , facet_var = "param_type"
                        , n_facet_row = 1
                        , y_scales = "free_y"
                        , p_title = ""
                        , colour_categ = ""
                        , colour_bp_strip = "khaki2"
                        , stat_grp_comp = c("DM", "OM")
                        , stat_method = "wilcox.test"
                        , my_paired = FALSE
                        , bp_width = c("auto", 0.5)
                        , dot_size = 3
                        , dot_transparency = 0.3
                        , stat_label = c("p.format", "p.signif")
                        , my_ats = 22 # axis text size
                        , my_als = 20 # axis label size
                        , my_fls = 20 # facet label size
                        , my_pts = 22 # plot title size
) {
  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
  }
  
  my_comparisonsL <- list( stat_grp_comp )

  bp_statP <- ggplot(lf_df, aes(x = eval(parse(text = x_grp))
                    , y = eval(parse(text = y_var)) ))  + 
    
    facet_wrap(~ eval(parse(text = facet_var))
               , nrow = n_facet_row
               , scales = y_scales) +
    
    geom_violin(trim = T
                , scale = "width"
                #, position = position_dodge(width = 0.9)
                , draw_quantiles = c(0.25, 0.5, 0.75)) + 
    
    # geom_boxplot(fill = "white"
    #              , outlier.colour = NA
    #              #, position = position_dodge(width = 0.9)
    #              , width = bp_width) +

    # geom_point(position = position_jitterdodge(dodge.width = 0.5)
    #            , alpha = 0.5
    #            , show.legend = FALSE
    #            , aes(colour = factor(eval(parse(text = colour_categ))) )) +

    # ggbeeswarm (better than geom_point)
      geom_beeswarm(priority = "density"
                    #, shape = 21
                    , size = dot_size
                    , alpha = dot_transparency
                    , show.legend = FALSE
                    , cex = 0.8
                    , aes(colour = factor(eval(parse(text = colour_categ))) )) +

    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 = "")+ 
  
    stat_compare_means(comparisons = my_comparisonsL
                       , method = stat_method
                       , paired = my_paired
                       , label = stat_label[1])
  
  return(bp_statP)

}