#!/usr/bin/Rscript   
getwd()
setwd("~/git/mosaic_2020/")
getwd()
############################################################
# TASK: Boxplots with stats 
# for each mediator, at each timepoint by group

# Handles some error: i.e will continue plotting even if there
# is stats error. However, needs fixing see below point 1):

# FIXME: 
# 1) For a given mediator, if there is error for ANY timepoint
# stats will not be added for the entire plot!

# 2) make the function more generic to take the following inputs
# df, column, group
# this way you can directly pass the log_calculated value column

# To be handled in 
# next iteration!
############################################################

is.error <- function(x) inherits(x, "try-error")

doMyPlotsStats <- function(df, custom_order=NULL) {
  if(!is.null(custom_order)){
    mediators = custom_order
  } else{
    mediators = levels(as.factor(df$mediator))
  }
  
  plots <- list()
  
  for (i in mediators) {
    cat("Creating plot for:", i, "\n")
    single=df[df$mediator==i,]
    
    max_y = max(single$value, na.rm = T)
    #cat("Plotting:", i, "max_y:", max_y, "\n")
    
    #----------
    # boxplot
    #----------
    p = ggplot(single)+ geom_boxplot(aes(x = timepoint
                                         , y = value
                                         , color = obesity
                                         #, palette = c("#00BFC4", "#F8766D")
    ))+
      scale_colour_manual(values=c("#00BFC4", "#F8766D")) + 
      theme(axis.text.x = element_text(size = 10)
            , axis.text.y = element_text(size = 15
                                         , angle = 0
                                         , hjust = 1
                                         , vjust = 0)
            , axis.title.x = element_blank()
            , axis.title.y = element_blank()
            , legend.position = "none"
            , plot.subtitle = element_text(size = 14, hjust = 0.5)
            , plot.title = element_text(size = 14, hjust = 0.5)
            #, panel.grid.major = element_blank()
            , panel.grid.minor = element_blank()
            ) +

      labs(title = i)
    
    #--------
    # stats
    #---------
    stats_state <- try({
      cat('Calculating stats for:', i, "\n")
      
      stat_df <- single %>%
        group_by(timepoint, mediator) %>%
        wilcox_test(value ~ obesity, paired = F) %>%
        add_significance("p")
      stat_df$p_format = round(stat_df$p, digits = 2)
      
      stat_df <- stat_df %>%
        add_xy_position(x = "timepoint", dodge = 0.8)
    }, silent=TRUE)
    #print(stats_state)
    if ( is.error(stats_state)) {cat("⚠️ Stats ERROR:", i, "\n")}
    if ( ! is.error(stats_state)) {
      cat('Adding stats to plot for:', i, "\n")
      
      p = p + stat_pvalue_manual(stat_df
                                 #, y.position = max_y
                                 , label = "{p_format} {p.signif}"
                                 , hide.ns = T
                                 , tip.length = 0)+
        scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
    }
    plots[[i]] <- p
    
  }
  return(plots)
}

###############################################################