# position_annotation takes a Data Frame (df) and returns a ggplot object.
# 
# This plots position tiles for the (up to) three ligands as well as drug
position_annotation=function(plot_df,
                             bg="transparent",
                             aa_pos_drug=1:100,
                             active_aa_pos=1:100,
                             aa_pos_lig1=1:100,
                             aa_pos_lig2=1:100,
                             aa_pos_lig3=1:100
)
{
  x_ats = 12 
  x_tangle = 90 
  x_tts = 20 
  y_tts = 23
  xtt_col    = "black"
  ytt_col    = "black"
  leg_dir = "horizontal" 
  leg_ts = 15 
  leg_tts = 16
  leg_pos = "none" 
  
  # plot_df=plot_df[order(plot_df$ligand_distance),]
  # 
  # plot_df$position = factor(plot_df$position)
  #plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
  # plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
  #                         "brown", "transparent")
  plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
                          "transparent", "transparent")
  
  plot_df$bg_all = plot_df$col_aa
  plot_df$bg_all = ifelse(plot_df[["position"]]%in%aa_pos_drug,
                          "green", plot_df$bg_all)
  
  plot_df$col_bg1 = plot_df$bg_all
  plot_df$col_bg1 = ifelse(plot_df[["position"]]%in%aa_pos_lig1,
                           "slategrey", plot_df$col_bg1)
  
  plot_df$col_bg2 = plot_df$col_bg1
  plot_df$col_bg2 = ifelse(plot_df[["position"]]%in%aa_pos_lig2,
                           "navyblue", plot_df$col_bg2)
  
  
  plot_df$col_bg3 = plot_df$col_bg2
  plot_df$col_bg3 =  ifelse(plot_df[["position"]]%in%aa_pos_lig3
                            , "purple", plot_df$col_bg3)
  
  plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
  
  cowplot::plot_grid(
    ggplot(plot_df, 
           aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
           )
    ) +
      geom_tile(aes(y=0), 
                fill=plot_df$ligD_colours) +
      #scale_x_discrete("Position", labels=factor(plot_df$position)) +
      #theme_nothing() +
      theme(plot.background = element_rect(fill = "transparent", colour=NA),
            plot.margin = margin(t=0,b=0),
            axis.ticks.x = element_blank(),
            axis.ticks.y = element_blank(),
            axis.text.y = element_blank(),
            panel.grid = element_blank(),
            panel.background = element_rect(fill = "transparent", colour=NA),
      ) +
      labs(x = NULL, y = NULL), #end of distance-heat-bar
    #NULL,
    ggplot(plot_df, 
           aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
               #reorder(ligand_distance)
           )
    ) +
      # geom_tile(aes(y = 0, fill = col_aa, colour = col_aa)
      # ) +
      geom_tile(aes(y = 1, fill = bg_all, colour = bg_all)
      ) +
      geom_tile(aes(y = 2, fill = col_bg1, colour = col_bg1)
      ) +
      geom_tile(aes(y = 3, fill = col_bg2, colour = col_bg2)
      ) +
      geom_tile(aes(y = 4, fill = col_bg3, colour = col_bg3)
      ) +
      
      #scale_x_discrete("Position", labels=factor(plot_df$position)) +
      scale_color_manual(values = c(
        "brown"="brown",
        "green"="#00ff00",
        "transparent"="transparent",
        "slategrey"="#2f4f4f",
        "navyblue"="#000080",
        "purple"="#a020f0"
      ),
      expand=c(0,0)
      ) +
      scale_fill_manual(values = c(
        "brown"="brown",
        "green"="#00ff00",
        "transparent"="transparent",
        "slategrey"="#2f4f4f",
        "navyblue"="#000080",
        "purple"="#a020f0"
      ),
      expand=c(0,0)
      ) +
      #scale_x_continuous(expand=c(0,0)) +
      #scale_y_continuous(expand=c(0,0)) +
      theme_nothing() +
      
      theme(plot.background = element_rect(fill = bg, colour=NA),
            plot.margin = margin(t=0,b=0)) +
      labs(x = NULL, y = NULL),
    ncol=1,
    rel_heights = c(1,
                    #-0.1,
                    1)
  )
}

position_annotation(merged_df3,
                    aa_pos_drug=aa_pos_drug,
                    active_aa_pos=active_aa_pos,
                    aa_pos_lig1=aa_pos_lig1,
                    aa_pos_lig2=aa_pos_lig2,
                    aa_pos_lig3=aa_pos_lig3
)
# 
# # proof that you can use this function to pass arbitrary lists of numbers :-)
# position_annotation(merged_df3,
#                     aa_pos_drug=1:1000,
#                     active_aa_pos=1:1000,
#                     aa_pos_lig1=1:1000,
#                     aa_pos_lig2=1:1000,
#                     aa_pos_lig3=1:1000
# )