# 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",
                             reorder_position = FALSE, # enable to reorder according to plot_df$pos_count
                             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,
                             drug_colour='green',
                             lig1_colour='slategrey',
                             lig2_colour='navyblue',
                             lig3_colour='purple'
)
{
  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$bg_all = ifelse(plot_df[["position"]]%in%aa_pos_drug,
                          "drug", plot_df$bg_all)
  
  plot_df$col_bg1 = plot_df$bg_all
  plot_df$col_bg1 = ifelse(plot_df[["position"]]%in%aa_pos_lig1,
                           "lig1", plot_df$col_bg1)
  
  plot_df$col_bg2 = plot_df$col_bg1
  plot_df$col_bg2 = ifelse(plot_df[["position"]]%in%aa_pos_lig2,
                           "lig2", plot_df$col_bg2)
  
  
  plot_df$col_bg3 = plot_df$col_bg2
  plot_df$col_bg3 =  ifelse(plot_df[["position"]]%in%aa_pos_lig3
                            , "lig3", plot_df$col_bg3)
  
  # the call to generate_distance_colour_map should probably be
  # wherever the outer DF is built, and not here.
  plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
  
  heat_bar = ggplot(plot_df) + # THIS STUPID FUCKING FACTOR THING
    
    # scale_x_discrete("Position", labels=factor(plot_df$position)) +
    theme_nothing() +
    theme(#axis.text.x = element_text(angle = 90, size = 6),
          title = element_blank()
    ) + # enable for alignment debug
    labs(x = NULL, y = NULL) +
    
    # if reorder_position is turned on then we need to reorder 'x'
    # according to the pos_count column (creating this column is
    # left as a fun exercise to whoever reads this next)
    if(reorder_position) {
      geom_tile(aes(y=0, x=reorder(position,-pos_count)), 
                fill=plot_df$ligD_colours)
    } else {
      geom_tile(aes(y=0, x=factor(position)), 
                fill=plot_df$ligD_colours)
    }
  #end of distance-heat-bar
  #NULL,
    if(reorder_position) {
      pos_tiles = ggplot(plot_df) +
        #scale_x_discrete("Position", labels=factor(plot_df$position)) +
        scale_color_manual(values = c(
          "brown"="brown",
          "drug"=drug_colour,
          "transparent"="transparent",
          "lig1"=lig1_colour,
          "lig2"=lig2_colour,
          "lig3"=lig3_colour
        ),
        #expand=c(0,0)
        ) +
        scale_fill_manual(values = c(
          "brown"="brown",
          "drug"=drug_colour,
          "transparent"="transparent",
          "lig1"=lig1_colour,
          "lig2"=lig2_colour,
          "lig3"=lig3_colour
        ),
        #expand=c(0,0)
        ) +
        theme_nothing() +
        theme(plot.background = element_rect(fill = bg, colour=NA),
              #plot.margin = margin(t=0,b=0),
              panel.background = element_rect(fill = bg, colour=NA),
              legend.position = "none"
        ) +
        labs(x = NULL, y= NULL) +
      geom_tile(aes(y = 1,x=reorder(position,-pos_count), fill = bg_all, colour = bg_all)
      ) +
        geom_tile(aes(y = 2, x=reorder(position,-pos_count), fill = col_bg1, colour = col_bg1)
        ) +
        geom_tile(aes(y = 3, x=reorder(position,-pos_count), fill = col_bg2, colour = col_bg2)
        ) +
        geom_tile(aes(y = 4, x=reorder(position,-pos_count), fill = col_bg3, colour = col_bg3)
        )
      
    } else {
      pos_tiles = ggplot(plot_df) +
        #scale_x_discrete("Position", labels=factor(plot_df$position)) +
        scale_color_manual(values = c(
          "brown"="brown",
          "drug"=drug_colour,
          "transparent"="transparent",
          "lig1"=lig1_colour,
          "lig2"=lig2_colour,
          "lig3"=lig3_colour
        ),
        #expand=c(0,0)
        ) +
        scale_fill_manual(values = c(
          "brown"="brown",
          "drug"=drug_colour,
          "transparent"="transparent",
          "lig1"=lig1_colour,
          "lig2"=lig2_colour,
          "lig3"=lig3_colour
        ),
        #expand=c(0,0)
        ) +
        theme_nothing() +
        theme(plot.background = element_rect(fill = bg, colour=NA),
              #plot.margin = margin(t=0,b=0),
              panel.background = element_rect(fill = bg, colour=NA),
              legend.position = "none"
        ) +
        labs(x = NULL, y= NULL) +
      geom_tile(aes(y = 1, x=factor(position), fill = bg_all, colour = bg_all)
      ) +
        geom_tile(aes(y = 2, x=factor(position), fill = col_bg1, colour = col_bg1)
        ) +
        geom_tile(aes(y = 3, x=factor(position), fill = col_bg2, colour = col_bg2)
        ) +
        geom_tile(aes(y = 4, x=factor(position), fill = col_bg3, colour = col_bg3)
        )
    }
# tile thingies end  

    heat_legend=get_legend(heat_bar)
  out_plot=cowplot::plot_grid(
    heat_bar,
    NULL,
    pos_tiles,
    ncol=1,
    align='v',
    rel_heights = c(1,
                    -0.1,
                    2)
  )
  
  return(out_plot)
}

# position_annotation(small_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
# )