#logo plots

# create functions

# one with OR
  # --> select/drop down option to remove empty positions
      # --> easy peasy, just select the merged_df3_comp
  # --> select/drop down option for colour
      # --> if clustalx and taylor,  set variable to black bg + white font
      # --> if chemistry and hydrophobicity, then grey bg +  black font 

  # --> select/drop down option for log scale
  # --> should include WT

# one for multiple muts
  # --> select/drop down option to filter count of nsSNPs
  # --> select/drop down  option for colour
  # --> should include WT

# Data used
#wide_df_or # or logo plot
#wide_df_or_mult # > 1 sites
#wide_df_logor_m #make it as a scale option. REDUNDANT
#tab_mt # mutant logo plot
#tab_wt # wt logo plot

# Make it hover over position and then get the corresponding data table!
#%%======================================================================

#==================
# logo data: OR
#==================
# NOTE: my_logo_col
# Can be one of these: 'chemistry', 'hydrophobicity', 'clustalx', 'taylor'
# if 'chemistry' or 'hydrophobicity' --> then bg is grey with  black font (x, y and labels)
# if 'clustalx'or 'taylor' --> then bg is black with white font (x, y and labels)
    #, theme_bgc = 
    #, xfont_bgc = 
    #, yfont_bgc = 
    #, xtt_col = 
    #, ytt_col = 

# ADD legend for hydrophobicity: done
# ADD option to remove empty positions

LogoPlotCustomH <- function(plotdf
                     , x_axis_colname = "position"
                     , y_axis_colname = "or_mychisq"
                     , symbol_colname = "mutant_type"
                     , y_axis_log  = T
                     , log_value = log10
                     , my_logo_col = "chemistry" 
                     , x_lab = "Position"
                     , y_lab = "Odds Ratio"
                     , x_ats = 12 # text size
                     , x_tangle = 90 # text angle
                     #, theme_bgc
                     #, xfont_bgc
                     #, yfont_bgc
                     , y_ats = 22
                     , y_tangle = 0
                     , x_tts = 20 # title size
                     , y_tts = 23
                     #, xtt_col = 
                     #, ytt_col = 
                     , leg_pos = "none" # can be top, left, right and bottom or c(0.8, 0.9)
                     , leg_dir = "horizontal" #can be vertical or horizontal
                     , leg_ts = 15 # leg text size
                     , leg_tts = 16 # leg title size
                     )

{
  #################################
  # Data processing for logo plot
  #################################
  
  logo_df = plotdf
  
  logo_data_plot2 = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
  
  #==================
  # logo data: OR
  #==================
  logo_data_plot2_or = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
  
  wide_df2_or  =  as.matrix(logo_data_plot2_or %>% spread(x_axis_colname, y_axis_colname, fill = 0.0))
  class(wide_df2_or)
  
  rownames(wide_df2_or) = wide_df2_or[,1]
  dim(wide_df2_or)
  
  wide_df2_or = wide_df2_or[,-1]
  str(wide_df2_or)
  
  colnames(wide_df2_or)
  position_or = as.numeric(colnames(wide_df2_or))

  #==================
  # logo data: logOR
  #==================
  if (y_axis_log){
    
    log_colname = paste0("log_", y_axis_colname)
    logo_df[log_colname] = log_value(logo_df[y_axis_colname])
    logo_data_plot2 = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname,log_colname )]
    
    logo_data_plot2_logor = logo_df[, c(x_axis_colname, symbol_colname, log_colname)]
  
    wide_df2_logor = as.matrix(logo_data_plot2_logor %>% spread(x_axis_colname, log_colname, fill = 0.0))
    class(wide_df2_logor)
    
    rownames(wide_df2_logor) = wide_df2_logor[,1]
    dim(wide_df2_logor)
    
    wide_df2_logor = wide_df2_logor[,-1]
    str(wide_df2_logor)
    
    colnames(wide_df2_logor)
    position_logor = as.numeric(colnames(wide_df2_logor))
  }

  ######################################
  # Generating plots with given y_axis
  #####################################
  #if (my_logo_col == 'clustalx || taylor'){
  
  if (my_logo_col %in% c('clustalx','taylor')) {
    cat("\nSelected colour scheme:", my_logo_col
        , "\nUsing black theme\n")
    theme_bgc  = "black"
    xfont_bgc  = "white"
    yfont_bgc  = "white"
    xtt_col    = "white"
    ytt_col    = "white"
  }

  if (my_logo_col %in% c('chemistry', 'hydrophobicity')) {
    cat('\nSelected colour scheme:', my_logo_col
        , "\nUsing grey theme")
    theme_bgc = "grey"
    xfont_bgc  = "black"
    yfont_bgc  = "black"
    xtt_col    = "black"
    ytt_col    = "black"
  }
 
  LogoPlot = ggseqlogo(wide_df2_or
                      , method = "custom"
                      , col_scheme = my_logo_col
                      , seq_type = "aa") + ylab("my custom height") +
    theme(axis.text.x = element_text(size = x_ats
                                      , angle = x_tangle
                                      , hjust = 1
                                      , vjust = 0.4
                                      , colour = xfont_bgc)
           , axis.text.y = element_text(size = y_ats
                                        , angle = y_tangle
                                        , hjust = 1
                                        , vjust = 0
                                        , colour = yfont_bgc)
           , axis.title.x = element_text(size = x_tts
                                        , colour = xtt_col)
           , axis.title.y = element_text(size = y_tts
                                        , colour = ytt_col)
           , legend.position = leg_pos
           , legend.direction = leg_dir
           , plot.background = element_rect(fill = theme_bgc))+
    #, legend.text = element_text(size = leg_ts)
    #, legend.title = element_text(size = leg_tts))+
    scale_x_discrete(x_lab
                     #, breaks
                     , labels = position_or
                     , limits = factor(1:length(position_or))) +
    ylab(y_lab)
  
  return(LogoPlot)

}