# source basic_barplots.R

#============
# Plot labels
#============
tit1 = "Stability outcome"
tit2 = "Affinity outcome"
tit3 = "Conservation outcome"
pt_size = 30


theme_georgia <- function(...) {
  theme_gray(base_family = "sans", ...) + 
    theme(plot.title = element_text(face = "bold"))
}


title_theme <- calc_element("plot.title", theme_georgia())

pt1 = ggdraw() + 
  draw_label(
    tit1,
    fontfamily = title_theme$family,
    fontface = title_theme$face,
    #size = title_theme$size
    size = pt_size
  )

pt2 = ggdraw() + 
  draw_label(
    tit2,
    fontfamily = title_theme$family,
    fontface = title_theme$face,
    size = pt_size
  )

pt3 = ggdraw() + 
  draw_label(
    tit3,
    fontfamily = title_theme$family,
    fontface = title_theme$face,
    size = pt_size
  )

# extract common legend
common_legend_outcome = get_legend(mLigP +
                                     guides(color = guide_legend(nrow = 1)) +
                                     theme(legend.position = "top"))



my_label_size = 25
#======================
# Output plot function
#======================
OutPlotBP = function(x){
cowplot::plot_grid(
  cowplot::plot_grid(pt1,
                     common_legend_outcome,
                     cowplot::plot_grid( duetP, foldxP
                                         , deepddgP, dynamut2P
                                         , nrow = 2
                                         , ncol = 2
                                         , labels = c("A", "B", "C","D")
                                         , label_size = my_label_size
                     )
                     , ncol = 1
                     , rel_heights = c(7, 3, 90)),
  
  cowplot::plot_grid(pt2,
                     cowplot::plot_grid(mLigP, mmLigP, ppi2P
                                        , nrow = 1
                                        , ncol = 3
                                        , labels = c("E","F", "G")
                                        , label_size = my_label_size
                     )
                     , ncol = 1
                     , rel_heights = c(1, 9)),              
  
  cowplot::plot_grid(pt3,
                     cowplot::plot_grid(consurfP, proveanP, snap2P
                                        , nrow = 1
                                        , ncol = 3
                                        , labels = c("H", "I", "J")
                                        , labels_x = 0.2
                                        , label_size = my_label_size
                                        , rel_widths = c(0.2, 0.2, 0.2)
                     )
                     , ncol = 1
                     , rel_heights = c(0.07, 0.93)
  ), 
  
  nrow = 3,
  rel_heights = c(0.58, 0.25, 0.27),
  align = "hv"
)
}

#=====================
# OutPlot: svg and png
#======================
#ratio 11.69 by 8.27
w = 8.27*2
h = 11.69*2

#svg
bp_all_CLP =  paste0(outdir_images
                     ,tolower(gene)
                     ,"_bp_all_CL.svg")
cat(paste0("plot filename:", bp_all_CLP))

svg(bp_all_CLP,  width = w, height = h)
OutPlotBP()
dev.off()

#png
bp_all_CLP_png =  paste0(outdir_images
                         ,tolower(gene)
                         ,"_bp_all_CL.png")
cat(paste0("plot filename:", bp_all_CLP_png))

png(bp_all_CLP_png, width = w, height = h, units = "in", res = 300 )
OutPlotBP()
dev.off()

#####################################################################
#####################################################################
# ------------------------------
# bp site site count: ALL
# <10 Ang ligand
# ------------------------------

posC_all = site_snp_count_bp(plotdf = df3
                  , df_colname = "position"
                  , xaxis_title = "Number of nsSNPs"
                  , yaxis_title = "Number of Sites"
                  , subtitle_size = 20)

# ------------------------------
# bp site site count: mCSM-lig
# < 10 Ang ligand
# ------------------------------
common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol)

posC_lig = site_snp_count_bp(plotdf = df3_lig
                  , df_colname = "position"
                  , xaxis_title = "Number of nsSNPs"
                  , yaxis_title = "Number of Sites"#+  annotate("text", x = 1.5, y = 2.2, label = "Text No. 1")
                  , subtitle_text = paste0(common_bp_title, " ligand")
                  , subtitle_size = 20
                  , subtitle_colour = subtitle_colour)
# ------------------------------
# bp site site count: ppi2
# < 10 Ang interface
# ------------------------------

posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2
                  , df_colname = "position"
                  , xaxis_title = "Number of nsSNPs"
                  , yaxis_title = "Number of Sites"
                  , subtitle_text = paste0(common_bp_title, " interface")
                  , subtitle_size = 20
                  , subtitle_colour = subtitle_colour)

# ------------------------------
#FIXME: bp site site count: na
# < 10 Ang TBC
# ------------------------------
# posC_na = site_snp_count_bp(plotdf = df3_na
#                   , df_colname = "position"
#                   , xaxis_title = ""
#                   , yaxis_title = "")


#===========================
# output: SITE SNP count:
# all + affinity
#==========================
my_label_size = 25
pos_count_combined_CLP =  paste0(outdir_images
                            ,tolower(gene)
                            ,"_pos_count_PS_AFF.svg")


svg(pos_count_combined_CLP, width = 20, height = 5.5)
print(paste0("plot filename:", pos_count_combined_CLP))

cowplot::plot_grid(posC_all, posC_lig, posC_ppi2
                     #, posC_na
                     , nrow = 1
                     , ncol = 3
                     , labels = "AUTO"
                     , label_size = my_label_size)

dev.off()


#===============================================================