source("~/git/LSHTM_analysis/config/embb.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")

my_gg_pairs=function(plot_df){
  ggpairs(plot_df,
          columns = 1:(ncol(plot_df)-1),
          upper = list(
            continuous = wrap('cor',
                              method = "spearman",
                              title="ρ",
                              digits=2,
                              justify_labels = "left",
                              title_args=c(colour="black")
            )
          ),
          lower = list(
            continuous = wrap("points",
                              alpha = 0.7,
                              size=0.5),
            combo     = wrap("dot",
                             alpha = 0.7,
                             size=0.5)
          ),
          aes(colour = factor(ifelse(plot_df$dst_mode==0,
                                     "S",
                                     "R") ),
              alpha = 0.5),
          title="Stability") +
    
    scale_colour_manual(values = c("red", "blue")) +
    scale_fill_manual(values = c("red", "blue")) +
    theme(text = element_text(size=12,
                              face="bold") )
}

DistCutOff = 10

merged_df3 = as.data.frame(merged_df3)
corr_plotdf = corr_data_extract(merged_df3
                                , gene = gene
                                , drug = drug
                                , extract_scaled_cols = F)

aff_dist_cols = colnames(corr_plotdf)[grep("Dist", colnames(corr_plotdf))]
static_cols =  c("Log10(MAF)"
                 , "Log10(OR)")

corr_ps_colnames = c(static_cols
                     , "DUET"
                     , "FoldX"
                     , "DeepDDG"
                     , "Dynamut2"
                     , aff_dist_cols
                     , "dst_mode")
corr_df_ps = corr_plotdf[, corr_ps_colnames]
complete_obs_ps = nrow(corr_df_ps) - sum(is.na(corr_df_ps$`Log(OR)`))
color_coln = which(colnames(corr_df_ps) == "dst_mode")
corr_end = color_coln-1

# Plot #1
plot_corr_df_ps = my_gg_pairs(corr_df_ps)


corr_conservation_cols = c( static_cols
                            , "ConSurf"
                            , "SNAP2"
                            , "PROVEAN"
                            , aff_dist_cols
                            , "dst_mode"
)

corr_df_cons = corr_plotdf[, corr_conservation_cols]
complete_obs_cons = nrow(corr_df_cons) - sum(is.na(corr_df_cons$`Log(OR)`))
color_coln = which(colnames(corr_df_cons) == "dst_mode")
corr_end = color_coln-1

# Plot #2

#my_gg_pairs(corr_df_cons)
plot_corr_df_cons = my_gg_pairs(corr_df_cons)


corr_df_lig = corr_plotdf[corr_plotdf["Lig-Dist"]<DistCutOff,]
corr_lig_colnames = c(static_cols
                      , "mCSM-lig"
                      , "mmCSM-lig"
                      , "dst_mode")

corr_df_lig = corr_plotdf[, corr_lig_colnames]

complete_obs_lig = nrow(corr_df_lig) - sum(is.na(corr_df_lig$`Log(OR)`))
color_coln = which(colnames(corr_df_lig) == "dst_mode")
corr_end = color_coln-1
# Plot #3

#my_gg_pairs(corr_df_lig)
plot_corr_df_lig = my_gg_pairs(corr_df_lig)

corr_df_ppi2 = corr_plotdf[corr_plotdf["PPI-Dist"]<DistCutOff,]
corr_ppi2_colnames = c(static_cols
                       , "mCSM-PPI2"
                       , "dst_mode"
)
corr_df_ppi2 = corr_plotdf[, corr_ppi2_colnames]
complete_obs_ppi2 = nrow(corr_df_ppi2) - sum(is.na(corr_df_ppi2$`Log(OR)`))
color_coln = which(colnames(corr_df_ppi2) == "dst_mode")
corr_end = color_coln-1

# NOTE: DELETE LOG OR FROM CORRELATION PLOTS!!!!!
# NOTE: ALSO MAYBE DELETE DISTANCES AS WELL
# NOTE: http://ggobi.github.io/ggally/reference/ggally_cor.html

# "***" if the p-value is < 0.001
# "**" if the p-value is < 0.01
# "*" if the p-value is < 0.05
# "." if the p-value is < 0.10
# "" otherwise
# 

# Plot #4
#my_gg_pairs(corr_df_ppi2)
plot_corr_df_ppi2 = my_gg_pairs(corr_df_ppi2)


# corr_df_na = corr_df_na[corr_df_na["NA-Dist"]<DistCutOff,]
# corr_na_colnames = c(static_cols
#                      , "mCSM-NA"
#                      , "dst_mode"
# )
# 
# corr_df_na = corr_plotdf[, corr_na_colnames]
# complete_obs_na = nrow(corr_df_na) - sum(is.na(corr_df_na$`Log(OR)`))
# color_coln = which(colnames(corr_df_na) == "dst_mode")
# corr_end = color_coln-1
# 
# # Plot #5
# #my_gg_pairs(corr_df_na)
# plot_corr_df_na = my_gg_pairs(corr_df_na) 
png("/tmp/gg_pairs_all.png", height = 8, width=11.75, unit="in",res=300)
cowplot::plot_grid(ggmatrix_gtable(plot_corr_df_ps),ggmatrix_gtable(plot_corr_df_cons),
                   ggmatrix_gtable(plot_corr_df_lig),ggmatrix_gtable(plot_corr_df_ppi2),
                   nrow=2, ncol=2, rel_heights = 7,7,3,3)
dev.off()