#!/usr/bin/env Rscript  

#########################################################
# TASK: Lineage plots [merged_df2]
# Count
# Diversity
# Average stability dist
# Avergae affinity dist: optional
#########################################################
#=======
# output
#=======
# outdir_images = paste0("~/git/Writing/thesis/images/results/"
#                        , tolower(gene), "/")
# cat("plots will output to:", outdir_images)
#########################################################

#===============
#Quick numbers checks
#===============
nsample_lin = merged_df2[merged_df2$lineage%in%c("L1", "L2", "L3", "L4"),]

if ( all(table(nsample_lin$sensitivity)== table(nsample_lin$mutation_info_labels)) ){
  cat("\nTotal no. of samples belonging to L1-l4 for", gene,":", nrow(nsample_lin)
      , "\nCounting R and S samples")
  if( sum(table(nsample_lin$sensitivity)) ==  nrow(nsample_lin) ){
    cat("\nPASSNumbers cross checked:")
    print(table(nsample_lin$sensitivity))
  }
}else{
  stop("Abort: Numbers mismatch. Please check")
}
########################################################################
###################################################
#                  Lineage barplots               #
###################################################

#===============================
# lineage sample and SNP count
#===============================
lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
             , all_lineages = F
             , x_categ = "sel_lineages"
             , y_count = "p_count"
             , use_lineages = c("L1", "L2", "L3", "L4")
             , bar_fill_categ = "count_categ"
             , display_label_col = "p_count"
             , bar_stat_stype = "identity"
             , d_lab_size = 8
             , d_lab_col = "black"
             , my_xats = 25 # x axis text size
             , my_yats = 25 # y axis text sized_lab_size
             , my_xals = 25 # x axis label size
             , my_yals = 25 # y axis label size
             , my_lls  = 25 # legend label size
             , bar_col_labels =  c("SNPs", "Total Samples")
             , bar_col_values = c("grey50", "gray75")
             , bar_leg_name = ""
             , leg_location = "top"
             , y_log10 = F
             , y_scale_percent = FALSE
             , y_label = c("Count")
             )

#===============================
# lineage SNP diversity count
#===============================
lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
                              , x_categ = "sel_lineages"
                              , y_count = "snp_diversity"
                              #, all_lineages = F
                              , use_lineages = c("L1", "L2", "L3", "L4")
                              , display_label_col = "snp_diversity_f"
                              , bar_stat_stype = "identity"
                              , x_lab_angle = 90
                              , d_lab_size =9
                              , my_xats = 25 # x axis text size
                              , my_yats = 25 # y axis text size
                              , my_xals = 25 # x axis label size
                              , my_yals = 25 # y axis label size
                              , my_lls  = 25 # legend label size
                              , y_log10 = F
                              , y_scale_percent = F
                              , leg_location = "top"
                              , y_label = "Percent" #"SNP diversity"
                              , bp_plot_title = "nsSNP diversity"
                              , title_colour = "black" #"chocolate4"
                              , subtitle_text = NULL
                              , sts = 20
                              , subtitle_colour = "#350E20FF")

#=============================================
# Output plots: Lineage count and Diversity
#=============================================
# lineage_bp_CL =  paste0(outdir_images
#                         ,tolower(gene)
#                         ,"_lineage_bp_CL_Tall.svg")
# 
# cat("Lineage barplots:", lineage_bp_CL)
# svg(lineage_bp_CL, width = 8, height = 15)
# 
# cowplot::plot_grid(lin_countP, lin_diversityP
#                      #, labels = c("(a)", "(b)", "(c)", "(d)")
#                       , nrow = 2
#                      # , ncols = 2
#                       , labels = "AUTO"
#                       , label_size = 25)
# 
# dev.off()
########################################################################


###################################################
#                   Stability dist                #
###################################################
# scaled_cols_stability = c("duet_scaled"       
#                           , "deepddg_scaled"   
#                           , "ddg_dynamut2_scaled"
#                           , "foldx_scaled"
#                           , "avg_stability_scaled")

my_xlabel = paste0("Average stability ", "(", stability_suffix, ")"); my_xlabel
#plotdf = merged_df2[merged_df2$lineage%in%c("L1", "L2", "L3", "L4"),]

linP_dm_om = lineage_distP(merged_df2
                           , with_facet = F
                           , x_axis = "avg_stability_scaled"
                           , y_axis = "lineage_labels"
                           , x_lab = my_xlabel
                           , use_lineages = c("L1", "L2", "L3", "L4")
                           #, fill_categ = "mutation_info_orig", fill_categ_cols = c("#E69F00", "#999999")
                           , fill_categ = "sensitivity"
                           , fill_categ_cols = c("red", "blue")
                           , label_categories = c("Resistant", "Sensitive")
                           , leg_label = "Mutation group"
                           , my_ats = 22 # axis text size
                           , my_als = 22 # axis label size
                           , my_leg_ts = 22
                           , my_leg_title = 22
                           , my_strip_ts = 22
                           , alpha = 0.56
)

linP_dm_om

###################################################
#                 Affinity dist [OPTIONAL]        #
###################################################
# scaled_cols_affinity = c("affinity_scaled" 
#                          , "mmcsm_lig_scaled" 
#                          , "mcsm_ppi2_scaled" 
#                          , "mcsm_na_scaled"
#                          , "avg_lig_affinity_scaled")

# lineage_distP(merged_df2
#               , with_facet = F
#               , x_axis = "avg_lig_affinity_scaled"
#               , y_axis = "lineage_labels"
#               , x_lab = my_xlabel
#               , use_lineages = c("L1", "L2", "L3", "L4")
#               #, fill_categ = "mutation_info_orig", fill_categ_cols = c("#E69F00", "#999999")
#               , fill_categ = "sensitivity"
#               , fill_categ_cols = c("red", "blue")
#               , label_categories = c("Resistant", "Sensitive")
#               , leg_label = "Mutation group"
#               , my_ats = 22 # axis text size
#               , my_als = 22 # axis label size
#               , my_leg_ts = 22
#               , my_leg_title = 22
#               , my_strip_ts = 22
#               , alpha = 0.56
# )