geneL_normal  = c("pnca")
geneL_na      = c("gid", "rpob")
geneL_ppi2    = c("alr", "embb", "katg", "rpob")

# LigDist_colname # from globals used
# ppi2Dist_colname #from globals used 
# naDist_colname #from globals used

common_cols = c("mutationinformation"
                , "id"
                , drug, "drug_name"
                , "mutation", "mutation_info"
                , "wild_type", "mutant_type", "position"
                , "pos_count"
                , "snp_frequency"
                , "total_id_ucount"
                , "drtype", "drtype_mode", "drtype_max"
                , "dst", "dst_mode"
                , "mutation_info_labels", "sensitivity"
                , "lineage", "lineage_labels", "lineage_count_all", "lineage_count_unique"
                , "ligand_id", LigDist_colname
                , "duet_stability_change", "duet_scaled", "duet_outcome"
                , "foldx_scaled_signC"
                , "ddg_foldx", "foldx_scaled", "foldx_outcome"
                , "deepddg", "deepddg_outcome", "deepddg_scaled"
                , "ddg_dynamut2", "ddg_dynamut2_scaled", "ddg_dynamut2_outcome"
                , "avg_stability", "avg_stability_outcome", "avg_stability_scaled"
                , "ligand_affinity_change", "ligand_outcome", "affinity_scaled"
                , "mmcsm_lig", "mmcsm_lig_scaled", "mmcsm_lig_outcome"
                , "avg_lig_affinity", "avg_lig_affinity_outcome", "avg_lig_affinity_scaled"
                , "consurf_score", "consurf_scaled", "consurf_outcome"
                , "consurf_colour_rev"
                , "provean_score", "provean_outcome", "provean_scaled"
                , "snap2_score", "snap2_scaled", "snap2_accuracy_pc", "snap2_outcome"
                , "asa", "rsa", "ss", "ss_class", "kd_values", "rd_values"
                , "maf" #, "af"
                , "or_logistic", "pval_logistic"
                , "or_mychisq", "log10_or_mychisq"
                , "or_fisher", "pval_fisher", "neglog_pval_fisher"
                , "consurf_colour", "consurf_ci_upper", "consurf_ci_lower"
                , "consurf_ci_colour", "consurf_msa_data", "consurf_aa_variety"
                , "wild_pos", "chain", "wild_chain_pos"
                , "wt_3upper", "mut_3upper"
                , "gene_name", "seq_offset4pdb", "pdb_file"
                )

##################################################################
#========================
# Common: affinity cols
#========================
common_raw_affinity_cols = c("ligand_affinity_change"
                             , "mmcsm_lig"
                             , "avg_lig_affinity")

common_scaled_affinity_cols = c("affinity_scaled" 
                              , "mmcsm_lig_scaled"
                              , "avg_lig_affinity_scaled")

common_outcome_affinity_cols = c( "ligand_outcome"
                               , "mmcsm_lig_outcome"
                               , "avg_lig_affinity_outcome")

#======================================================
# Plotting cols + affinity cols: conditional on gene
#======================================================
if (tolower(gene)%in%geneL_normal){
  plotting_cols = common_cols
  
  raw_affinity_cols = common_raw_affinity_cols
  scaled_affinity_cols = common_scaled_affinity_cols
  outcome_affinity_cols = common_outcome_affinity_cols
  affinity_dist_colnames = LigDist_colname
  
}
# ppi2 genes
if (tolower(gene)%in%geneL_ppi2){
  plotting_cols = c(common_cols,
                    ppi2Dist_colname,
                    "mcsm_ppi2_affinity", "mcsm_ppi2_scaled", "mcsm_ppi2_outcome")
  
  raw_affinity_cols     = c(common_raw_affinity_cols     , "mcsm_ppi2_affinity")
  scaled_affinity_cols  = c(common_scaled_affinity_cols  , "mcsm_ppi2_scaled" )
  outcome_affinity_cols = c(common_outcome_affinity_cols , "mcsm_ppi2_outcome")
  affinity_dist_colnames      = c(LigDist_colname, ppi2Dist_colname)
  
  
}

#na_genes
if (tolower(gene)%in%geneL_na){
  plotting_cols = c(common_cols,
                    naDist_colname,
                    "mcsm_na_affinity", "mcsm_na_scaled", "mcsm_na_outcome")

  raw_affinity_cols     = c(common_raw_affinity_cols         , "mcsm_na_affinity")
  scaled_affinity_cols  = c(common_scaled_affinity_cols   , "mcsm_na_scaled")
  outcome_affinity_cols = c(common_outcome_affinity_cols , "mcsm_na_outcome")
  affinity_dist_colnames      = c(LigDist_colname, ppi2Dist_colname, naDist_colname)
  
  }

if (tolower(gene)%in%c("rpob")){
  plotting_cols = c(plotting_cols, "X5uhc_position","X5uhc_offset")
}
#=======================================
# All: affinity cols: based on above confition
#========================================

all_affinity_cols = c(raw_affinity_cols
                      , scaled_affinity_cols
                      , outcome_affinity_cols)

#=======================================
# All: stability cols
# these are common, no condition on gene
#========================================
raw_stability_cols =  c("duet_stability_change"
                        , "deepddg"
                        , "ddg_dynamut2"
                        , "ddg_foldx"
                        , "avg_stability")

scaled_stability_cols = c("duet_scaled"       
                        , "deepddg_scaled"   
                        , "ddg_dynamut2_scaled"
                        , "foldx_scaled"
                        , "foldx_scaled_signC" # needed to get avg stability
                        , "avg_stability_scaled")

outcome_stability_cols = c("duet_outcome"
                        , "deepddg_outcome"
                        , "ddg_dynamut2_outcome"
                        , "foldx_outcome"
                        , "avg_stability_outcome")

all_stability_cols = c(raw_stability_cols
                       , scaled_stability_cols
                       , outcome_stability_cols)