155 lines
6.3 KiB
R
155 lines
6.3 KiB
R
geneL_normal = c("pnca")
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geneL_na = c("gid", "rpob")
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geneL_ppi2 = c("alr", "embb", "katg", "rpob")
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# LigDist_colname # from globals used
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# ppi2Dist_colname #from globals used
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# naDist_colname #from globals used
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common_cols = c("mutationinformation"
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, "id"
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, drug, "drug_name"
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, "mutation", "mutation_info"
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, "wild_type", "mutant_type", "position"
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, "pos_count"
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, "snp_frequency"
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, "total_id_ucount"
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, "drtype", "drtype_mode", "drtype_max"
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, "dst", "dst_mode"
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, "mutation_info_labels", "sensitivity"
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, "lineage", "lineage_labels", "lineage_count_all", "lineage_count_unique"
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, "ligand_id", LigDist_colname
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, "duet_stability_change", "duet_scaled", "duet_outcome"
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, "foldx_scaled_signC"
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, "ddg_foldx", "foldx_scaled", "foldx_outcome"
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, "deepddg", "deepddg_outcome", "deepddg_scaled"
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, "ddg_dynamut2", "ddg_dynamut2_scaled", "ddg_dynamut2_outcome"
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, "avg_stability", "avg_stability_outcome", "avg_stability_scaled"
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, "ligand_affinity_change", "ligand_outcome", "affinity_scaled"
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, "mmcsm_lig", "mmcsm_lig_scaled", "mmcsm_lig_outcome"
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, "avg_lig_affinity", "avg_lig_affinity_outcome", "avg_lig_affinity_scaled"
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, "consurf_score", "consurf_scaled", "consurf_outcome"
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, "consurf_colour_rev"
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, "provean_score", "provean_outcome", "provean_scaled"
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, "snap2_score", "snap2_scaled", "snap2_accuracy_pc", "snap2_outcome"
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, "asa", "rsa", "ss", "ss_class", "kd_values", "rd_values"
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, "maf" #, "af"
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, "or_logistic", "pval_logistic"
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, "or_mychisq", "log10_or_mychisq"
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, "or_fisher", "pval_fisher", "neglog_pval_fisher"
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, "consurf_colour", "consurf_ci_upper", "consurf_ci_lower"
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, "consurf_ci_colour", "consurf_msa_data", "consurf_aa_variety"
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, "wild_pos", "chain", "wild_chain_pos"
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, "wt_3upper", "mut_3upper"
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, "gene_name", "seq_offset4pdb", "pdb_file"
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)
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##################################################################
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#========================
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# Common: affinity cols
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#========================
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common_raw_affinity_cols = c("ligand_affinity_change"
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, "mmcsm_lig"
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, "avg_lig_affinity")
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common_scaled_affinity_cols = c("affinity_scaled"
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, "mmcsm_lig_scaled"
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, "avg_lig_affinity_scaled")
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common_outcome_affinity_cols = c( "ligand_outcome"
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, "mmcsm_lig_outcome"
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, "avg_lig_affinity_outcome")
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#======================================================
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# Plotting cols + affinity cols: conditional on gene
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#======================================================
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if (tolower(gene)%in%geneL_normal){
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plotting_cols = common_cols
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raw_affinity_cols = common_raw_affinity_cols
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scaled_affinity_cols = common_scaled_affinity_cols
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outcome_affinity_cols = common_outcome_affinity_cols
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affinity_dist_colnames = LigDist_colname
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}
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# ppi2 genes
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if (tolower(gene)%in%geneL_ppi2){
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plotting_cols = c(common_cols,
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ppi2Dist_colname,
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"mcsm_ppi2_affinity", "mcsm_ppi2_scaled", "mcsm_ppi2_outcome")
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raw_affinity_cols = c(common_raw_affinity_cols , "mcsm_ppi2_affinity")
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scaled_affinity_cols = c(common_scaled_affinity_cols , "mcsm_ppi2_scaled" )
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outcome_affinity_cols = c(common_outcome_affinity_cols , "mcsm_ppi2_outcome")
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affinity_dist_colnames = c(LigDist_colname, ppi2Dist_colname)
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}
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#na_genes
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if (tolower(gene)%in%geneL_na){
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plotting_cols = c(common_cols,
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naDist_colname,
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"mcsm_na_affinity", "mcsm_na_scaled", "mcsm_na_outcome")
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raw_affinity_cols = c(common_raw_affinity_cols , "mcsm_na_affinity")
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scaled_affinity_cols = c(common_scaled_affinity_cols , "mcsm_na_scaled")
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outcome_affinity_cols = c(common_outcome_affinity_cols , "mcsm_na_outcome")
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affinity_dist_colnames = c(LigDist_colname, ppi2Dist_colname, naDist_colname)
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}
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if (tolower(gene)%in%c("rpob")){
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plotting_cols = c(plotting_cols, "X5uhc_position","X5uhc_offset")
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}
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#=======================================
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# All: affinity cols: based on above confition
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#========================================
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all_affinity_cols = c(raw_affinity_cols
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, scaled_affinity_cols
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, outcome_affinity_cols)
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#=======================================
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# All: stability cols
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# these are common, no condition on gene
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#========================================
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raw_stability_cols = c("duet_stability_change"
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, "deepddg"
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, "ddg_dynamut2"
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, "ddg_foldx"
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, "avg_stability")
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scaled_stability_cols = c("duet_scaled"
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, "deepddg_scaled"
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, "ddg_dynamut2_scaled"
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, "foldx_scaled"
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, "foldx_scaled_signC" # needed to get avg stability
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, "avg_stability_scaled")
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outcome_stability_cols = c("duet_outcome"
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, "deepddg_outcome"
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, "ddg_dynamut2_outcome"
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, "foldx_outcome"
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, "avg_stability_outcome")
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raw_conservation_cols = c("consurf_score"
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, "provean_score"
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, "snap2_score")
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scaled_conservation_cols = c("consurf_scaled"
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,"provean_scaled"
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, "snap2_scaled")
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outcome_conservation_cols = c("consurf_outcome", "consurf_colour_rev"
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,"provean_outcome"
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, "snap2_outcome")
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all_stability_cols = c(raw_stability_cols
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, scaled_stability_cols
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, outcome_stability_cols
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, raw_conservation_cols
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, scaled_conservation_cols
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, outcome_conservation_cols)
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