From d6766d9d9c4671453fe548b42efec455be1d8cd1 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Thu, 11 Aug 2022 21:08:54 +0100 Subject: [PATCH] added plotting_colnames.R in scripts/plotting --- scripts/plotting/plotting_colnames.R | 138 +++++++++++++++++++++++++++ 1 file changed, 138 insertions(+) create mode 100644 scripts/plotting/plotting_colnames.R diff --git a/scripts/plotting/plotting_colnames.R b/scripts/plotting/plotting_colnames.R new file mode 100644 index 0000000..ea15973 --- /dev/null +++ b/scripts/plotting/plotting_colnames.R @@ -0,0 +1,138 @@ +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)