added katg and rpob files
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scripts/plotting/plotting_thesis/rpob/rpob_ORandSNP_results.R
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226
scripts/plotting/plotting_thesis/rpob/rpob_ORandSNP_results.R
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#!/usr/bin/env Rscript
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#source("~/git/LSHTM_analysis/config/katg.R")
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#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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#=======
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# output
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#=======
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outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
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outdir_stats = paste0(outdir_images,"stats/")
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###################################################################
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# FIXME: ADD distance to NA when SP replies
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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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dist_columns = c(LigDist_colname, ppi2Dist_colname, naDist_colname )
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common_cols = c("mutationinformation"
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, "X5uhc_position"
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, "X5uhc_offset"
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, "position"
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, "dst_mode"
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, "mutation_info_labels"
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, "sensitivity", dist_columns )
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########################################
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categ_cols_to_factor = grep( "_outcome|_info", colnames(merged_df3) )
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fact_cols = colnames(merged_df3)[categ_cols_to_factor]
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if (any(lapply(merged_df3[, fact_cols], class) == "character")){
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cat("\nChanging", length(categ_cols_to_factor), "cols to factor")
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merged_df3[, fact_cols] <- lapply(merged_df3[, fact_cols], as.factor)
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if (all(lapply(merged_df3[, fact_cols], class) == "factor")){
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cat("\nSuccessful: cols changed to factor")
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}
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}else{
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cat("\nRequested cols aready factors")
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}
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cat("\ncols changed to factor are:\n", colnames(merged_df3)[categ_cols_to_factor] )
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####################################
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# merged_df3: NECESSARY pre-processing
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###################################
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#df3 = merged_df3
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all_cols = c(common_cols
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, all_stability_cols
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, all_affinity_cols
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, all_conserv_cols)
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plot_cols = c("mutationinformation", "mutation_info_labels", "position", "dst_mode"
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#, all_cols
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)
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# counting
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foo = merged_df3[, c("mutationinformation"
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, "wild_pos"
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, "position"
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, "sensitivity"
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, "avg_lig_affinity"
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, "avg_lig_affinity_scaled"
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, "avg_lig_affinity_outcome"
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, "ligand_distance"
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, "ligand_affinity_change"
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, "affinity_scaled"
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, "ligand_outcome"
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, "consurf_colour_rev"
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, "consurf_outcome")]
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table(foo$consurf_outcome)
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foo2 = foo[foo$ligand_distance<10,]
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table(foo2$ligand_outcome)
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#############################
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# wide plots SNP
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# DRUG
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length(aa_pos_drug); aa_pos_drug
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drug = foo[foo$position%in%aa_pos_drug,]
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drug$wild_pos
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#CA
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###############################################
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# OR
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###############################################
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# OR plot
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df3_or = merged_df3
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df3_or$maf_percent = df3_or$maf*100
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bar = df3_or[, c("mutationinformation"
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, "wild_pos"
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, "position"
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, "sensitivity"
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, drug
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, affinity_dist_colnames
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, "maf_percent"
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, "or_mychisq"
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, "pval_fisher"
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#, "pval_chisq"
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, "neglog_pval_fisher"
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, "log10_or_mychisq")]
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# bar$p_adj_bonferroni = p.adjust(bar$pval_fisher, method = "bonferroni")
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# bar$signif_bon = bar$p_adj_bonferroni
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# bar = dplyr::mutate(bar
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# , signif_bon = case_when(signif_bon == 0.05 ~ "."
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# , signif_bon <=0.0001 ~ '****'
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# , signif_bon <=0.001 ~ '***'
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# , signif_bon <=0.01 ~ '**'
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# , signif_bon <0.05 ~ '*'
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# , TRUE ~ 'ns'))
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bar$p_adj_fdr = p.adjust(bar$pval_fisher, method = "BH")
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bar$signif_fdr = bar$p_adj_fdr
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bar = dplyr::mutate(bar
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, signif_fdr = case_when(signif_fdr == 0.05 ~ "."
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, signif_fdr <=0.0001 ~ '****'
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, signif_fdr <=0.001 ~ '***'
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, signif_fdr <=0.01 ~ '**'
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, signif_fdr <0.05 ~ '*'
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, TRUE ~ 'ns'))
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# sort df
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bar = bar[order(bar$or_mychisq, decreasing = T), ]
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bar = bar[, c("mutationinformation"
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, "wild_pos"
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, "position"
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, "sensitivity"
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, drug
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, affinity_dist_colnames
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, "maf_percent"
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, "or_mychisq"
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#, "pval_fisher"
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#, "pval_chisq"
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#, "neglog_pval_fisher"
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#, "log10_or_mychisq"
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#, "signif_bon"
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, "p_adj_fdr"
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, "signif_fdr")]
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table(bar$sensitivity)
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str(bar)
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sen = bar[bar$or_mychisq<1,]
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sen = na.omit(sen)
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res = bar[bar$or_mychisq>1,]
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res = na.omit(res)
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# comp
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bar_or = bar[!is.na(bar$or_mychisq),]
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table(bar_or$sensitivity)
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sen1 = bar_or[bar_or$or_mychisq<1,] # sen and res ~OR
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res1 = bar_or[bar_or$or_mychisq>1,] # sen and res ~OR
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# sanity check
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if (nrow(bar_or) == nrow(sen1) + nrow(res1) ){
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cat("\nPASS: df with or successfully sourced"
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, "\nCalculating % of muts with OR>1")
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}else{
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stop("Abort: df with or numbers mimatch")
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}
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# percent for OR muts
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pc_orR = nrow(res1)/(nrow(sen1) + nrow(res1)); pc_orR
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cat("\nNo.of DST muts:", nrow(bar_or)
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, "\nNo of DST (R):", table(bar_or$sensitivity)[[1]]
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, "\nNo of DST (S):", table(bar_or$sensitivity)[[2]]
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, "\nNumber of R muts with OR >1 (n = ", nrow(res1),")"
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, "\nPercentage of muts with OR>1 i.e resistant:" , pc_orR *100 )
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table(bar_or$sensitivity)
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# muts with highest OR
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head(bar_or$mutationinformation, 10)
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# sort df
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bar_or = bar_or[order(bar_or$or_mychisq
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, bar_or$ligand_distance
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, bar_or$nca_distance
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, bar_or$interface_dist
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, decreasing = T), ]
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nrow(bar_or)
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bar_or$drug_site = ifelse(bar_or$position%in%aa_pos_drug, "drug", "no")
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table(bar_or$drug_site)
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top10_or = bar_or[1:10,]
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top10_or
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write.csv(bar_or, paste0(outdir_stats, "rpob_OR_10.csv"))
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# are these active sites
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top10_or$position[top10_or$position%in%active_aa_pos]
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# most frequent
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bar_maf = bar_or[order(bar_or$maf_percent
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, bar_or$ligand_distance
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, bar_or$nca_distance
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, bar_or$interface_dist
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, decreasing = T), ]
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bar_maf$drug_site = ifelse(bar_maf$position%in%aa_pos_drug, "drug", "no")
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table(bar_maf$drug_site)
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bar_maf[1:10,]
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#########################################################
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# closest most sig
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bar_or_lig = bar_or[bar_or$ligand_distance<10,]
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bar_or_lig = bar_or_lig[order(bar_or_lig$ligand_distance, -bar_or_lig$or_mychisq), ]
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table(bar_or_lig$signif_fdr)
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bar_or_nca = bar_or[bar_or$nca_distance<10,]
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bar_or_nca = bar_or_nca[order(bar_or_nca$nca_distance, -bar_or_ppi$or_mychisq), ]
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table(bar_or_nca$signif_fdr)
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bar_or_ppi = bar_or[bar_or$interface_dist<10,]
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bar_or_ppi = bar_or_ppi[order(bar_or_ppi$interface_dist, -bar_or_ppi$or_mychisq), ]
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table(bar_or_ppi$signif_fdr)
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