added output tables with active site
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4 changed files with 43 additions and 17 deletions
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@ -224,8 +224,8 @@ cat(s3)
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# 1
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# s3 = c("\nSuccessfully sourced lineage_data.R")
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# cat(s3)
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merged_df3 = as.data.frame(merged_df3)
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#
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merged_df3 = as.data.frame(merged_df3)
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corr_df_m3_f = corr_data_extract(merged_df3
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, gene = gene
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, drug = drug
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@ -1,7 +1,15 @@
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#source("~/git/LSHTM_analysis/config/embb.R")
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#source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
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#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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#=======
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# Input
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#=======
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source("~/git/LSHTM_analysis/config/gid.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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cat("\nOutput dir for plots:", outdir_images)
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#### corr plot function: ggpairs ####
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my_gg_pairs=function(plot_df, plot_title
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, tt_args_size = 2.5
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, gp_args_size = 2.5){
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@ -38,8 +46,10 @@ my_gg_pairs=function(plot_df, plot_title
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# face="bold"))
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}
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#### Data for ggpairs ####
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DistCutOff = 10
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###########################################################################
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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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@ -53,7 +63,7 @@ corr_plotdf = corr_data_extract(merged_df3
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aff_dist_cols = colnames(corr_plotdf)[grep("Dist", colnames(corr_plotdf))]
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static_cols = c("Log10(MAF)"
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, "Log10(OR)"
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#, "Log10(OR)"
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)
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############################################################
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#=============================================
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@ -148,7 +158,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
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#, gp_args_size = 4
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)
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#### Combine plots #####
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#### Combine plots (OLD, AB + C) #####
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# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
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# png(paste0(outdir_images
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# ,tolower(gene)
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@ -136,8 +136,6 @@ bar = bar[, c("mutationinformation"
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table(bar$sensitivity)
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table(bar$or_mychisq>1&bar$signif_fdr) # sen and res ~ OR
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str(bar)
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sen = bar[bar$or_mychisq<1,]
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sen = na.omit(sen)
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@ -162,7 +160,9 @@ if (nrow(bar_or) == nrow(sen1) + nrow(res1) ){
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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("\nPercentage of muts with OR>1 i.e resistant:"
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cat("Number of R muts with OR>1:", nrow(res1)
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, "\nPercentage of muts with OR>1 i.e resistant:"
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, pc_orR *100 )
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# muts with highest OR
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@ -171,22 +171,23 @@ 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$ligand_distance
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, bar_or$interface_dist
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, bar_or$nca_dist
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#, bar_or$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$drug_site)
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bar_or$dsl_site = ifelse(bar_or$position%in%aa_pos_dsl, "dsl", "no")
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bar_or$rna_site = ifelse(bar_or$position%in%aa_pos_rna, "rna", "no")
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table(bar_or$dsl_site)
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bar_or$ca_site = ifelse(bar_or$position%in%aa_pos_ca, "ca", "no")
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bar_or$sam_site = ifelse(bar_or$position%in%aa_pos_sam, "sam", "no")
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table(bar_or$ca_site)
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bar_or$cdl_site = ifelse(bar_or$position%in%aa_pos_cdl, "cdl", "no")
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bar_or$amp_site = ifelse(bar_or$position%in%aa_pos_amp, "amp", "no")
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table(bar_or$cdl_site)
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top10_or = bar_or[1:10,]
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# are these active sites
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@ -285,6 +285,7 @@ if (identical(colnames(mut_h_avs_dd), colnames(mut_h_avs_ss)) ){
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#-------------------
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# Filtered columns
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# most DD/SS: ligand
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# FIXME DUBIOUS as min and max can be both negative
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#-------------------
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df3_effects_lig = df3_effects[df3_effects[[LigDist_colname]]<DistCutOff,]
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nrow(df3_effects_lig)
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@ -296,7 +297,7 @@ if (identical(colnames(mut_h_lig_dd), colnames(mut_h_lig_ss)) ){
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# add cols
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mut_h_lig_dd$mutational_effect = "Most Destabilising for Ligand affinity"
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mut_h_lig_ss$mutational_effect = "Most Stabilising for Ligand affinity"
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mut_h_lig_ss$mutational_effect = "CAUTION: Most DE/Stabilising for Ligand affinity"
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cat("\nPass: avg ligand affinity")
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}else{
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@ -415,6 +416,20 @@ if ( length(colnames(combined_table)) == length(colsNames_combined_table) ) {
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stop("\nAbort: No. of cols mismatch. Cannot assign pretty colnames for output")
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}
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nrow(combined_table)
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combined_table$drug_site = ifelse(combined_table$position%in%aa_pos_drug, "drug", "no")
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table(combined_table$drug_site)
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combined_table$rna_site = ifelse(combined_table$position%in%aa_pos_rna, "rna", "no")
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table(combined_table$rna_site)
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combined_table$sam_site = ifelse(combined_table$position%in%aa_pos_sam, "sam", "no")
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table(combined_table$sam_site)
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combined_table$amp_site = ifelse(combined_table$position%in%aa_pos_amp, "amp", "no")
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table(combined_table$amp_site)
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#--------------------
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# write output file: KS test within grpup
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#----------------------
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