rearranged corr plot cols and also added example for ggpairs
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parent
fdb3f00503
commit
b302daaa60
7 changed files with 227 additions and 681 deletions
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@ -8,6 +8,7 @@ source("~/git/LSHTM_analysis/config/embb.R")
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# get plottting dfs
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source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
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####################################################
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#=======
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# output
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@ -23,55 +24,126 @@ corr_plotdf = corr_data_extract(merged_df3
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, drug = drug
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, extract_scaled_cols = F)
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colnames(corr_plotdf)
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colnames(corr_df_m3_f)
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corr_plotdf = corr_df_m3_f #for downstream code
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if (all(colnames(corr_df_m3_f) == colnames(corr_plotdf))){
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cat("PASS: corr plot colnames match for dashboard")
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}else{
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stop("Abort: corr plot colnames DO NOT match for dashboard")
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}
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#corr_plotdf = corr_df_m3_f #for downstream code
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aff_dist_cols = colnames(corr_plotdf)[grep("Dist", colnames(corr_plotdf))]
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aff_dist_cols
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static_cols = c("Log(MAF)"
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, "Log(OR)"
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#, "-Log(P)"
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)
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#================
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# stability
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#================
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corr_ps_colnames = c("DUET"
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#affinity_dist_colnames# lIg DIst and ppi Di
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corr_ps_colnames = c(static_cols
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, "DUET"
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, "FoldX"
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, "DeepDDG"
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, "Dynamut2"
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, "MAF"
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, "Log(OR)"
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, "-Log(P)"
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#, "ligand_distance"
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, "dst_mode"
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, drug)
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, aff_dist_cols
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, "dst_mode")
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corr_ps_colnames%in%colnames(corr_plotdf)
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if (all(corr_ps_colnames%in%colnames(corr_plotdf))){
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cat("PASS: all colnames exist for correlation")
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}else{
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stop("Abort: all colnames DO NOT exist for correlation")
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}
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corr_df_ps = corr_plotdf[, corr_ps_colnames]
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complete_obs_ps = nrow(corr_df_ps) - sum(is.na(corr_df_ps$`Log(OR)`))
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cat("\nComplete muts for Conservation for", gene, ":", complete_obs_ps)
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color_coln = which(colnames(corr_df_ps) == "dst_mode")
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end = which(colnames(corr_df_ps) == drug)
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ncol_omit = 2
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corr_end = end-ncol_omit
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#end = which(colnames(corr_df_ps) == drug)
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#ncol_omit = 2
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#corr_end = end-ncol_omit
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corr_end = color_coln-1
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#------------------------
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# Output: stability corrP
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#------------------------
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corr_psP = paste0(outdir_images
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,tolower(gene)
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,"_corr_stability.svg" )
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,tolower(gene)
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,"_corr_stability.svg" )
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cat("Corr plot stability with coloured dots:", corr_psP)
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svg(corr_psP, width = 15, height = 15)
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my_corr_pairs(corr_data_all = corr_df_ps
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, corr_cols = colnames(corr_df_ps[1:corr_end])
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, corr_method = "spearman"
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, colour_categ_col = colnames(corr_df_ps[color_coln]) #"dst_mode"
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, categ_colour = c("red", "blue")
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, density_show = F
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, hist_col = "coral4"
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, dot_size = 1.6
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, ats = 1.5
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, corr_lab_size = 3
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, corr_value_size = 1)
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, corr_cols = colnames(corr_df_ps[1:corr_end])
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, corr_method = "spearman"
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, colour_categ_col = colnames(corr_df_ps[color_coln]) #"dst_mode"
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, categ_colour = c("red", "blue")
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, density_show = F
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, hist_col = "coral4"
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, dot_size = 1.6
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, ats = 1.5
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, corr_lab_size = 3
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, corr_value_size = 1)
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dev.off()
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#===============
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# CONSERVATION
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#==============
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corr_conservation_cols = c( static_cols
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, "ConSurf"
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, "SNAP2"
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, "PROVEAN"
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, aff_dist_cols
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, "dst_mode"
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, drug)
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if (all(corr_conservation_cols%in%colnames(corr_plotdf))){
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cat("PASS: all colnames exist for ConSurf-correlation")
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}else{
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stop("Abort: all colnames DO NOT exist for ConSurf-correlation")
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}
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corr_df_cons = corr_plotdf[, corr_conservation_cols]
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complete_obs_cons = nrow(corr_df_cons) - sum(is.na(corr_df_cons$`Log(OR)`))
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cat("\nComplete muts for Conservation for", gene, ":", complete_obs_cons)
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color_coln = which(colnames(corr_df_cons) == "dst_mode")
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# end = which(colnames(corr_df_cons) == drug)
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# ncol_omit = 2
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# corr_end = end-ncol_omit
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corr_end = color_coln-1
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#---------------------------
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# Output: Conservation corrP
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#----------------------------
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corr_consP = paste0(outdir_images
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,tolower(gene)
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,"_corr_conservation.svg" )
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cat("Corr plot conservation coloured dots:", corr_consP)
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svg(corr_consP, width = 10, height = 10)
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my_corr_pairs(corr_data_all = corr_df_cons
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, corr_cols = colnames(corr_df_cons[1:corr_end])
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, corr_method = "spearman"
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, colour_categ_col = colnames(corr_df_cons[color_coln]) #"dst_mode"
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, categ_colour = c("red", "blue")
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, density_show = F
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, hist_col = "coral4"
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, dot_size =1.1
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, ats = 1.5
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, corr_lab_size = 2.15
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, corr_value_size = 1)
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dev.off()
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#####################################################
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#DistCutOff = 10
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#LigDist_colname # = "ligand_distance" # from globals
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@ -82,31 +154,36 @@ dev.off()
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#================
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# ligand affinity
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#================
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corr_lig_colnames = c("mCSM-lig"
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, "MAF"
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, "Log(OR)"
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, "-Log(P)"
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, "Lig-Dist"
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, "dst_mode"
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, drug)
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corr_df_lig = corr_plotdf[corr_plotdf["Lig-Dist"]<DistCutOff,]
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corr_lig_colnames = c(static_cols
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, "mCSM-lig"
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, "mmCSM-lig"
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, "dst_mode")
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#, drug)
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if (all(corr_lig_colnames%in%colnames(corr_plotdf))){
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cat("PASS: all colnames exist for Lig-correlation")
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}else{
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stop("Abort: all colnames DO NOT exist for Lig-correlation")
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}
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corr_lig_colnames%in%colnames(corr_plotdf)
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corr_df_lig = corr_plotdf[, corr_lig_colnames]
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corr_df_lig = corr_df_lig[corr_df_lig["Lig-Dist"]<DistCutOff,]
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complete_obs_lig = nrow(corr_df_lig) - sum(is.na(corr_df_lig$`Log(OR)`))
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cat("\nComplete muts for lig affinity for", gene, ":", complete_obs_lig)
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color_coln = which(colnames(corr_df_lig) == "dst_mode")
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end = which(colnames(corr_df_lig) == drug)
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ncol_omit = 3 #omit dist col
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corr_end = end-ncol_omit
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# end = which(colnames(corr_df_lig) == drug)
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# ncol_omit = 2
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# corr_end = end-ncol_omit
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corr_end = color_coln-1
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#------------------------
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# Output: ligand corrP
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#------------------------
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corr_ligP = paste0(outdir_images
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,tolower(gene)
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,"_corr_lig.svg" )
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,tolower(gene)
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,"_corr_lig.svg" )
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cat("Corr plot affinity with coloured dots:", corr_ligP)
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svg(corr_ligP, width = 10, height = 10)
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@ -127,32 +204,38 @@ dev.off()
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#================
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# ppi2 affinity
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#================
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if (tolower(gene)%in%geneL_ppi2){
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corr_ppi2_colnames = c("mCSM-PPI2"
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, "MAF"
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, "Log(OR)"
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, "-Log(P)"
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, "PPI-Dist" # "interface_dist"
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corr_df_ppi2 = corr_plotdf[corr_plotdf["PPI-Dist"]<DistCutOff,]
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corr_ppi2_colnames = c(static_cols
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, "mCSM-PPI2"
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, "dst_mode"
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, drug)
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corr_ppi2_colnames%in%colnames(corr_plotdf)
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if (all(corr_ppi2_colnames%in%colnames(corr_plotdf))){
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cat("PASS: all colnames exist for mcsm-ppi2 correlation")
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}else{
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stop("Abort: all colnames DO NOT exist for mcsm-ppi2 correlation")
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}
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corr_df_ppi2 = corr_plotdf[, corr_ppi2_colnames]
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corr_df_ppi2 = corr_df_ppi2[corr_df_ppi2["PPI-Dist"]<DistCutOff,]
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complete_obs_ppi2 = nrow(corr_df_ppi2) - sum(is.na(corr_df_ppi2$`Log(OR)`))
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cat("\nComplete muts for ppi2 affinity for", gene, ":", complete_obs_ppi2)
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color_coln = which(colnames(corr_df_ppi2) == "dst_mode")
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end = which(colnames(corr_df_ppi2) == drug)
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ncol_omit = 3 #omit dist col
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corr_end = end-ncol_omit
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# end = which(colnames(corr_df_ppi2) == drug)
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# ncol_omit = 2
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# corr_end = end-ncol_omit
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corr_end = color_coln-1
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#------------------------
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# Output: ppi2 corrP
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#------------------------
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corr_ppi2P = paste0(outdir_images
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,tolower(gene)
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,"_corr_ppi2.svg" )
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,tolower(gene)
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,"_corr_ppi2.svg" )
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cat("Corr plot ppi2 with coloured dots:", corr_ppi2P)
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svg(corr_ppi2P, width = 10, height = 10)
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@ -180,25 +263,29 @@ if (tolower(gene)%in%geneL_ppi2){
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# NA affinity
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#================
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if (tolower(gene)%in%geneL_na){
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corr_na_colnames = c("mCSM-NA"
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, "MAF"
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, "Log(OR)"
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, "-Log(P)"
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, "NA-Dist" # "NA_dist"
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corr_df_na = corr_df_na[corr_df_na["NA-Dist"]<DistCutOff,]
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corr_na_colnames = c(static_cols
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, "mCSM-NA"
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, "dst_mode"
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, drug)
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if (all(corr_na_colnames%in%colnames(corr_plotdf))){
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cat("PASS: all colnames exist for mcsm-NA-correlation")
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}else{
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stop("Abort: all colnames DO NOT exist for mcsm-NA-correlation")
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}
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corr_na_colnames%in%colnames(corr_plotdf)
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corr_df_na = corr_plotdf[, corr_na_colnames]
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corr_df_na = corr_df_na[corr_df_na["NA-Dist"]<DistCutOff,]
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complete_obs_na = nrow(corr_df_na) - sum(is.na(corr_df_na$`Log(OR)`))
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cat("\nComplete muts for NA affinity for", gene, ":", complete_obs_na)
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color_coln = which(colnames(corr_df_na) == "dst_mode")
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end = which(colnames(corr_df_na) == drug)
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ncol_omit = 3 #omit dist col
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corr_end = end-ncol_omit
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# end = which(colnames(corr_df_na) == drug)
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# ncol_omit = 2
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# corr_end = end-ncol_omit
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corr_end = color_coln-1
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#------------------------
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# Output: mCSM-NA corrP
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@ -224,51 +311,21 @@ if (tolower(gene)%in%geneL_na){
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dev.off()
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}
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####################################################
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# CONSERVATION
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corr_conservation_cols = c("ConSurf"
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, "SNAP2"
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, "PROVEAN"
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, "MAF"
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, "Log(OR)"
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, "-Log(P)"
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, "dst_mode"
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, drug)
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#===============
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#ggpairs:
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#================
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#corr_df_ps$dst_mode = ifelse(corr_df_cons$dst_mode=="1", "R", "S")
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colnames(corr_plotdf)
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corr_conservation_cols%in%colnames(corr_plotdf)
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corr_df_cons = corr_plotdf[, corr_conservation_cols]
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complete_obs_cons = nrow(corr_df_cons) - sum(is.na(corr_df_cons$`Log(OR)`))
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cat("\nComplete muts for Conservation for", gene, ":", complete_obs_cons)
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svg('/tmp/foo.svg', width=10, height=10, )
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color_coln = which(colnames(corr_df_cons) == "dst_mode")
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end = which(colnames(corr_df_cons) == drug)
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ncol_omit = 2
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corr_end = end-ncol_omit
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ggpairs(corr_df_ps, columns = 1:(ncol(corr_df_ps)-corr_end)
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, upper = list(continuous = wrap('cor', method = "spearman"))
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, aes(colour = factor(dst_mode), alpha = 0.5)
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, title="correlogram with ggpairs()") +
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scale_colour_manual(values = c("red", "blue")) +
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scale_fill_manual(values = c("red", "blue"))
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#---------------------------
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# Output: Conservation corrP
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#----------------------------
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corr_consP = paste0(outdir_images
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,tolower(gene)
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,"_corr_conservation.svg" )
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cat("Corr plot conservation coloured dots:", corr_consP)
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svg(corr_consP, width = 10, height = 10)
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my_corr_pairs(corr_data_all = corr_df_cons
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, corr_cols = colnames(corr_df_cons[1:corr_end])
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, corr_method = "spearman"
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, colour_categ_col = colnames(corr_df_cons[color_coln]) #"dst_mode"
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, categ_colour = c("red", "blue")
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, density_show = F
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, hist_col = "coral4"
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, dot_size =1.1
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, ats = 1.5
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, corr_lab_size = 2.5
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, corr_value_size = 1)
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dev.off()
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@ -9,6 +9,7 @@ source("~/git/LSHTM_analysis/config/embb.R")
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# get plottting dfs
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source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
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#=======
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# output
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#=======
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