saving other_plots.R
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c9040cad21
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5 changed files with 227 additions and 241 deletions
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@ -33,7 +33,7 @@ my_max = max(df_ps[,n]); my_max
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df_ps$foldx_scaled = ifelse(df_ps[,n] < 0
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, df_ps[,n]/abs(my_min)
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, df_ps[,n]/my_max) #335, 15
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#sanity check
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# sanity check
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my_min = min(df_ps$foldx_scaled); my_min
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my_max = max(df_ps$foldx_scaled); my_max
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@ -50,7 +50,6 @@ if ( all(c1 == c2) ){
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exit()
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}
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# name tidying
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df_ps$mutation_info = as.factor(df_ps$mutation_info)
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df_ps$duet_outcome = as.factor(df_ps$duet_outcome)
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@ -60,6 +59,21 @@ df_ps$ligand_outcome = as.factor(df_ps$ligand_outcome)
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# check
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table(df_ps$mutation_info)
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# further checks to make sure dr and other muts are indeed unique
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dr_muts = df_ps[df_ps$mutation_info == dr_muts_col,]
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dr_muts_names = unique(dr_muts$mutation)
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other_muts = df_ps[df_ps$mutation_info == other_muts_col,]
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other_muts_names = unique(other_muts$mutation)
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if ( table(dr_muts_names%in%other_muts_names)[[1]] == length(dr_muts_names) &&
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table(other_muts_names%in%dr_muts_names)[[1]] == length(other_muts_names) ){
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cat("PASS: dr and other muts are indeed unique")
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}else{
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cat("FAIL: dr adn others muts are NOT unique!")
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quit()
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}
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#%%%%%%%%%%%%%%%%%%%
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# REASSIGNMENT: LIG
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#%%%%%%%%%%%%%%%%%%%%
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@ -133,78 +147,25 @@ levels(df_lf_ps$mutation_info)[levels(df_lf_ps$mutation_info)==other_muts_col] <
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levels(df_lf_ps$mutation_info); table(df_lf_ps$mutation_info)
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############################################################################
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#===========
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# Data: foldx
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#===========
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# keep similar dtypes cols together
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cols_to_select_foldx = c("mutationinformation", "mutation", "position", "mutation_info"
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, "foldx_outcome"
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, "foldx_scaled"
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, "ligand_distance"
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, "asa"
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, "rsa"
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, "rd_values"
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, "kd_values")
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df_wf_foldx = df_ps[, cols_to_select_foldx]
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pivot_cols_foldx = cols_to_select_foldx[1:5]; pivot_cols_foldx
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expected_rows_lf_foldx = nrow(df_wf_foldx) * (length(df_wf_foldx) - length(pivot_cols_foldx))
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expected_rows_lf_foldx
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# LF data: foldx
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df_lf_foldx = gather(df_wf_foldx, param_type, param_value, foldx_scaled:kd_values, factor_key=TRUE)
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if (nrow(df_lf_foldx) == expected_rows_lf_foldx){
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cat("PASS: long format data created for foldx")
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}else{
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cat("FAIL: long format data could not be created for foldx")
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exit()
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}
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# assign pretty labels: param type
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levels(df_lf_foldx$param_type); table(df_lf_foldx$param_type)
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levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="foldx_scaled"] <- "Foldx"
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levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="ligand_distance"] <- "Ligand Distance"
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levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="asa"] <- "ASA"
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levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="rsa"] <- "RSA"
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levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="rd_values"] <- "RD"
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levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="kd_values"] <- "KD"
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# check
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levels(df_lf_foldx$param_type); table(df_lf_foldx$param_type)
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# assign pretty labels: mutation_info
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levels(df_lf_foldx$mutation_info); table(df_lf_foldx$mutation_info)
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sum(table(df_lf_foldx$mutation_info)) == nrow(df_lf_foldx)
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levels(df_lf_foldx$mutation_info)[levels(df_lf_foldx$mutation_info)==dr_muts_col] <- "DM"
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levels(df_lf_foldx$mutation_info)[levels(df_lf_foldx$mutation_info)==other_muts_col] <- "OM"
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# check
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levels(df_lf_foldx$mutation_info); table(df_lf_foldx$mutation_info)
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############################################################################
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#===========
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# LF data: LIG
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#===========
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# keep similar dtypes cols together
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cols_to_select_lig = c("mutationinformation", "mutation", "position", "mutation_info"
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, "ligand_outcome"
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, "affinity_scaled"
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, "ligand_distance"
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, "asa"
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, "rsa"
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, "rd_values"
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, "kd_values")
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, "ligand_outcome"
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, "affinity_scaled"
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, "ligand_distance"
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, "asa"
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, "rsa"
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, "rd_values"
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, "kd_values")
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df_wf_lig = df_lig[, cols_to_select_lig]
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pivot_cols_lig = cols_to_select_lig[1:5]; pivot_cols_lig
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expected_rows_lf_lig = nrow(df_wf_lig) * (length(df_wf_lig) - length(pivot_cols_lig))
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expected_rows_lf_lig
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@ -239,7 +200,61 @@ levels(df_lf_lig$mutation_info)[levels(df_lf_lig$mutation_info)==other_muts_col]
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# check
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levels(df_lf_lig$mutation_info); table(df_lf_lig$mutation_info)
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###############################################################################
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#############################################################################
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#===========
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# Data: foldx
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#===========
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# keep similar dtypes cols together
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cols_to_select_foldx = c("mutationinformation", "mutation", "position", "mutation_info"
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, "foldx_outcome"
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, "foldx_scaled")
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#, "ligand_distance"
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#, "asa"
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#, "rsa"
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#, "rd_values"
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#, "kd_values")
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df_wf_foldx = df_ps[, cols_to_select_foldx]
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pivot_cols_foldx = cols_to_select_foldx[1:5]; pivot_cols_foldx
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expected_rows_lf_foldx = nrow(df_wf_foldx) * (length(df_wf_foldx) - length(pivot_cols_foldx))
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expected_rows_lf_foldx
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# LF data: foldx
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df_lf_foldx = gather(df_wf_foldx, param_type, param_value, foldx_scaled, factor_key=TRUE)
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if (nrow(df_lf_foldx) == expected_rows_lf_foldx){
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cat("PASS: long format data created for foldx")
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}else{
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cat("FAIL: long format data could not be created for foldx")
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exit()
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}
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# assign pretty labels: param type
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levels(df_lf_foldx$param_type); table(df_lf_foldx$param_type)
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levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="foldx_scaled"] <- "Foldx"
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#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="ligand_distance"] <- "Ligand Distance"
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#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="asa"] <- "ASA"
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#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="rsa"] <- "RSA"
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#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="rd_values"] <- "RD"
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#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="kd_values"] <- "KD"
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# check
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levels(df_lf_foldx$param_type); table(df_lf_foldx$param_type)
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# assign pretty labels: mutation_info
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levels(df_lf_foldx$mutation_info); table(df_lf_foldx$mutation_info)
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sum(table(df_lf_foldx$mutation_info)) == nrow(df_lf_foldx)
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levels(df_lf_foldx$mutation_info)[levels(df_lf_foldx$mutation_info)==dr_muts_col] <- "DM"
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levels(df_lf_foldx$mutation_info)[levels(df_lf_foldx$mutation_info)==other_muts_col] <- "OM"
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# check
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levels(df_lf_foldx$mutation_info); table(df_lf_foldx$mutation_info)
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############################################################################
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# clear excess variables
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rm(cols_to_select_ps, cols_to_select_foldx, cols_to_select_lig
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