From b2e035d9bc93a7e8c4ba84cc29b840c05cf7a70f Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Mon, 31 Jan 2022 17:52:29 +0000 Subject: [PATCH] moved old dm_om_data_nf to redundant/ --- scripts/plotting/redundant/dm_om_data_nf.R | 416 +++++++++++++++++++++ 1 file changed, 416 insertions(+) create mode 100644 scripts/plotting/redundant/dm_om_data_nf.R diff --git a/scripts/plotting/redundant/dm_om_data_nf.R b/scripts/plotting/redundant/dm_om_data_nf.R new file mode 100644 index 0000000..4bd82e7 --- /dev/null +++ b/scripts/plotting/redundant/dm_om_data_nf.R @@ -0,0 +1,416 @@ +#!/usr/bin/env Rscript +######################################################### +# TASK: Script to format data for dm om plots: +# generating LF data +# sourced by get_plotting_dfs.R +######################################################### +##======================================================================== +# cols to select: +# THINK: whu + +comb_df <- merged_df3[, c("mutationinformation", "mutation" + , "mutation_info","mutation_info_labels" + , "position" + , LigDist_colname + , "duet_stability_change", "duet_scaled", "duet_outcome" + , "ligand_affinity_change", "affinity_scaled", "ligand_outcome" + , "ddg_foldx", "foldx_scaled", "foldx_outcome" + , "deepddg", "deepddg_scaled", "deepddg_outcome" + , "asa", "rsa" + , "rd_values", "kd_values" + , "log10_or_mychisq", "neglog_pval_fisher", "af" + , "mcsm_na_affinity", "mcsm_na_scaled", "mcsm_na_outcome" + , "ddg_dynamut", "ddg_dynamut_scaled","ddg_dynamut_outcome" + , "ddg_encom", "ddg_encom_scaled", "ddg_encom_outcome" + , "dds_encom", "dds_encom_scaled", "dds_encom_outcome" + , "ddg_mcsm", "ddg_mcsm_scaled", "ddg_mcsm_outcome" + , "ddg_sdm", "ddg_sdm_scaled", "ddg_sdm_outcome" + , "ddg_duet", "ddg_duet_scaled", "ddg_duet_outcome" + , "ddg_dynamut2","ddg_dynamut2_scaled", "ddg_dynamut2_outcome")] + + +comb_df_s = arrange(comb_df, position) + +#======================================================================= +fact_cols = colnames(comb_df_s)[grepl( "_outcome|_info", colnames(comb_df_s) )] +fact_cols +lapply(comb_df_s[, fact_cols], class) +comb_df_s[, fact_cols] <- lapply(comb_df_s[, fact_cols], as.factor) + +if (any(lapply(comb_df_s[, fact_cols], class) == "character")){ + cat("\nChanging cols to factor") + comb_df_s[, fact_cols] <- lapply(comb_df_s[, fact_cols],as.factor) + if (all(lapply(comb_df_s[, fact_cols], class) == "factor")){ + cat("\nSuccessful: cols changed to factor") + } +} +lapply(comb_df_s[, fact_cols], class) + +#======================================================================= +table(comb_df_s$mutation_info) + + # further checks to make sure dr and other muts are indeed unique +dr_muts = comb_df_s[comb_df_s$mutation_info == dr_muts_col,] +dr_muts_names = unique(dr_muts$mutation) + +other_muts = comb_df_s[comb_df_s$mutation_info == other_muts_col,] +other_muts_names = unique(other_muts$mutation) + +if ( table(dr_muts_names%in%other_muts_names)[[1]] == length(dr_muts_names) && + table(other_muts_names%in%dr_muts_names)[[1]] == length(other_muts_names) ){ + cat("PASS: dr and other muts are indeed unique") +}else{ + cat("FAIL: dr and others muts are NOT unique!") + quit() +} + +# pretty display names i.e. labels to reduce major code duplication later +foo_cnames = data.frame(colnames(comb_df_s)) +names(foo_cnames) <- "old_name" + +stability_suffix <- paste0(delta_symbol, delta_symbol, "G") +flexibility_suffix <- paste0(delta_symbol, delta_symbol, "S") + +lig_dn = paste0("Ligand distance (", angstroms_symbol, ")"); lig_dn +duet_dn = paste0("DUET ", stability_suffix); duet_dn +foldx_dn = paste0("FoldX ", stability_suffix); foldx_dn +deepddg_dn = paste0("Deepddg " , stability_suffix); deepddg_dn +mcsm_na_dn = paste0("mCSM-NA affinity ", stability_suffix); mcsm_na_dn +dynamut_dn = paste0("Dynamut ", stability_suffix); dynamut_dn +dynamut2_dn = paste0("Dynamut2 " , stability_suffix); dynamut2_dn +encom_ddg_dn = paste0("EnCOM " , stability_suffix); encom_ddg_dn +encom_dds_dn = paste0("EnCOM " , flexibility_suffix ); encom_dds_dn +sdm_dn = paste0("SDM " , stability_suffix); sdm_dn +mcsm_dn = paste0("mCSM " , stability_suffix ); mcsm_dn + +# Change colnames of some columns using datatable +comb_df_sl = comb_df_s +names(comb_df_sl) + +setnames(comb_df_sl + , old = c("asa", "rsa", "rd_values", "kd_values" + , "log10_or_mychisq", "neglog_pval_fisher", "af" + , LigDist_colname + , "duet_scaled" + , "foldx_scaled" + , "deepddg_scaled" + , "mcsm_na_scaled" + , "ddg_dynamut_scaled" + , "ddg_dynamut2_scaled" + , "ddg_encom_scaled" + , "dds_encom_scaled" + , "ddg_sdm" + , "ddg_mcsm") + + , new = c("ASA", "RSA", "RD", "KD" + , "Log10 (OR)", "-Log (P)", "MAF" + , lig_dn + , duet_dn + , foldx_dn + , deepddg_dn + , mcsm_na_dn + , dynamut_dn + , dynamut2_dn + , encom_ddg_dn + , encom_dds_dn + , sdm_dn + , mcsm_dn) + ) + +foo_cnames <- cbind(foo_cnames, colnames(comb_df_sl)) + +# some more pretty labels +table(comb_df_sl$mutation_info) + +levels(comb_df_sl$mutation_info)[levels(comb_df_sl$mutation_info)==dr_muts_col] <- "DM" +levels(comb_df_sl$mutation_info)[levels(comb_df_sl$mutation_info)==other_muts_col] <- "OM" + +table(comb_df_sl$mutation_info) + +####################################################################### +#====================== +# Selecting dfs +# with appropriate cols +#======================= +static_cols_start = c("mutationinformation" + , "position" + , "mutation" + , "mutation_info") + +static_cols_end = c(lig_dn + , "ASA" + , "RSA" + , "RD" + , "KD") + +# ordering is important! + +######################################################################### +#============== +# DUET: LF +#============== +cols_to_select_duet = c(static_cols_start, c("duet_outcome", duet_dn), static_cols_end) +wf_duet = comb_df_sl[, cols_to_select_duet] + +#pivot_cols_ps = cols_to_select_ps[1:5]; pivot_cols_ps +pivot_cols_duet = cols_to_select_duet[1: (length(static_cols_start) + 1)]; pivot_cols_duet + +expected_rows_lf = nrow(wf_duet) * (length(wf_duet) - length(pivot_cols_duet)) +expected_rows_lf + +# LF data: duet +lf_duet = gather(wf_duet + , key = param_type + , value = param_value + , all_of(duet_dn):tail(static_cols_end,1) + , factor_key = TRUE) + +if (nrow(lf_duet) == expected_rows_lf){ + cat("\nPASS: long format data created for ", duet_dn) +}else{ + cat("\nFAIL: long format data could not be created for duet") + quit() +} + +############################################################################ +#============== +# FoldX: LF +#============== +cols_to_select_foldx= c(static_cols_start, c("foldx_outcome", foldx_dn), static_cols_end) +wf_foldx = comb_df_sl[, cols_to_select_foldx] + +pivot_cols_foldx = cols_to_select_foldx[1: (length(static_cols_start) + 1)]; pivot_cols_foldx + +expected_rows_lf = nrow(wf_foldx) * (length(wf_foldx) - length(pivot_cols_foldx)) +expected_rows_lf + +# LF data: Foldx +lf_foldx <<- gather(wf_foldx + , key = param_type + , value = param_value + , all_of(foldx_dn):tail(static_cols_end,1) + , factor_key = TRUE) + +if (nrow(lf_foldx) == expected_rows_lf){ + cat("\nPASS: long format data created for ", foldx_dn) +}else{ + cat("\nFAIL: long format data could not be created for duet") + quit() +} + +############################################################################ +#============== +# Deepddg: LF +#============== +cols_to_select_deepddg = c(static_cols_start, c("deepddg_outcome", deepddg_dn), static_cols_end) +wf_deepddg = comb_df_sl[, cols_to_select_deepddg] + +pivot_cols_deepddg = cols_to_select_deepddg[1: (length(static_cols_start) + 1)]; pivot_cols_deepddg + +expected_rows_lf = nrow(wf_deepddg) * (length(wf_deepddg) - length(pivot_cols_deepddg)) +expected_rows_lf + +# LF data: Deepddg +lf_deepddg = gather(wf_deepddg + , key = param_type + , value = param_value + , all_of(deepddg_dn):tail(static_cols_end,1) + , factor_key = TRUE) + +if (nrow(lf_deepddg) == expected_rows_lf){ + cat("\nPASS: long format data created for ", deepddg_dn) +}else{ + cat("\nFAIL: long format data could not be created for duet") + quit() +} + +############################################################################ +#============== +# mCSM-NA: LF +#============== +cols_to_select_mcsm_na = c(static_cols_start, c("mcsm_na_outcome", mcsm_na_dn), static_cols_end) +wf_mcsm_na = comb_df_sl[, cols_to_select_mcsm_na] + +pivot_cols_mcsm_na = cols_to_select_mcsm_na[1: (length(static_cols_start) + 1)]; pivot_cols_mcsm_na + +expected_rows_lf = nrow(wf_mcsm_na) * (length(wf_mcsm_na) - length(pivot_cols_mcsm_na)) +expected_rows_lf + +# LF data: mcsm_na +lf_mcsm_na = gather(wf_mcsm_na + , key = param_type + , value = param_value + , all_of(mcsm_na_dn):tail(static_cols_end,1) + , factor_key = TRUE) + +if (nrow(lf_mcsm_na) == expected_rows_lf){ + cat("\nPASS: long format data created for ", mcsm_na_dn) +}else{ + cat("\nFAIL: long format data could not be created for duet") + quit() +} + +############################################################################ +#============== +# Dynamut: LF +#============== +cols_to_select_dynamut = c(static_cols_start, c("ddg_dynamut_outcome", dynamut_dn), static_cols_end) +wf_dynamut = comb_df_sl[, cols_to_select_dynamut] + +pivot_cols_dynamut = cols_to_select_dynamut[1: (length(static_cols_start) + 1)]; pivot_cols_dynamut + +expected_rows_lf = nrow(wf_dynamut) * (length(wf_dynamut) - length(pivot_cols_dynamut)) +expected_rows_lf + +# LF data: dynamut +lf_dynamut = gather(wf_dynamut + , key = param_type + , value = param_value + , all_of(dynamut_dn):tail(static_cols_end,1) + , factor_key = TRUE) + +if (nrow(lf_dynamut) == expected_rows_lf){ + cat("\nPASS: long format data created for ", dynamut_dn) +}else{ + cat("\nFAIL: long format data could not be created for duet") + quit() +} + +############################################################################ +#============== +# Dynamut2: LF +#============== +cols_to_select_dynamut2 = c(static_cols_start, c("ddg_dynamut2_outcome", dynamut2_dn), static_cols_end) + +wf_dynamut2 = comb_df_sl[, cols_to_select_dynamut2] + +pivot_cols_dynamut2 = cols_to_select_dynamut2[1: (length(static_cols_start) + 1)]; pivot_cols_dynamut2 + +expected_rows_lf = nrow(wf_dynamut2) * (length(wf_dynamut2) - length(pivot_cols_dynamut2)) +expected_rows_lf + +# LF data: dynamut2 +lf_dynamut2 = gather(wf_dynamut2 + , key = param_type + , value = param_value + , all_of(dynamut2_dn):tail(static_cols_end,1) + , factor_key = TRUE) + +if (nrow(lf_dynamut2) == expected_rows_lf){ + cat("\nPASS: long format data created for ", dynamut2_dn) +}else{ + cat("\nFAIL: long format data could not be created for duet") + quit() +} + +############################################################################ +#============== +# EnCOM ddg: LF +#============== +cols_to_select_encomddg = c(static_cols_start, c("ddg_encom_outcome", encom_ddg_dn), static_cols_end) +wf_encomddg = comb_df_sl[, cols_to_select_encomddg] + +pivot_cols_encomddg = cols_to_select_encomddg[1: (length(static_cols_start) + 1)]; pivot_cols_encomddg + +expected_rows_lf = nrow(wf_encomddg ) * (length(wf_encomddg ) - length(pivot_cols_encomddg)) +expected_rows_lf + +# LF data: encomddg +lf_encomddg = gather(wf_encomddg + , key = param_type + , value = param_value + , all_of(encom_ddg_dn):tail(static_cols_end,1) + , factor_key = TRUE) + +if (nrow(lf_encomddg) == expected_rows_lf){ + cat("\nPASS: long format data created for ", encom_ddg_dn) +}else{ + cat("\nFAIL: long format data could not be created for duet") + quit() +} +############################################################################ +#============== +# EnCOM dds: LF +#============== +cols_to_select_encomdds = c(static_cols_start, c("dds_encom_outcome", encom_dds_dn), static_cols_end) +wf_encomdds = comb_df_sl[, cols_to_select_encomdds] + +pivot_cols_encomdds = cols_to_select_encomdds[1: (length(static_cols_start) + 1)]; pivot_cols_encomdds + +expected_rows_lf = nrow(wf_encomdds) * (length(wf_encomdds) - length(pivot_cols_encomdds)) +expected_rows_lf + +# LF data: encomdds +lf_encomdds = gather(wf_encomdds + , key = param_type + , value = param_value + , all_of(encom_dds_dn):tail(static_cols_end,1) + , factor_key = TRUE) + +if (nrow(lf_encomdds) == expected_rows_lf){ + cat("\nPASS: long format data created for", encom_dds_dn) +}else{ + cat("\nFAIL: long format data could not be created for duet") + quit() +} + +############################################################################ +#============== +# SDM: LF +#============== +cols_to_select_sdm = c(static_cols_start, c("ddg_sdm_outcome", sdm_dn), static_cols_end) +wf_sdm = comb_df_sl[, cols_to_select_sdm] + +pivot_cols_sdm = cols_to_select_sdm[1: (length(static_cols_start) + 1)]; pivot_cols_sdm + +expected_rows_lf = nrow(wf_sdm) * (length(wf_sdm) - length(pivot_cols_sdm)) +expected_rows_lf + +# LF data: sdm +lf_sdm = gather(wf_sdm + , key = param_type + , value = param_value + , all_of(sdm_dn):tail(static_cols_end,1) + , factor_key = TRUE) + +if (nrow(lf_sdm) == expected_rows_lf){ + cat("\nPASS: long format data created for", sdm_dn) +}else{ + cat("\nFAIL: long format data could not be created for duet") + quit() +} + +############################################################################ +#============== +# mCSM: LF +#============== +cols_to_select_mcsm = c(static_cols_start, c("ddg_mcsm_outcome", mcsm_dn), static_cols_end) +wf_mcsm = comb_df_sl[, cols_to_select_mcsm] + +pivot_cols_mcsm = cols_to_select_mcsm[1: (length(static_cols_start) + 1)]; pivot_cols_mcsm + +expected_rows_lf = nrow(wf_mcsm) * (length(wf_mcsm) - length(pivot_cols_mcsm)) +expected_rows_lf + +# LF data: mcsm +lf_mcsm = gather(wf_mcsm + , key = param_type + , value = param_value + , all_of(mcsm_dn):tail(static_cols_end,1) + , factor_key = TRUE) + +if (nrow(lf_mcsm) == expected_rows_lf){ + cat("\nPASS: long format data created for", mcsm_dn) +}else{ + cat("\nFAIL: long format data could not be created for duet") + quit() +} + +#========================== +# Duet-d(from Dynamut): LF +#=========================== + +#Not created, redundant and chaos! + +############################################################################ +