diff --git a/scripts/plotting/dm_om_data.R b/scripts/plotting/dm_om_data.R index 4bd82e7..97e5e7a 100644 --- a/scripts/plotting/dm_om_data.R +++ b/scripts/plotting/dm_om_data.R @@ -1,416 +1,62 @@ #!/usr/bin/env Rscript ######################################################### # TASK: Script to format data for dm om plots: -# generating LF data +# generating WF LF data # sourced by get_plotting_dfs.R +# calls my function: dm_om_wf_lf_data() ######################################################### -##======================================================================== -# cols to select: -# THINK: whu + #geneL_normal = c("pnca") + #geneL_na_dy = c("gid") + geneL_na = c("gid", "rpob") + geneL_dy = c("gid") + geneL_ppi2 = c("alr", "embb", "katg", "rpob") + +all_dm_om_df = dm_om_wf_lf_data(df = merged_df3, gene_name = gene) -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")] - +wf_duet = all_dm_om_df[['wf_duet']] +lf_duet = all_dm_om_df[['lf_duet']] -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) +wf_mcsm_lig = all_dm_om_df[['wf_mcsm_lig']] +lf_mcsm_lig = all_dm_om_df[['lf_mcsm_lig']] -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) +wf_foldx = all_dm_om_df[['wf_foldx']] +lf_foldx = all_dm_om_df[['lf_foldx']] -#======================================================================= -table(comb_df_s$mutation_info) +wf_deepddg = all_dm_om_df[['wf_deepddg']] +lf_deepddg = all_dm_om_df[['lf_deepddg']] - # further checks to make sure dr and other muts are indeed unique -dr_muts = comb_df_s[comb_df_s$mutation_info == dr_muts_col,] -dr_muts_names = unique(dr_muts$mutation) +wf_dynamut2 = all_dm_om_df[['wf_dynamut2']] +lf_dynamut2 = all_dm_om_df[['lf_dynamut2']] -other_muts = comb_df_s[comb_df_s$mutation_info == other_muts_col,] -other_muts_names = unique(other_muts$mutation) +wf_consurf = all_dm_om_df[['wf_consurf']] +lf_consurf = all_dm_om_df[['lf_consurf']] -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() +wf_snap2 = all_dm_om_df[['wf_snap2']] +lf_snap2 = all_dm_om_df[['lf_snap2']] + +if (tolower(gene)%in%geneL_na){ +wf_mcsm_na = all_dm_om_df[['wf_mcsm_na']] +lf_mcsm_na = all_dm_om_df[['lf_mcsm_na']] } -# 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() +if (tolower(gene)%in%geneL_ppi2){ +wf_mcsm_ppi2 = all_dm_om_df[['wf_mcsm_ppi2']] +lf_mcsm_ppi2 = all_dm_om_df[['lf_mcsm_ppi2']] } -############################################################################ -#============== -# 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] +if (tolower(gene)%in%geneL_dy){ +wf_dynamut = all_dm_om_df[['wf_dynamut']] +lf_dynamut = all_dm_om_df[['lf_dynamut']] -pivot_cols_foldx = cols_to_select_foldx[1: (length(static_cols_start) + 1)]; pivot_cols_foldx +wf_encomddg = all_dm_om_df[['wf_encomddg']] +lf_encomddg = all_dm_om_df[['lf_encomddg']] -expected_rows_lf = nrow(wf_foldx) * (length(wf_foldx) - length(pivot_cols_foldx)) -expected_rows_lf +wf_encomdds = all_dm_om_df[['wf_encomdds']] +lf_encomdds = all_dm_om_df[['lf_encomdds']] -# 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) +wf_sdm = all_dm_om_df[['wf_sdm']] +lf_sdm = all_dm_om_df[['lf_sdm']] -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() +wf_mcsm = all_dm_om_df[['wf_mcsm']] +lf_mcsm = all_dm_om_df[['lf_mcsm']] } - -############################################################################ -#============== -# 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! - -############################################################################ - diff --git a/scripts/plotting/get_plotting_dfs.R b/scripts/plotting/get_plotting_dfs.R index 9d7f395..01c21be 100644 --- a/scripts/plotting/get_plotting_dfs.R +++ b/scripts/plotting/get_plotting_dfs.R @@ -122,38 +122,31 @@ s1 = c("\nSuccessfully sourced logo_data_msa.R") cat(s1) #################################################################### -# Data for DM OM Plots: Long format dfs +# Data for DM OM Plots: WF and LF dfs +# My function: dm_om_wf_lf_data() #################################################################### #source("other_plots_data.R") - -# FIXME -#source(paste0(plot_script_path, "dm_om_data.R")) +# converted to a function +# moved old one to redundant. Added suffix to filename i.e. _nf(non-function) +source(paste0(plot_script_path, "dm_om_data.R")) -#s2 = c("\nSuccessfully sourced other_plots_data.R") -#cat(s2) +s2 = c("\nSuccessfully sourced other_plots_data.R") +cat(s2) #################################################################### # Data for Lineage barplots: WF and LF dfs #################################################################### -#source(paste0(plot_script_path, "lineage_data.R")) +source(paste0(plot_script_path, "lineage_data.R")) -#s3 = c("\nSuccessfully sourced lineage_data.R") -#cat(s3) +s3 = c("\nSuccessfully sourced lineage_data.R") +cat(s3) #################################################################### # Data for corr plots: +# My function: corr_data_extract() #################################################################### # make sure the above script works because merged_df2_combined is needed -#source(paste0(plot_script_path, "corr_data.R")) - -#s4 = c("\nSuccessfully sourced corr_data.R") -#cat(s4) - -# Moved "logo_data.R" to redundant/ -#----------------------------------------- -# Replaced above with my function -# corr_data_extract() corr_df_m3_f = corr_data_extract(merged_df3, extract_scaled_cols = F) head(corr_df_m3_f)