Standardize output filenames

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -1295,9 +1295,9 @@ main <- function() {
         group_vars = c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor")
         )$df_with_stats
       reference_results <- calculate_interaction_scores(df_reference_stats, max_conc, bg_stats, group_vars = c("OrfRep", "Gene", "num"))
-      zscores_calculations_reference <- reference_results$calculations
-      zscores_interactions_reference <- reference_results$interactions
-      zscores_interactions_reference_joined <- reference_results$interactions_joined
+      zscore_calculations_reference <- reference_results$calculations
+      zscore_interactions_reference <- reference_results$interactions
+      zscore_interactions_reference_joined <- reference_results$interactions_joined
 
       message("Calculating deletion strain(s) interactions scores")
       df_deletion_stats <- calculate_summary_stats(
@@ -1306,97 +1306,97 @@ main <- function() {
         group_vars = c("OrfRep", "Gene", "conc_num", "conc_num_factor")
         )$df_with_stats
       deletion_results <- calculate_interaction_scores(df_deletion_stats, max_conc, bg_stats, group_vars = c("OrfRep"))
-      zscores_calculations <- deletion_results$calculations
-      zscores_interactions <- deletion_results$interactions
-      zscores_interactions_joined <- deletion_results$interactions_joined
+      zscore_calculations <- deletion_results$calculations
+      zscore_interactions <- deletion_results$interactions
+      zscore_interactions_joined <- deletion_results$interactions_joined
 
       # Writing Z-Scores to file
-      write.csv(zscores_calculations_reference, file = file.path(out_dir, "RF_ZScores_Calculations.csv"), row.names = FALSE)
-      write.csv(zscores_calculations, file = file.path(out_dir, "ZScores_Calculations.csv"), row.names = FALSE)
-      write.csv(zscores_interactions_reference, file = file.path(out_dir, "RF_ZScores_Interaction.csv"), row.names = FALSE)
-      write.csv(zscores_interactions, file = file.path(out_dir, "ZScores_Interaction.csv"), row.names = FALSE)
+      write.csv(zscore_calculations_reference, file = file.path(out_dir, "zscore_calculations_reference.csv"), row.names = FALSE)
+      write.csv(zscore_calculations, file = file.path(out_dir, "zscore_calculations.csv"), row.names = FALSE)
+      write.csv(zscore_interactions_reference, file = file.path(out_dir, "zscore_interactions_reference.csv"), row.names = FALSE)
+      write.csv(zscore_interactions, file = file.path(out_dir, "zscore_interactions.csv"), row.names = FALSE)
 
       # Create interaction plots
       message("Generating reference interaction plots")
-      reference_plot_configs <- generate_interaction_plot_configs(zscores_interactions_reference_joined, interaction_vars)
-      generate_and_save_plots(out_dir, "RF_interactionPlots", reference_plot_configs, grid_layout = list(ncol = 4, nrow = 3))
+      reference_plot_configs <- generate_interaction_plot_configs(zscore_interactions_reference_joined, interaction_vars)
+      generate_and_save_plots(out_dir, "interaction_plots_reference", reference_plot_configs, grid_layout = list(ncol = 4, nrow = 3))
 
       message("Generating deletion interaction plots")
-      deletion_plot_configs <- generate_interaction_plot_configs(zscores_interactions_joined, interaction_vars)
-      generate_and_save_plots(out_dir, "InteractionPlots", deletion_plot_configs, grid_layout = list(ncol = 4, nrow = 3))
+      deletion_plot_configs <- generate_interaction_plot_configs(zscore_interactions_joined, interaction_vars)
+      generate_and_save_plots(out_dir, "interaction_plots", deletion_plot_configs, grid_layout = list(ncol = 4, nrow = 3))
 
       # Define conditions for enhancers and suppressors
       # TODO Add to study config?
       threshold <- 2
-      enhancer_condition_L <- zscores_interactions$Avg_Zscore_L >= threshold
-      suppressor_condition_L <- zscores_interactions$Avg_Zscore_L <= -threshold
-      enhancer_condition_K <- zscores_interactions$Avg_Zscore_K >= threshold
-      suppressor_condition_K <- zscores_interactions$Avg_Zscore_K <= -threshold
+      enhancer_condition_L <- zscore_interactions$Avg_Zscore_L >= threshold
+      suppressor_condition_L <- zscore_interactions$Avg_Zscore_L <= -threshold
+      enhancer_condition_K <- zscore_interactions$Avg_Zscore_K >= threshold
+      suppressor_condition_K <- zscore_interactions$Avg_Zscore_K <= -threshold
       
       # Subset data
-      enhancers_L <- zscores_interactions[enhancer_condition_L, ]
-      suppressors_L <- zscores_interactions[suppressor_condition_L, ]
-      enhancers_K <- zscores_interactions[enhancer_condition_K, ]
-      suppressors_K <- zscores_interactions[suppressor_condition_K, ]
+      enhancers_L <- zscore_interactions[enhancer_condition_L, ]
+      suppressors_L <- zscore_interactions[suppressor_condition_L, ]
+      enhancers_K <- zscore_interactions[enhancer_condition_K, ]
+      suppressors_K <- zscore_interactions[suppressor_condition_K, ]
       
       # Save enhancers and suppressors
       message("Writing enhancer/suppressor csv files")
-      write.csv(enhancers_L, file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_L.csv"), row.names = FALSE)
-      write.csv(suppressors_L, file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_L.csv"), row.names = FALSE)
-      write.csv(enhancers_K, file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_K.csv"), row.names = FALSE)
-      write.csv(suppressors_K, file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K.csv"), row.names = FALSE)
+      write.csv(enhancers_L, file = file.path(out_dir, "zscore_interactions_deletion_enhancers_L.csv"), row.names = FALSE)
+      write.csv(suppressors_L, file = file.path(out_dir, "zscore_interactions_deletion_suppressors_L.csv"), row.names = FALSE)
+      write.csv(enhancers_K, file = file.path(out_dir, "zscore_interactions_deletion_enhancers_K.csv"), row.names = FALSE)
+      write.csv(suppressors_K, file = file.path(out_dir, "zscore_interactions_deletion_suppressors_K.csv"), row.names = FALSE)
       
       # Combine conditions for enhancers and suppressors
-      enhancers_and_suppressors_L <- zscores_interactions[enhancer_condition_L | suppressor_condition_L, ]
-      enhancers_and_suppressors_K <- zscores_interactions[enhancer_condition_K | suppressor_condition_K, ]
+      enhancers_and_suppressors_L <- zscore_interactions[enhancer_condition_L | suppressor_condition_L, ]
+      enhancers_and_suppressors_K <- zscore_interactions[enhancer_condition_K | suppressor_condition_K, ]
       
       # Save combined enhancers and suppressors
       write.csv(enhancers_and_suppressors_L,
-        file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_and_Suppressors_L.csv"), row.names = FALSE)
+        file = file.path(out_dir, "zscore_interactions_deletion_enhancers_and_suppressors_L.csv"), row.names = FALSE)
       write.csv(enhancers_and_suppressors_K,
-        file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_and_Suppressors_K.csv"), row.names = FALSE)
+        file = file.path(out_dir, "zscore_interaction_deletion_enhancers_and_suppressors_K.csv"), row.names = FALSE)
       
       # Handle linear model based enhancers and suppressors
       lm_threshold <- 2
-      enhancers_lm_L <- zscores_interactions[zscores_interactions$Z_lm_L >= lm_threshold, ]
-      suppressors_lm_L <- zscores_interactions[zscores_interactions$Z_lm_L <= -lm_threshold, ]
-      enhancers_lm_K <- zscores_interactions[zscores_interactions$Z_lm_K >= lm_threshold, ]
-      suppressors_lm_K <- zscores_interactions[zscores_interactions$Z_lm_K <= -lm_threshold, ]
+      enhancers_lm_L <- zscore_interactions[zscore_interactions$Z_lm_L >= lm_threshold, ]
+      suppressors_lm_L <- zscore_interactions[zscore_interactions$Z_lm_L <= -lm_threshold, ]
+      enhancers_lm_K <- zscore_interactions[zscore_interactions$Z_lm_K >= lm_threshold, ]
+      suppressors_lm_K <- zscore_interactions[zscore_interactions$Z_lm_K <= -lm_threshold, ]
       
       # Save linear model based enhancers and suppressors
       message("Writing linear model enhancer/suppressor csv files")
       write.csv(enhancers_lm_L,
-        file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_L_lm.csv"), row.names = FALSE)
+        file = file.path(out_dir, "zscore_interactions_deletion_enhancers_lm_L.csv"), row.names = FALSE)
       write.csv(suppressors_lm_L,
-        file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_L_lm.csv"), row.names = FALSE)
+        file = file.path(out_dir, "zscore_interactions_deletion_suppressors_lm_L.csv"), row.names = FALSE)
       write.csv(enhancers_lm_K,
-        file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_K_lm.csv"), row.names = FALSE)
+        file = file.path(out_dir, "zscore_interactions_deletion_enhancers_lm_K.csv"), row.names = FALSE)
       write.csv(suppressors_lm_K,
-        file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K_lm.csv"), row.names = FALSE)
+        file = file.path(out_dir, "zscore_interactions_deletion_suppressors_lm_K.csv"), row.names = FALSE)
 
       message("Generating rank plots")
       rank_plot_configs <- generate_rank_plot_configs(
-        df = zscores_interactions_joined,
+        df = zscore_interactions_joined,
         variables = interaction_vars,
         is_lm = FALSE,
         adjust = TRUE
       )
-      generate_and_save_plots(out_dir = out_dir, filename = "RankPlots",
+      generate_and_save_plots(out_dir = out_dir, filename = "rank_plots",
         plot_configs = rank_plot_configs, grid_layout = list(ncol = 3, nrow = 2))
 
       message("Generating ranked linear model plots")
       rank_lm_plot_configs <- generate_rank_plot_configs(
-        df = zscores_interactions_joined,
+        df = zscore_interactions_joined,
         variables = interaction_vars,
         is_lm = TRUE,
         adjust = TRUE
       )
-      generate_and_save_plots(out_dir = out_dir, filename = "RankPlots_lm",
+      generate_and_save_plots(out_dir = out_dir, filename = "rank_plots_lm",
         plot_configs = rank_lm_plot_configs, grid_layout = list(ncol = 3, nrow = 2))
 
       message("Filtering and reranking plots")
       # Formerly X_NArm
-      zscores_interactions_filtered <- zscores_interactions_joined %>%
+      zscore_interactions_filtered <- zscore_interactions_joined %>%
         filter(!is.na(Z_lm_L) & !is.na(Avg_Zscore_L)) %>%
         mutate(
           Overlap = case_when(
@@ -1418,7 +1418,7 @@ main <- function() {
 
       message("Generating filtered ranked plots")
       rank_plot_filtered_configs <- generate_rank_plot_configs(
-        df = zscores_interactions_filtered,
+        df = zscore_interactions_filtered,
         variables = interaction_vars,
         is_lm = FALSE,
         adjust = FALSE,
@@ -1433,7 +1433,7 @@ main <- function() {
 
       message("Generating filtered ranked linear model plots")
       rank_plot_lm_filtered_configs <- generate_rank_plot_configs(
-        df = zscores_interactions_filtered,
+        df = zscore_interactions_filtered,
         variables = interaction_vars,
         is_lm = TRUE,
         adjust = FALSE,
@@ -1441,15 +1441,15 @@ main <- function() {
       )
       generate_and_save_plots(
         out_dir = out_dir,
-        filename = "RankPlots_lm_na_rm",
+        filename = "rank_plots_lm_na_rm",
         plot_configs = rank_plot_lm_filtered_configs,
         grid_layout = list(ncol = 3, nrow = 2))
 
-      message("Generating correlation plots")
-      correlation_plot_configs <- generate_correlation_plot_configs(zscores_interactions_filtered)
+      message("Generating correlation curve parameter pair plots")
+      correlation_plot_configs <- generate_correlation_plot_configs(zscore_interactions_filtered)
       generate_and_save_plots(
         out_dir = out_dir,
-        filename = "Correlation_CPPs",
+        filename = "correlation_cpps",
         plot_configs = correlation_plot_configs,
         grid_layout = list(ncol = 2, nrow = 2))
     })

qhtcp-workflow/apps/r/join_interaction_zscores.R

@@ -9,11 +9,11 @@ suppressMessages({
 parse_arguments <- function() {
   if (interactive()) {
     args <- c(
-      "/home/bryan/documents/develop/scripts/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD",
+      "/home/bryan/documents/develop/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD",
       3, # sd value
-      "/home/bryan/documents/develop/scripts/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD/20240822_jhartman2_DoxoHLD/exp1",
+      "/home/bryan/documents/develop/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD/20240822_jhartman2_DoxoHLD/exp1",
       "Experiment 1: Doxo versus HLD",
-      "/home/bryan/documents/develop/scripts/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD/20240822_jhartman2_DoxoHLD/exp2",
+      "/home/bryan/documents/develop/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD/20240822_jhartman2_DoxoHLD/exp2",
       "Experiment 2: HLD versus Doxo"
     )
   } else {
@@ -42,7 +42,7 @@ dir.create(args$out_dir, showWarnings = FALSE, recursive = TRUE)
 combine_zscores <- function(experiments, out_dir) {
   combined_data <- lapply(names(experiments), function(exp_name) {
     exp_dir <- experiments[[exp_name]]
-    zscore_file <- file.path(exp_dir, "zscores", "zscores_interaction.csv")
+    zscore_file <- file.path(exp_dir, "zscores", "zscore_interactions.csv")
 
     if (!file.exists(zscore_file)) {
       stop("Z-score file does not exist for ", exp_name, " at ", zscore_file)

qhtcp-workflow/qhtcp-workflow

@@ -1432,6 +1432,7 @@ wrapper calculate_interaction_zscores
 # * More variables can be read in from the config file to allow more configuration
 # * Add gene names, other threshold values, etc.
 # * Dataframe columns and output file columns should be standardized in calculate_interactions()
+# * Need to decide if conc_num_factor is numeric or factor 
 #
 # INPUT
 #