Rollup before java debug

workflow/apps/r/joinInteractExps.R

@@ -26,8 +26,8 @@ args <- parse_arguments()
 
 # Create an array for the zscores files
 get_zscores_files <- function(dirs) {
-  files <- sapply(dirs, function(study) {
-    file_path <- file.path(study, "zscores", "zscores_interaction.csv")
+  files <- sapply(dirs, function(exp) {
+    file_path <- file.path(exp, "zscores", "zscores_interaction.csv")
     if (file.exists(file_path)) file_path else NULL
   }, simplify = TRUE, USE.NAMES = FALSE)
   

workflow/apps/r/join_interaction_zscores.R

@@ -0,0 +1,113 @@
+suppressMessages({
+  library("dplyr")
+  library("data.table")
+  library("readr")
+  library("stringr")
+})
+
+# Function to parse arguments
+parse_arguments <- function() {
+  if (interactive()) {
+    args <- c(
+      "/home/bryan/documents/develop/scripts/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD",
+      3, # sd value
+      "/home/bryan/documents/develop/scripts/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",
+      "Experiment 2: HLD versus Doxo"
+    )
+  } else {
+    args <- commandArgs(trailingOnly = TRUE)
+  }
+
+  out_dir <- normalizePath(args[1], mustWork = FALSE)
+  sd <- as.numeric(args[2])
+  paths <- normalizePath(args[seq(3, length(args), by = 2)], mustWork = FALSE)
+  names <- args[seq(4, length(args), by = 2)]
+  experiments <- setNames(paths, names)
+
+  list(
+    out_dir = out_dir,
+    sd = sd,
+    experiments = experiments
+  )
+}
+
+args <- parse_arguments()
+
+# Ensure main output directory exists
+dir.create(args$out_dir, showWarnings = FALSE, recursive = TRUE)
+
+# Function to read and combine z-score interaction files
+combine_zscores <- function(experiments, out_dir) {
+  combined_data <- lapply(names(experiments), function(exp_name) {
+    exp_dir <- experiments[[exp_name]]
+    zscore_file <- file.path(exp_dir, "zscores", "zscores_interaction.csv")
+
+    if (!file.exists(zscore_file)) {
+      stop("Z-score file does not exist for ", exp_name, " at ", zscore_file)
+    }
+
+    message("Reading z-score file for ", exp_name, " from ", zscore_file)
+    data <- fread(zscore_file)
+    data$Experiment <- exp_name
+
+    return(data)
+  }) %>%
+    bind_rows()
+
+  combined_output_file <- file.path(out_dir, "combined_zscores.csv")
+  fwrite(combined_data, combined_output_file, row.names = FALSE)
+
+  message("Combined z-score file saved to: ", combined_output_file)
+}
+
+# Function to read and combine summary statistics files
+combine_summary_stats <- function(experiments, out_dir) {
+  combined_stats <- lapply(names(experiments), function(exp_name) {
+    exp_dir <- experiments[[exp_name]]
+    summary_file <- file.path(exp_dir, "zscores", "summary_stats_all_strains.csv")
+
+    if (!file.exists(summary_file)) {
+      stop("Summary stats file does not exist for ", exp_name, " at ", summary_file)
+    }
+
+    message("Reading summary stats file for ", exp_name, " from ", summary_file)
+    data <- fread(summary_file)
+    data$Experiment <- exp_name
+
+    return(data)
+  }) %>%
+    bind_rows()
+
+  combined_output_file <- file.path(out_dir, "combined_summary_stats.csv")
+  fwrite(combined_stats, combined_output_file, row.names = FALSE)
+
+  message("Combined summary stats file saved to: ", combined_output_file)
+}
+
+# Function to generate final summary report
+generate_final_report <- function(out_dir) {
+  combined_zscores <- file.path(out_dir, "combined_zscores.csv")
+  combined_stats <- file.path(out_dir, "combined_summary_stats.csv")
+
+  if (!file.exists(combined_zscores) || !file.exists(combined_stats)) {
+    stop("Combined z-scores or summary stats files do not exist.")
+  }
+
+  zscores_data <- fread(combined_zscores)
+  stats_data <- fread(combined_stats)
+
+  message("Merging z-score and summary stats data...")
+  final_report <- merge(zscores_data, stats_data, by = c("OrfRep", "Experiment"), all = TRUE, allow.cartesian = TRUE)
+
+  final_report_file <- file.path(out_dir, "final_combined_report.csv")
+  fwrite(final_report, final_report_file, row.names = FALSE)
+
+  message("Final combined report saved to: ", final_report_file)
+}
+
+# Process all experiments and generate outputs
+combine_zscores(args$experiments, args$out_dir)
+combine_summary_stats(args$experiments, args$out_dir)
+generate_final_report(args$out_dir)