From 0eb460b4ee87f0bcd95fc8b5d60354d7dd428368 Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Wed, 4 Sep 2024 20:49:39 -0400
Subject: [PATCH] Add rank plots

---
 .../apps/r/calculate_interaction_zscores5.R   | 50 ++++++++++++++++---
 1 file changed, 43 insertions(+), 7 deletions(-)

diff --git a/workflow/apps/r/calculate_interaction_zscores5.R b/workflow/apps/r/calculate_interaction_zscores5.R
index 6ecbb378..89eefb2e 100644
--- a/workflow/apps/r/calculate_interaction_zscores5.R
+++ b/workflow/apps/r/calculate_interaction_zscores5.R
@@ -565,6 +565,46 @@ generate_plots <- function(df, x_var, y_vars, plot_type, color_var = "conc_num",
   save_plots(file_prefix, plot_list, output_dir)
 }
 
+# Function to generate rank plots for the provided dataframe
+generate_rank_plots <- function(df, output_dir) {
+  # Adjust missing values and calculate ranks
+  df_adjusted <- adjust_missing_and_rank(df)
+  
+  # List of variables for which we need to generate rank plots
+  variables <- c("L", "K", "r", "AUC")
+  
+  # Generate rank plots for Avg_Zscore and Z_lm
+  for (var in variables) {
+    plot_rank_avg <- generate_plot(
+      df = df_adjusted,
+      x_var = paste0(var, "_Rank"),
+      y_var = paste0("Avg_Zscore_", var),
+      plot_type = "scatter",
+      title = paste("Average Z score vs Rank for", var)
+    )
+    
+    plot_rank_lm <- generate_plot(
+      df = df_adjusted,
+      x_var = paste0(var, "_Rank_lm"),
+      y_var = paste0("Z_lm_", var),
+      plot_type = "scatter",
+      title = paste("Interaction Z score vs Rank for", var)
+    )
+    
+    # Save the plots for Avg_Zscore and Z_lm
+    save_plots(paste0("RankPlots_", var), list(
+      plot_rank_avg = plot_rank_avg,
+      plot_rank_lm = plot_rank_lm
+    ), output_dir)
+  }
+}
+
+# Function to call rank plot generation in the main function
+create_ranked_plots <- function(df, output_dir) {
+  message("Generating rank plots")
+  generate_rank_plots(df, output_dir)
+}
+
 
 main <- function() {
   lapply(names(args$experiments), function(exp_name) {
@@ -614,9 +654,6 @@ main <- function() {
     write.csv(stats, file = file.path(out_dir, "SummaryStats_ALLSTRAINS.csv"), row.names = FALSE)
     stats_joined <- left_join(df_na, stats, by = c("OrfRep", "conc_num", "conc_num_factor"))
 
-    # Create interaction plots
-    generate_interaction_plots(stats_joined, output_file = file.path(output_dir, "InteractionPlots.pdf"))
-
     print("stats:")
     print(head(stats))
 
@@ -710,11 +747,10 @@ main <- function() {
       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)
-      
-
-      
-
 
+      # Create interaction plots
+      generate_interaction_plots(df_reference, output_file = file.path(output_dir, "RF_InteractionPlots.pdf"))
+      generate_interaction_plots(df_deletion, output_file = file.path(output_dir, "InteractionPlots.pdf"))
 
       # Define conditions for enhancers and suppressors
       # TODO Add to study config file?