From ed1e3cf7566a318c61f9d0b4272e82ae86f4a6dd Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Sun, 1 Sep 2024 02:31:49 -0400
Subject: [PATCH] Auto-commit: apps/r/calculate_interaction_zscores5.R

---
 .../apps/r/calculate_interaction_zscores5.R   | 83 ++++++++++++++++++-
 1 file changed, 81 insertions(+), 2 deletions(-)

diff --git a/workflow/apps/r/calculate_interaction_zscores5.R b/workflow/apps/r/calculate_interaction_zscores5.R
index 49183c71..16a1cf70 100644
--- a/workflow/apps/r/calculate_interaction_zscores5.R
+++ b/workflow/apps/r/calculate_interaction_zscores5.R
@@ -285,7 +285,6 @@ process_strains <- function(df, df_stats_by_l_within_2sd_k, strain, output_dir)
     }
     df_strains <- bind_rows(df, df_temp)
   }
-
   return(df_strains)
 }
 
@@ -412,7 +411,7 @@ generate_summary_plots <- function(df, output_dir) {
 generate_cpp_correlation_plots <- function(df_na_rm, lm_list, output_dir) {
   lm_summaries <- lapply(lm_list, summary)
   plot_titles <- c("Interaction L vs. Interaction K", "Interaction L vs. Interaction r", "Interaction L vs. Interaction AUC",
-                   "Interaction K vs. Interaction r", "Interaction K vs. Interaction AUC", "Interaction r vs. Interaction AUC")
+    "Interaction K vs. Interaction r", "Interaction K vs. Interaction AUC", "Interaction r vs. Interaction AUC")
   
   plot_list <- lapply(seq_along(lm_list), function(i) {
     ggplot(df_na_rm, aes_string(x = names(lm_list)[i][1], y = names(lm_list)[i][2])) +
@@ -426,6 +425,81 @@ generate_cpp_correlation_plots <- function(df_na_rm, lm_list, output_dir) {
   save_plots("Correlation_CPPs", plot_list, output_dir)
 }
 
+
+# Adjust missing values and calculate ranks
+adjust_missing_and_rank <- function(df) {
+  df <- df %>%
+    mutate(
+      Avg_Zscore_L = ifelse(is.na(Avg_Zscore_L), 0.001, Avg_Zscore_L),
+      Avg_Zscore_K = ifelse(is.na(Avg_Zscore_K), 0.001, Avg_Zscore_K),
+      Avg_Zscore_r = ifelse(is.na(Avg_Zscore_r), 0.001, Avg_Zscore_r),
+      Avg_Zscore_AUC = ifelse(is.na(Avg_Zscore_AUC), 0.001, Avg_Zscore_AUC),
+      Z_lm_L = ifelse(is.na(Z_lm_L), 0.001, Z_lm_L),
+      Z_lm_K = ifelse(is.na(Z_lm_K), 0.001, Z_lm_K),
+      Z_lm_r = ifelse(is.na(Z_lm_r), 0.001, Z_lm_r),
+      Z_lm_AUC = ifelse(is.na(Z_lm_AUC), 0.001, Z_lm_AUC),
+      L_Rank = rank(Avg_Zscore_L),
+      K_Rank = rank(Avg_Zscore_K),
+      r_Rank = rank(Avg_Zscore_r),
+      AUC_Rank = rank(Avg_Zscore_AUC),
+      L_Rank_lm = rank(Z_lm_L),
+      K_Rank_lm = rank(Z_lm_K),
+      r_Rank_lm = rank(Z_lm_r),
+      AUC_Rank_lm = rank(Z_lm_AUC)
+    )
+  return(df)
+}
+
+# Generate ranked plots for a specific metric
+generate_ranked_plot <- function(df, rank_var, zscore_var, sd_threshold, title_prefix) {
+  ggplot(df, aes(x = {{rank_var}}, y = {{zscore_var}})) +
+    ggtitle(paste(title_prefix, "above", sd_threshold, "SD")) +
+    xlab("Rank") + ylab(paste("Avg Z score", title_prefix)) +
+    annotate("rect", xmin = -Inf, xmax = Inf, ymin = sd_threshold, ymax = Inf, fill = "#542788", alpha = 0.3) +
+    annotate("rect", xmin = -Inf, xmax = Inf, ymin = -sd_threshold, ymax = -Inf, fill = "orange", alpha = 0.3) +
+    geom_hline(yintercept = c(-sd_threshold, sd_threshold)) +
+    geom_point(size = 0.1, shape = 3) +
+    theme_publication()
+}
+
+# Generate and save all ranked plots
+generate_and_save_ranked_plots <- function(df, output_dir, prefix) {
+  rank_metrics <- list(
+    list("L_Rank", "Avg_Zscore_L", "L"),
+    list("K_Rank", "Avg_Zscore_K", "K"),
+    list("r_Rank", "Avg_Zscore_r", "r"),
+    list("AUC_Rank", "Avg_Zscore_AUC", "AUC"),
+    list("L_Rank_lm", "Z_lm_L", "L"),
+    list("K_Rank_lm", "Z_lm_K", "K"),
+    list("r_Rank_lm", "Z_lm_r", "r"),
+    list("AUC_Rank_lm", "Z_lm_AUC", "AUC")
+  )
+  
+  pdf(file.path(output_dir, paste0(prefix, ".pdf")), width = 18, height = 12, onefile = TRUE)
+  
+  for (sd_threshold in c(1, 2, 3)) {
+    for (metric in rank_metrics) {
+      plot <- generate_ranked_plot(df, sym(metric[[1]]), sym(metric[[2]]), sd_threshold, metric[[3]])
+      print(plot)
+    }
+  }
+  
+  dev.off()
+}
+
+# Function to create and save all ranked plots
+create_ranked_plots <- function(df, output_dir) {
+  df_adjusted <- adjust_missing_and_rank(df)
+  
+  # Generate and save ranked plots
+  generate_and_save_ranked_plots(df_adjusted, output_dir, "RankPlots")
+  generate_and_save_ranked_plots(df_adjusted, output_dir, "RankPlots_lm")
+  generate_and_save_ranked_plots(df_adjusted, output_dir, "RankPlots_naRM")
+  generate_and_save_ranked_plots(df_adjusted, output_dir, "RankPlots_lm_naRM")
+}
+
+
+
 main <- function() {
   # Applying to all experiments
   lapply(names(args$experiments), function(exp_name) {
@@ -642,7 +716,12 @@ main <- function() {
         lm(Z_lm_AUC ~ Z_lm_K, data = zscores_interactions_filtered),
         lm(Z_lm_AUC ~ Z_lm_r, data = zscores_interactions_filtered)
       )
+
+      # Generate cpp correlation plots
       generate_cpp_correlation_plots(zscores_interactions_filtered, lm_list, out_dir)
+
+      # Generate ranked plots
+      create_ranked_plots(zscores_interactions_filtered, out_dir)
     })
   })
 }