Add some debug for rank plots

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -585,11 +585,14 @@ adjust_missing_and_rank <- function(df, variables) {
       df[[z_lm_col]] <- if_else(is.na(df[[z_lm_col]]), 0.001, df[[z_lm_col]])
       
       # Compute ranks and create new columns
-      df[[rank_col]] <- rank(df[[avg_zscore_col]], na.last = "keep")
-      df[[rank_lm_col]] <- rank(df[[z_lm_col]], na.last = "keep")
+      df[[rank_col]] <- rank(df[[avg_zscore_col]])
+      df[[rank_lm_col]] <- rank(df[[z_lm_col]])
     } else {
       warning(paste("Columns", avg_zscore_col, "or", z_lm_col, "not found in data frame"))
     }
+    # Print some debugging output
+    print(df %>% select("OrfRep", "Gene", "conc_num", "conc_num_factor",
+      avg_zscore_col, z_lm_col, rank_col, rank_lm_col))
   }
 
   return(df)
@@ -771,8 +774,7 @@ generate_rank_plot_configs <- function(df, rank_var, zscore_var, var, is_lm = FA
     enhancer_label = NULL,
     suppressor_label = NULL,
     shape = 3,
-    size = 0.1,
-    position = "jitter"
+    size = 0.1
   )
 
   return(configs)
@@ -1213,8 +1215,10 @@ main <- function() {
         file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K_lm.csv"), row.names = FALSE)
 
       # TODO needs explanation
+      message("Adjusting and ranking interactions scores")
       zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions, variables = interaction_vars)
       
+      message("Generating rank plots")
       rank_plot_configs <- c(
         generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_L", "Avg_Zscore_L", "L"),
         generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_K", "Avg_Zscore_K", "K")