Loosen R linter

qhtcp-workflow/.lintr

@@ -1,4 +1,5 @@
 linters: linters_with_defaults(
+  object_length_linter = object_length_linter(40),
   object_name_linter = NULL,
   object_usage_linter = NULL,
   commented_code_linter = NULL,

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -514,9 +514,12 @@ generate_interaction_plot_configs <- function(df, variables) {
   return(plot_configs)
 }
 
-generate_rank_plot_config <- function(df, rank_var, zscore_var, label_prefix) {
+generate_rank_plot_configs <- function(df, rank_var, zscore_var, label_prefix, is_lm = FALSE) {
   configs <- list()
   
+  # Adjust titles for _lm plots if is_lm is TRUE
+  plot_title_prefix <- if (is_lm) "Interaction Z score vs. Rank for" else "Average Z score vs. Rank for"
+  
   for (sd_band in c(1, 2, 3)) {
     # Annotated version (with text)
     configs[[length(configs) + 1]] <- list(
@@ -524,7 +527,7 @@ generate_rank_plot_config <- function(df, rank_var, zscore_var, label_prefix) {
       x_var = rank_var,
       y_var = zscore_var,
       plot_type = "rank",
-      title = paste("Average Z score vs. Rank for", label_prefix, "above", sd_band, "SD"),
+      title = paste(plot_title_prefix, label_prefix, "above", sd_band, "SD"),
       sd_band = sd_band,
       enhancer_label = list(
         x = nrow(df) / 2, y = 10,
@@ -542,16 +545,17 @@ generate_rank_plot_config <- function(df, rank_var, zscore_var, label_prefix) {
       x_var = rank_var,
       y_var = zscore_var,
       plot_type = "rank",
-      title = paste("Average Z score vs. Rank for", label_prefix, "above", sd_band, "SD"),
+      title = paste(plot_title_prefix, label_prefix, "above", sd_band, "SD"),
       sd_band = sd_band,
-      enhancer_label = NULL,  # Remove annotations for _notext
-      suppressor_label = NULL  # Remove annotations for _notext
+      enhancer_label = NULL,  # No annotations for _notext
+      suppressor_label = NULL  # No annotations for _notext
     )
   }
   
   return(configs)
 }
 
+
 # Generate all rank plot configurations for L and K (annotated and _notext)
 rank_plot_config <- c(
   create_rank_plot_config(zscores_interactions_adjusted, "L_Rank", "Avg_Zscore_L", "L"),
@@ -928,16 +932,23 @@ main <- function() {
 
       zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions)
       
-      # Generate all rank plot configurations for L and K
       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")
       )
-
-      # Generate and save rank plots
       generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots",
         plot_configs = rank_plot_config, grid_layout = list(ncol = 3, nrow = 2))
 
+      rank_lm_plot_config <- c(
+        generate_rank_lm_plot_configs(zscores_interactions_adjusted, "Rank_lm_L", "Z_lm_L", "L"),
+        generate_rank_lm_plot_configs(zscores_interactions_adjusted, "Rank_lm_K", "Z_lm_K", "K")
+      )
+      generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots_lm",
+        plot_configs = rank_lm_plot_config, grid_layout = list(ncol = 3, nrow = 2))
+      
+
+      
+
       # # Correlation plots
       # lm_list <- list(
       #   lm(Z_lm_K ~ Z_lm_L, data = zscores_interactions_filtered),