Simplify R Squared calculations

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -1231,6 +1231,7 @@ main <- function() {
       generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots",
         plot_configs = rank_plot_configs, grid_layout = list(ncol = 3, nrow = 2))
 
+      message("Generating ranked linear model plots")
       # Generate rank plots for L and K using linear model (`lm`) ranks
       rank_lm_plot_configs <- generate_rank_plot_configs(
         df = zscores_interactions,
@@ -1243,7 +1244,7 @@ main <- function() {
       generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots_lm",
         plot_configs = rank_lm_plot_configs, grid_layout = list(ncol = 3, nrow = 2))
 
-      message("Filtering and regenerating rank plots")
+      message("Filtering and reranking plots")
       # Filter rows where either Z_lm_L or Avg_Zscore_L is not NA
       # Formerly X_NArm
       zscores_interactions_filtered <- zscores_interactions %>%
@@ -1252,10 +1253,10 @@ main <- function() {
         ungroup() %>%
         rowwise() %>%
         mutate(
-          lm_R_squared_L = if (n() > 1) summary(lm(Z_lm_L ~ Avg_Zscore_L))$r.squared else NA,
-          lm_R_squared_K = if (n() > 1) summary(lm(Z_lm_K ~ Avg_Zscore_K))$r.squared else NA,
-          lm_R_squared_r = if (n() > 1) summary(lm(Z_lm_r ~ Avg_Zscore_r))$r.squared else NA,
-          lm_R_squared_AUC = if (n() > 1) summary(lm(Z_lm_AUC ~ Avg_Zscore_AUC))$r.squared else NA,
+          lm_R_squared_L = summary(lm(Z_lm_L ~ Avg_Zscore_L))$r.squared,
+          lm_R_squared_K = summary(lm(Z_lm_K ~ Avg_Zscore_K))$r.squared,
+          lm_R_squared_r = summary(lm(Z_lm_r ~ Avg_Zscore_r))$r.squared,
+          lm_R_squared_AUC = summary(lm(Z_lm_AUC ~ Avg_Zscore_AUC))$r.squared,
 
           Overlap = case_when(
             Z_lm_L >= 2 & Avg_Zscore_L >= 2 ~ "Deletion Enhancer Both",
@@ -1269,23 +1270,24 @@ main <- function() {
         ) %>%
         ungroup()
 
-      message("Generating filtered rank plots")
+      message("Generating filtered ranked plots")
       rank_plot_filtered_configs <- generate_rank_plot_configs(
         df = zscores_interactions_filtered,
         interaction_vars = interaction_vars,
         is_lm = FALSE,
         adjust = FALSE
-      )$plot_configs
+      )
       generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots_na_rm",
         plot_configs = rank_plot_filtered_configs,
         grid_layout = list(ncol = 3, nrow = 2))
-          
+
+      message("Generating filtered ranked linear model plots")
       rank_plot_lm_filtered_configs <- generate_rank_plot_configs(
         df = zscores_interactions_filtered,
         interaction_vars = interaction_vars,
         is_lm = TRUE,
         adjust = FALSE
-      )$plot_configs
+      )
       generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots_lm_na_rm",
         plot_configs = rank_plot_lm_filtered_configs,
         grid_layout = list(ncol = 3, nrow = 2))