Add missing correlation plot layers

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -401,7 +401,6 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
         if (!is.null(config$coord_cartesian)) {
           plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
         }
-
         plot
       },
       
@@ -424,13 +423,21 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
         if (!is.null(config$suppressor_label)) {
           plot <- plot + annotate("text", x = config$suppressor_label$x, y = config$suppressor_label$y, label = config$suppressor_label$label)
         }
-        
         plot
       },
       
-      "correlation" = plot + geom_point(shape = config$shape %||% 3, color = "gray70") +
-        geom_abline(intercept = config$lm_line$intercept, slope = config$lm_line$slope, color = "tomato3") +
-        annotate("text", x = 0, y = 0, label = config$correlation_text),
+      "correlation" = {
+        plot <- plot + geom_point(shape = config$shape %||% 3, color = "gray70") +
+          geom_abline(intercept = config$lm_line$intercept, slope = config$lm_line$slope, color = "tomato3") +
+          annotate("text", x = config$annotate_position$x, y = config$annotate_position$y, label = config$correlation_text)
+        
+        if (!is.null(config$rect)) {
+          plot <- plot + geom_rect(aes(xmin = config$rect$xmin,
+            xmax = config$rect$xmax, ymin = config$rect$ymin, ymax = config$rect$ymax),
+            color = "grey20", size = 0.25, alpha = 0.1, fill = NA, inherit.aes = FALSE)
+        }
+        plot
+      },
       
       "box" = {
         plot <- plot + geom_boxplot()
@@ -590,8 +597,7 @@ generate_rank_plot_configs <- function(df, rank_var, zscore_var, var, is_lm = FA
         label = paste("Deletion Suppressors =", nrow(df[df[[zscore_var]] <= -sd_band, ]))
       ),
       shape = 3,
-      size = 0.1,
-      position = "jitter"
+      size = 0.1
     )
   }
   
@@ -633,6 +639,8 @@ generate_correlation_plot_configs <- function(df, variables) {
       correlation_text = paste("R-squared =", round(df[[lm_r_squared_col]][1], 2)),
       shape = 3,
       geom_smooth = TRUE,
+      rect = list(xmin = -2, xmax = 2, ymin = -2, ymax = 2),  # To add the geom_rect layer
+      annotate_position = list(x = 0, y = 0),  # Position for the R-squared text
       legend_position = "right"
     )
   }