Move annotations to global scope

.gitignore

@@ -2,4 +2,6 @@
 centos-upgrade-plan.txt
 qhtcp-workflow/out/
 qhtcp-workflow/scans/
+qhctp-workflow/oom
 last.dump.rda
+

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -554,6 +554,23 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
       if (!is.null(config$y_label)) plot <- plot + ylab(config$y_label)
       if (!is.null(config$coord_cartesian)) plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
 
+      # Add annotations if specified
+      if (!is.null(config$annotations)) {
+        for (annotation in config$annotations) {
+          plot <- plot +
+            annotate(
+              "text",
+              x = ifelse(is.null(annotation$x), 0, annotation$x),
+              y = ifelse(is.null(annotation$y), Inf, annotation$y),
+              label = annotation$label,
+              hjust = ifelse(is.null(annotation$hjust), 0.5, annotation$hjust),
+              vjust = ifelse(is.null(annotation$vjust), 1, annotation$vjust),
+              size = ifelse(is.null(annotation$size), 3, annotation$size),
+              color = ifelse(is.null(annotation$color), "black", annotation$color)
+            )
+        }
+      }
+
       # Add error bars if specified
       if (!is.null(config$error_bar) && config$error_bar) {
         # Check if a fixed color is provided or if it should come from a data column
@@ -567,19 +584,15 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
               ymin = config$error_bar_params$ymin,
               ymax = config$error_bar_params$ymax
             )
-            # Apply fixed color if specified
-            if (!is.null(error_bar_color)) {
-              plot <- plot + scale_color_manual(values = error_bar_color)
-            }
           } else {
-            # If config$color_var exists, map the color aesthetic
+            # Map color_var to data if available
             if (!is.null(config$color_var)) {
               plot <- plot + geom_errorbar(
                 aes(
                   x = .data[[config$x_var]],
                   ymin = .data[[config$error_bar_params$ymin]],
                   ymax = .data[[config$error_bar_params$ymax]],
-                  color = .data[[config$color_var]]  # Map color_var to data
+                  color = .data[[config$color_var]]
                 )
               )
             } else {
@@ -593,19 +606,18 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
             }
           }
         } else {
-          # Ensure the mean and sd columns exist
+          # Use mean and SD columns from df
           y_mean_col <- paste0("mean_", config$y_var)
           y_sd_col <- paste0("sd_", config$y_var)
 
           if (y_mean_col %in% colnames(df) && y_sd_col %in% colnames(df)) {
-            # If config$color_var exists, map the color aesthetic
             if (!is.null(config$color_var)) {
               plot <- plot + geom_errorbar(
                 aes(
                   x = .data[[config$x_var]],
                   ymin = .data[[y_mean_col]] - .data[[y_sd_col]],
                   ymax = .data[[y_mean_col]] + .data[[y_sd_col]],
-                  color = .data[[config$color_var]]  # Color based on aes()
+                  color = .data[[config$color_var]]
                 )
               )
             } else {
@@ -617,10 +629,6 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
                 )
               )
             }
-            # Apply fixed color if specified
-            if (!is.null(error_bar_color)) {
-              plot <- plot + scale_color_manual(values = error_bar_color)
-            }
           }
         }
       }
@@ -773,23 +781,6 @@ generate_scatter_plot <- function(plot, config) {
     plot <- plot + scale_y_continuous(limits = config$ylim_vals)
   }
   
-  # Add annotations if specified
-  if (!is.null(config$annotations)) {
-    for (annotation in config$annotations) {
-      plot <- plot +
-        annotate(
-          "text",
-          x = ifelse(is.null(annotation$x), 0, annotation$x),
-          y = ifelse(is.null(annotation$y), 0, annotation$y),
-          label = annotation$label,
-          hjust = ifelse(is.null(annotation$hjust), 0.5, annotation$hjust),
-          vjust = ifelse(is.null(annotation$vjust), 0.5, annotation$vjust),
-          size = ifelse(is.null(annotation$size), 3, annotation$size),
-          color = ifelse(is.null(annotation$color), "black", annotation$color)
-        )
-    }
-  }
-  
   return(plot)
 }
 
@@ -901,9 +892,9 @@ generate_interaction_plot_configs <- function(df, type) {
         plot_config$position <- "jitter"
 
       annotations <- list(
-        list(x = 0.25, y = y_limits[1] + 0.1 * y_span, label = "              NG ="), # Slightly above y-min
+        list(x = 0.25, y = y_limits[1] + 0.1 * y_span, label = "               NG ="), # Slightly above y-min
-        list(x = 0.25, y = y_limits[1] + 0.05 * y_span, label = "              DB ="),
+        list(x = 0.25, y = y_limits[1] + 0.05 * y_span, label = "               DB ="),
-        list(x = 0.25, y = y_limits[1], label = "              SM =")
+        list(x = 0.25, y = y_limits[1], label = "               SM =")
       )
 
       # Loop over unique x values and add NG, DB, SM values at calculated y positions