Begin scatter plot refactoring

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -411,20 +411,24 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
   saveWidget(combined_plot, file = file.path(output_dir, paste0(file_name, ".html")), selfcontained = TRUE)
 }
 
-generate_scatter_plot <- function(plot, config) {
+generate_scatter_plot <- function(plot, config, interactive = FALSE) {
 
-  # Add the interactive text aesthetics to the scatter points
-  plot <-
-    if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
+  # Add the interactive `text` aesthetic if `interactive` is TRUE
+  if (interactive) {
+    plot <- if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
       plot + geom_point(aes(text = paste("ORF:", OrfRep, "Gene:", Gene, "delta_bg:", delta_bg)),
         shape = config$shape %||% 3, size = config$size %||% 0.2)
     } else if (!is.null(config$gene_point) && config$gene_point) {
       plot + geom_point(aes(text = paste("ORF:", OrfRep, "Gene:", Gene)),
         shape = config$shape %||% 3, size = config$size %||% 0.2, position = "jitter")
     } else {
-      plot + geom_point(shape = config$shape %||% 3, size = config$size %||% 0.2,
-        position = config$position %||% "identity")
+      plot + geom_point(shape = config$shape %||% 3, size = config$size %||% 0.2)
     }
+  } else {
+    # For non-interactive plots, just add `geom_point`
+    plot <- plot + geom_point(shape = config$shape %||% 3, size = config$size %||% 0.2,
+      position = if (!is.null(config$position) && config$position == "jitter") "jitter" else "identity")
+  }
 
   # Add smooth line if specified
   if (!is.null(config$add_smooth) && config$add_smooth) {
@@ -573,17 +577,28 @@ generate_interaction_plot_configs <- function(df, variables) {
     )
 
     # Dynamically create annotations based on variable
+    # Dynamically create annotations based on variable
     annotations <- lapply(names(annotation_positions[[variable]]), function(annotation_name) {
       y_pos <- annotation_positions[[variable]][[annotation_name]]
-      label <- annotation_labels[[annotation_name]](df, variable)
-      list(x = 1, y = y_pos, label = label)
+      
+      # Check if the annotation_name exists in annotation_labels
+      if (!is.null(annotation_labels[[annotation_name]])) {
+        label <- annotation_labels[[annotation_name]](df, variable)
+        list(x = 1, y = y_pos, label = label)
+      } else {
+        message(paste("Warning: No annotation function found for", annotation_name))
+        NULL
+      }
     })
 
+    # Filter out any NULL annotations
+    annotations <- Filter(Negate(is.null), annotations)
+
     # Add scatter plot configuration for this variable
     configs[[length(configs) + 1]] <- list(
       df = df,
       x_var = "conc_num_factor",
-      y_var = var_info$delta_var,
+      y_var = variable,
       plot_type = "scatter",
       title = sprintf("%s      %s", df$OrfRep[1], df$Gene[1]),
       ylim_vals = var_info$ylim,
@@ -593,8 +608,6 @@ generate_interaction_plot_configs <- function(df, variables) {
       x_breaks = unique(df$conc_num_factor),
       x_labels = unique(as.character(df$conc_num)),
       x_label = unique(df$Drug[1]),
-      shape = 3,
-      size = 0.6,
       position = "jitter",
       coord_cartesian = c(0, max(var_info$ylim))  # You can customize this per plot as needed
     )