Skip empty plots to fix grid.arrange() error

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -509,30 +509,23 @@ calculate_interaction_scores <- function(df, df_bg, type, overlap_threshold = 2)
 generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width = 12, page_height = 8) {
   message("Generating ", filename, ".pdf and ", filename, ".html")
 
-  # Check if we're dealing with multiple plot groups
   plot_groups <- if ("plots" %in% names(plot_configs)) {
     list(plot_configs)  # Single group
   } else {
     plot_configs  # Multiple groups
   }
 
-  # Open the PDF device once for all plots
   pdf(file.path(out_dir, paste0(filename, ".pdf")), width = page_width, height = page_height)
 
-  # Loop through each plot group
   for (group in plot_groups) {
     static_plots <- list()
     plotly_plots <- list()
 
-    # Retrieve grid layout if it exists, otherwise skip
-    grid_layout <- group$grid_layout
-    plots <- group$plots
-
-    for (i in seq_along(plots)) {
-      config <- plots[[i]]
+    for (i in seq_along(group$plots)) {
+      config <- group$plots[[i]]
       df <- config$df
 
-      # Filter points outside of y-limits if specified
+      # Filter and debug out-of-bounds data
       if (!is.null(config$ylim_vals)) {
         out_of_bounds <- df %>%
           filter(
@@ -540,14 +533,11 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
             .data[[config$y_var]] < config$ylim_vals[1] |
             .data[[config$y_var]] > config$ylim_vals[2]
           )
-        
-        # Print rows being filtered out
         if (nrow(out_of_bounds) > 0) {
           message("Filtered ", nrow(out_of_bounds), " row(s) from '", config$title, "' because ", config$y_var,
-            " is outside of y-limits: [", config$ylim_vals[1], ", ", config$ylim_vals[2], "]:")
-          print(out_of_bounds %>% select(OrfRep, Gene, num, Drug, scan, Plate, Row, Col, conc_num, all_of(config$y_var)), width = 1000)
+                  " is outside of y-limits: [", config$ylim_vals[1], ", ", config$ylim_vals[2], "]:")
+          # print(out_of_bounds %>% select(OrfRep, Gene, num, Drug, scan, Plate, Row, Col, conc_num, all_of(config$y_var)), width = 1000)
         }
-
         df <- df %>%
           filter(
             !is.na(.data[[config$y_var]]) &
@@ -556,13 +546,17 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
           )
       }
 
-      # Filter NAs if specified
+      # Filter NAs
       if (!is.null(config$filter_na) && config$filter_na) {
         df <- df %>%
           filter(!is.na(.data[[config$y_var]]))
       }
 
-      # Set up aes mapping based on plot type
+      if (nrow(df) == 0) {
+        message("No data available after filtering for plot ", config$title)
+        next  # Skip this plot if no data is available
+      }
+
       aes_mapping <- if (config$plot_type == "bar") {
         if (!is.null(config$color_var)) {
           aes(x = .data[[config$x_var]], fill = .data[[config$color_var]], color = .data[[config$color_var]])
@@ -587,16 +581,14 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
 
       plot <- ggplot(df, aes_mapping) + theme_publication(legend_position = config$legend_position)
 
-      # Add appropriate plot layer or helper function based on plot type
       plot <- switch(config$plot_type,
         "scatter" = generate_scatter_plot(plot, config),
         "box" = generate_boxplot(plot, config),
         "density" = plot + geom_density(),
         "bar" = plot + geom_bar(),
-        plot  # default (unused)
+        plot  # default
       )
 
-      # Add labels and title
       if (!is.null(config$title)) {
         plot <- plot + ggtitle(config$title)
         if (!is.null(config$title_size)) {
@@ -607,44 +599,21 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
       if (!is.null(config$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)
-            )
-        }
-      }
-
-      # Convert ggplot to plotly for interactive version
       plotly_plot <- suppressWarnings(plotly::ggplotly(plot))
 
-      # Store both static and interactive versions
       static_plots[[i]] <- plot
       plotly_plots[[i]] <- plotly_plot
     }
 
-    # Print the plots in the current group to the PDF
+    grid_layout <- group$grid_layout
     if (!is.null(grid_layout)) {
-      # Set grid_ncol to 1 if not specified
       if (is.null(grid_layout$ncol)) {
         grid_layout$ncol <- 1
       }
 
-      # If ncol is set but nrow is not, calculate nrow dynamically based on num_plots
       if (!is.null(grid_layout$ncol) && is.null(grid_layout$nrow)) {
         num_plots <- length(static_plots)
-        nrow <- ceiling(num_plots / grid_layout$ncol)
-        # message("No nrow provided, automatically using nrow = ", nrow)
-        grid_layout$nrow <- nrow
+        grid_layout$nrow <- ceiling(num_plots / grid_layout$ncol)
       }
       
       total_spots <- grid_layout$nrow * grid_layout$ncol
@@ -655,24 +624,26 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
         static_plots <- c(static_plots, replicate(total_spots - num_plots, nullGrob(), simplify = FALSE))
       }
 
-      # Print a page of gridded plots
-      grid.arrange(
-        grobs = static_plots,
-        ncol = grid_layout$ncol,
-        nrow = grid_layout$nrow)
-        
+      tryCatch({
+        grid.arrange(
+          grobs = static_plots,
+          ncol = grid_layout$ncol,
+          nrow = grid_layout$nrow
+        )
+      }, error = function(e) {
+        message("Error in grid.arrange: ", e$message)
+        print(static_plots)
+      })
+      
     } else {
-      # Print individual plots on separate pages if no grid layout
       for (plot in static_plots) {
         print(plot)
       }
     }
   }
 
-  # Close the PDF device after all plots are done
   dev.off()
 
-  # Save HTML file with interactive plots if needed
   out_html_file <- file.path(out_dir, paste0(filename, ".html"))
   message("Saving combined HTML file: ", out_html_file)
   htmltools::save_html(
@@ -681,6 +652,7 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
   )
 }
 
+
 generate_scatter_plot <- function(plot, config) {
 
   # Define the points
@@ -1118,7 +1090,7 @@ generate_interaction_plot_configs <- function(df_summary, df_interactions, type)
         x_breaks = unique(group_data$conc_num_factor_factor),
         x_labels = as.character(unique(group_data$conc_num)),
         ylim_vals = y_limits,
-        filter_na = TRUE,
+        # filter_na = TRUE,
         lm_line = list(
           intercept = lm_intercept_value,
           slope = lm_slope_value,