Vecotrize plot generation

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -155,9 +155,8 @@ update_gene_names <- function(df, sgd_gene_list) {
 
 # Calculate summary statistics for all variables
 calculate_summary_stats <- function(df, variables, group_vars = c("conc_num", "conc_num_factor")) {
-  df <- df %>%
-    mutate(across(all_of(variables), ~ ifelse(. == 0, NA, .)))
 
+  # Summarize the variables within the grouped data
   summary_stats <- df %>%
     group_by(across(all_of(group_vars))) %>%
     summarise(
@@ -165,16 +164,18 @@ calculate_summary_stats <- function(df, variables, group_vars = c("conc_num", "c
       across(all_of(variables), list(
         mean = ~mean(., na.rm = TRUE),
         median = ~median(., na.rm = TRUE),
-        max = ~max(., na.rm = TRUE),
-        min = ~min(., na.rm = TRUE),
+        max = ~ ifelse(all(is.na(.)), NA, max(., na.rm = TRUE)),
+        min = ~ ifelse(all(is.na(.)), NA, min(., na.rm = TRUE)),
         sd = ~sd(., na.rm = TRUE),
-        se = ~sd(., na.rm = TRUE) / sqrt(sum(!is.na(.)) - 1)
+        se = ~ ifelse(all(is.na(.)), NA, sd(., na.rm = TRUE) / sqrt(sum(!is.na(.)) - 1))
       ), .names = "{.fn}_{.col}")
     )
-
+  
+  # Prevent .x and .y suffix issues by renaming columns
   df_cleaned <- df %>%
-    select(-any_of(names(summary_stats)))
-
+    select(-any_of(setdiff(names(summary_stats), group_vars))) # Avoid duplicate columns in the final join
+  
+  # Join the stats back to the original dataframe
   df_with_stats <- left_join(df_cleaned, summary_stats, by = group_vars)
 
   return(list(summary_stats = summary_stats, df_with_stats = df_with_stats))
@@ -336,45 +337,57 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
 
 generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_layout = NULL) {
   
-  `%||%` <- function(a, b) if (!is.null(a)) a else b
-
-  plots <- lapply(plot_configs, function(config) {
-    df <- config$df
-    plot <- ggplot(df, aes(x = !!sym(config$x_var), y = !!sym(config$y_var), color = as.factor(!!sym(config$color_var))))
-
-    # Handle plot types like "rank", "correlation", and default scatter/box/density
-    if (config$plot_type == "rank") {
-      plot <- plot + geom_point(size = 0.1, shape = 3)
-      if (!is.null(config$sd_band)) {
-        for (i in seq_len(config$sd_band)) {
-          plot <- plot +
-            annotate("rect", xmin = -Inf, xmax = Inf, ymin = i, ymax = Inf, fill = "#542788", alpha = 0.3) +
-            annotate("rect", xmin = -Inf, xmax = Inf, ymin = -i, ymax = -Inf, fill = "orange", alpha = 0.3) +
-            geom_hline(yintercept = c(-i, i), color = "gray")
+  # Helper function for plot type logic
+  apply_plot_type <- function(plot, config) {
+    switch(config$plot_type,
+      "rank" = {
+        plot <- plot + geom_point(size = 0.1, shape = 3)
+        if (!is.null(config$sd_band)) {
+          for (i in seq_len(config$sd_band)) {
+            plot <- plot +
+              annotate("rect", xmin = -Inf, xmax = Inf, ymin = i, ymax = Inf, fill = "#542788", alpha = 0.3) +
+              annotate("rect", xmin = -Inf, xmax = Inf, ymin = -i, ymax = -Inf, fill = "orange", alpha = 0.3) +
+              geom_hline(yintercept = c(-i, i), color = "gray")
+          }
         }
-      }
-      if (!is.null(config$enhancer_label)) {
-        plot <- plot + annotate("text", x = config$enhancer_label$x, y = config$enhancer_label$y, label = config$enhancer_label$label) +
-          annotate("text", x = config$suppressor_label$x, y = config$suppressor_label$y, label = config$suppressor_label$label)
-      }
-    } else if (config$plot_type == "correlation") {
-      plot <- plot + geom_point(shape = 3, color = "gray70") + geom_smooth(method = "lm", color = "tomato3") +
-        annotate("text", x = 0, y = 0, label = config$correlation_text)
-    } else {
-      plot <- plot + aes(y = !!sym(config$y_var)) +
-        if (config$plot_type == "box") geom_boxplot() else
-        if (config$plot_type == "density") geom_density() else
-        if (config$plot_type == "bar") geom_bar(stat = "identity") else geom_point(shape = 3) + geom_smooth(method = "lm", se = FALSE)
-    }
+        plot
+      },
+      "correlation" = {
+        plot + geom_point(shape = 3, color = "gray70") + geom_smooth(method = "lm", color = "tomato3") +
+          annotate("text", x = 0, y = 0, label = config$correlation_text)
+      },
+      "box" = plot + geom_boxplot(),
+      "density" = plot + geom_density(),
+      "bar" = plot + geom_bar(stat = "identity"),
+      plot + geom_point(shape = 3) + geom_smooth(method = "lm", se = FALSE)  # Default scatter plot
+    )
+  }
 
-    # Add error bars for "delta_bg" or general cases
-    if (config$error_bar %||% FALSE) {
+  # Helper function for error bars
+  apply_error_bars <- function(plot, config) {
+    if (!is.null(config$error_bar) && config$error_bar) {
       y_mean_col <- paste0("mean_", config$y_var)
       y_sd_col <- paste0("sd_", config$y_var)
       plot <- plot + geom_errorbar(aes(ymin = !!sym(y_mean_col) - !!sym(y_sd_col),
-        ymax = !!sym(y_mean_col) + !!sym(y_sd_col)), width = 0.1) +
+                                      ymax = !!sym(y_mean_col) + !!sym(y_sd_col)), width = 0.1) +
         geom_point(aes(y = !!sym(y_mean_col)), size = 0.6)
     }
+    plot
+  }
+
+  # Helper function for annotations
+  apply_annotations <- function(plot, config) {
+    if (!is.null(config$annotations)) {
+      plot <- plot + geom_text(aes(x = config$annotations$x, y = config$annotations$y, label = config$annotations$label))
+    }
+    plot
+  }
+
+  # Generate each plot
+  plots <- lapply(plot_configs, function(config) {
+    plot <- ggplot(config$df, aes(x = !!sym(config$x_var), y = !!sym(config$y_var), color = as.factor(!!sym(config$color_var))))
+    plot <- apply_plot_type(plot, config)
+    plot <- apply_error_bars(plot, config)
 
     # Apply y-limits if provided
     if (!is.null(config$ylim_vals)) {
@@ -382,27 +395,25 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
     }
 
     # Apply labels, titles, and legends
-    plot <- plot + ggtitle(config$title) + theme_publication(legend_position = config$legend_position %||% "bottom") +
-      if (!is.null(config$x_label)) xlab(config$x_label) else NULL +
-      if (!is.null(config$y_label)) ylab(config$y_label) else NULL
+    plot <- plot + ggtitle(config$title) +
+      theme_publication(legend_position = if (!is.null(config$legend_position)) config$legend_position else "bottom") +
+      xlab(config$x_label %||% "") + ylab(config$y_label %||% "")
 
-    # Add annotations if available
-    if (!is.null(config$annotations)) {
-      plot <- plot + geom_text(aes(x = config$annotations$x, y = config$annotations$y, label = config$annotations$label))
-    }
+    plot <- apply_annotations(plot, config)
 
     return(plot)
   })
 
-  # Save the plots
+  # Save plots to PDF
   pdf(file.path(output_dir, paste0(file_name, ".pdf")), width = 14, height = 9)
   lapply(plots, print)
   dev.off()
 
+  # Generate Plotly versions for interactive HTML
   plotly_plots <- lapply(plots, function(plot) suppressWarnings(ggplotly(plot) %>% layout(legend = list(orientation = "h"))))
 
   # Handle grid layout
-  combined_plot <- subplot(plotly_plots, nrows = grid_layout$nrow %||% length(plots), margin = 0.05)
+  combined_plot <- subplot(plotly_plots, nrows = if (!is.null(grid_layout)) grid_layout$nrow else length(plots), margin = 0.05)
   saveWidget(combined_plot, file = file.path(output_dir, paste0(file_name, ".html")), selfcontained = TRUE)
 }
 
@@ -727,7 +738,7 @@ main <- function() {
       }
 
     l_outside_2sd_k_plots <- list(
-      list(df = X_outside_2SD_K, x_var = "l", y_var = "K", plot_type = "scatter",
+      list(df = df_na_l_outside_2sd_k_stats, x_var = "l", y_var = "K", plot_type = "scatter",
         title = "Raw L vs K for strains falling outside 2SD of the K mean at each Conc",
         color_var = "conc_num",
         legend_position = "right"
@@ -735,7 +746,7 @@ main <- function() {
     )
 
     delta_bg_outside_2sd_k_plots <- list(
-      list(df = X_outside_2SD_K, x_var = "delta_bg", y_var = "K", plot_type = "scatter",
+      list(df = df_na_l_outside_2sd_k_stats, x_var = "delta_bg", y_var = "K", plot_type = "scatter",
         title = "Delta Background vs K for strains falling outside 2SD of the K mean at each Conc",
         color_var = "conc_num",
         legend_position = "right"