Allow missing y_var for some plot types

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -336,58 +336,58 @@ 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) {
+  plots <- lapply(plot_configs, function(config) {
+    df <- config$df
     
-  # Helper function for plot type logic
+    # Check if y_var is NULL and adjust the aes mapping
-  apply_plot_type <- function(plot, config) {
+    aes_mapping <- if (is.null(config$y_var)) {
-    switch(config$plot_type,
+      aes(x = !!sym(config$x_var), color = as.factor(!!sym(config$color_var)))
-      "rank" = {
+    } else {
-        plot <- plot + geom_point(size = 0.1, shape = 3)
+      aes(x = !!sym(config$x_var), y = !!sym(config$y_var), color = as.factor(!!sym(config$color_var)))
-        if (!is.null(config$sd_band)) {
+    }
-          for (i in seq_len(config$sd_band)) {
+    
-            plot <- plot +
+    plot <- ggplot(df, aes_mapping)
-              annotate("rect", xmin = -Inf, xmax = Inf, ymin = i, ymax = Inf, fill = "#542788", alpha = 0.3) +
+    
-              annotate("rect", xmin = -Inf, xmax = Inf, ymin = -i, ymax = -Inf, fill = "orange", alpha = 0.3) +
+    # Handle plot types like "rank", "correlation", and default scatter/box/density
-              geom_hline(yintercept = c(-i, i), color = "gray")
+    if (config$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")
         }
-        plot
+      }
-      },
+      if (!is.null(config$enhancer_label)) {
-      "correlation" = {
+        plot <- plot + annotate("text", x = config$enhancer_label$x, y = config$enhancer_label$y,
-        plot + geom_point(shape = 3, color = "gray70") + geom_smooth(method = "lm", color = "tomato3") +
+          label = config$enhancer_label$label) +
-          annotate("text", x = 0, y = 0, label = config$correlation_text)
+          annotate("text", x = config$suppressor_label$x, y = config$suppressor_label$y, label = config$suppressor_label$label)
-      },
+      }
-      "box" = plot + geom_boxplot(),
+    } else if (config$plot_type == "correlation") {
-      "density" = plot + geom_density(),
+      plot <- plot + geom_point(shape = 3, color = "gray70") + geom_smooth(method = "lm", color = "tomato3") +
-      "bar" = plot + geom_bar(stat = "identity"),
+        annotate("text", x = 0, y = 0, label = config$correlation_text)
-      plot + geom_point(shape = 3) + geom_smooth(method = "lm", se = FALSE)  # Default scatter plot
+    } else {
-    )
+      # Adjust based on plot types that may or may not need y_var
-  }
+      if (config$plot_type == "box") {
+        plot <- plot + geom_boxplot()
+      } else if (config$plot_type == "density") {
+        plot <- plot + geom_density()
+      } else if (config$plot_type == "bar") {
+        plot <- plot + geom_bar(stat = "identity")
+      } else {
+        plot <- plot + geom_point(shape = 3) + geom_smooth(method = "lm", se = FALSE)
+      }
+    }
 
-  # Helper function for error bars
+    # Add error bars for "delta_bg" or general cases
-  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$ylim_vals)) {
@@ -399,17 +399,19 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
       theme_publication(legend_position = if (!is.null(config$legend_position)) config$legend_position else "bottom") +
       xlab(config$x_label %||% "") + ylab(config$y_label %||% "")
 
-    plot <- apply_annotations(plot, config)
+    # 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))
+    }
 
     return(plot)
   })
 
-  # Save plots to PDF
+  # Save the plots
   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
@@ -417,6 +419,7 @@ 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_interaction_plot_configs <- function(df, variables) {
   configs <- list()
 
@@ -661,11 +664,9 @@ main <- function() {
         title = paste("Raw L vs K for strains above delta background threshold of", df_above_tolerance$delta_bg_tolerance[[1]], "or above"),
         color_var = "conc_num",
         annotations = list(
-          list(
+          x = L_half_median,
-            x = L_half_median,
+          y = K_half_median,
-            y = K_half_median,
+          label = paste("Strains above delta background tolerance =", nrow(df_above_tolerance))
-            label = paste("Strains above delta background tolerance =", nrow(df_above_tolerance))
-          )
         ),
         error_bar = FALSE,
         legend_position = "right"