Use htmltools to combine html widgets into single file

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -406,14 +406,6 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
     config <- plot_configs$plots[[i]]
     df <- config$df
 
-    message("Processing plot ", i, ": ", config$title)
-    message("Plot type: ", config$plot_type)
-
-    if (is.null(df)) {
-      message("Dataframe for plot ", i, " is NULL.")
-      next
-    }
-
     # Define aes_mapping, ensuring y_var is only used when it's not NULL
     aes_mapping <- switch(config$plot_type,
       "bar" = if (!is.null(config$color_var)) {
@@ -490,14 +482,16 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
 
   dev.off()
 
-  # Save individual interactive HTML plots
-  for (i in seq_along(plotly_plots)) {
-    html_file <- file.path(out_dir, paste0(filename, "_plot_", i, ".html"))
-    message("Saving HTML plot ", i, ": ", html_file)
-    htmlwidgets::saveWidget(plotly_plots[[i]], file = html_file, selfcontained = TRUE)
-  }
+  # Save combined HTML plot
+  out_html_file <- file.path(out_dir, paste0(filename, ".html"))
+  message("Saving combined HTML file: ", out_html_file)
+  htmltools::save_html(
+    htmltools::tagList(plotly_plots),
+    file = out_html_file
+  )
 }
 
+
 generate_scatter_plot <- function(plot, config) {
 
   # Define the points
@@ -804,136 +798,75 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL, plot_type =
 
 generate_rank_plot_configs <- function(df, variables, is_lm = FALSE, adjust = FALSE, overlap_color = FALSE) {
   sd_bands <- c(1, 2, 3)
-  avg_zscore_cols <- paste0("Avg_Zscore_", variables)
-  z_lm_cols <- paste0("Z_lm_", variables)
-
   configs <- list()
-
-  # Adjust values if necessary
-  if (adjust) {
-    df <- df %>%
-      mutate(across(all_of(avg_zscore_cols), ~ ifelse(is.na(.), 0.001, .))) %>%
-      mutate(across(all_of(z_lm_cols), ~ ifelse(is.na(.), 0.001, .)))
-  }
-
-  # Calculate rank columns for Avg_Zscore and Z_lm columns
-  df_ranked <- df %>%
-    mutate(across(all_of(avg_zscore_cols), rank, .names = "Rank_{col}")) %>%
-    mutate(across(all_of(z_lm_cols), rank, .names = "Rank_lm_{col}"))
-
-  # Generate plots for SD-based L and K variables
-  for (variable in c("L", "K")) {
-    rank_var <- if (is_lm) paste0("Rank_lm_", variable) else paste0("Rank_", variable)
-    zscore_var <- if (is_lm) paste0("Z_lm_", variable) else paste0("Avg_Zscore_", variable)
-    y_label <- if (is_lm) paste("Int Z score", variable) else paste("Avg Z score", variable)
-
-    for (sd_band in sd_bands) {
-      num_enhancers <- sum(df_ranked[[zscore_var]] >= sd_band, na.rm = TRUE)
-      num_suppressors <- sum(df_ranked[[zscore_var]] <= -sd_band, na.rm = TRUE)
-
-      # Plot with annotations
-      configs[[length(configs) + 1]] <- list(
-        df = df_ranked,
-        x_var = rank_var,
-        y_var = zscore_var,
-        plot_type = "scatter",
-        title = paste(y_label, "vs. Rank for", variable, "above", sd_band, "SD"),
-        sd_band = sd_band,
-        fill_positive = "#542788",
-        fill_negative = "orange",
-        alpha_positive = 0.3,
-        alpha_negative = 0.3,
-        annotations = list(
-          list(
-            x = median(df_ranked[[rank_var]], na.rm = TRUE),
-            y = max(df_ranked[[zscore_var]], na.rm = TRUE) * 0.9,
-            label = paste("Deletion Enhancers =", num_enhancers)
-          ),
-          list(
-            x = median(df_ranked[[rank_var]], na.rm = TRUE),
-            y = min(df_ranked[[zscore_var]], na.rm = TRUE) * 0.9,
-            label = paste("Deletion Suppressors =", num_suppressors)
-          )
-        ),
-        shape = 3,
-        size = 0.1,
-        y_label = y_label,
-        x_label = "Rank",
-        legend_position = "none"
-      )
-
-      # Plot without annotations
-      configs[[length(configs) + 1]] <- list(
-        df = df_ranked,
-        x_var = rank_var,
-        y_var = zscore_var,
-        plot_type = "scatter",
-        title = paste(y_label, "vs. Rank for", variable, "above", sd_band, "SD No Annotations"),
-        sd_band = sd_band,
-        fill_positive = "#542788",
-        fill_negative = "orange",
-        alpha_positive = 0.3,
-        alpha_negative = 0.3,
-        annotations = NULL,
-        shape = 3,
-        size = 0.1,
-        y_label = y_label,
-        x_label = "Rank",
-        legend_position = "none"
-      )
+  
+  # Adjust (if necessary) and rank columns
+  for (variable in variables) {
+    if (adjust) {
+      df[[paste0("Avg_Zscore_", variable)]] <- ifelse(is.na(df[[paste0("Avg_Zscore_", variable)]]), 0.001, df[[paste0("Avg_Zscore_", variable)]])
+      df[[paste0("Z_lm_", variable)]] <- ifelse(is.na(df[[paste0("Z_lm_", variable)]]), 0.001, df[[paste0("Z_lm_", variable)]])
     }
+    df[[paste0("Rank_", variable)]] <- rank(df[[paste0("Avg_Zscore_", variable)]], na.last = "keep")
+    df[[paste0("Rank_lm_", variable)]] <- rank(df[[paste0("Z_lm_", variable)]], na.last = "keep")
   }
 
-  # Generate Avg ZScore and Rank Avg ZScore plots for each variable
-  for (variable in variables) {
-    for (plot_type in c("Avg Zscore vs lm", "Rank Avg Zscore vs lm")) {
-      title <- paste(plot_type, variable)
-
-      # Define specific variables based on plot type
-      x_var <- if (plot_type == "Avg Zscore vs lm") paste0("Avg_Zscore_", variable) else paste0("Rank_", variable)
-      y_var <- if (plot_type == "Avg Zscore vs lm") paste0("Z_lm_", variable) else paste0("Rank_lm_", variable)
-
-      # Fit the linear model
-      lm_model <- lm(as.formula(paste(y_var, "~", x_var)), data = df_ranked)
-      intercept <- coef(lm_model)[1]
-      slope <- coef(lm_model)[2]
-      r_squared <- summary(lm_model)$r.squared
-
-      annotations <- list(
+  # Helper function to create a plot configuration
+  create_plot_config <- function(variable, rank_var, zscore_var, y_label, sd_band, with_annotations = TRUE) {
+    num_enhancers <- sum(df[[zscore_var]] >= sd_band, na.rm = TRUE)
+    num_suppressors <- sum(df[[zscore_var]] <= -sd_band, na.rm = TRUE)
+    
+    # Default plot config
+    plot_config <- list(
+      df = df,
+      x_var = rank_var,
+      y_var = zscore_var,
+      plot_type = "scatter",
+      title = paste(y_label, "vs. Rank for", variable, "above", sd_band),
+      sd_band = sd_band,
+      fill_positive = "#542788",
+      fill_negative = "orange",
+      alpha_positive = 0.3,
+      alpha_negative = 0.3,
+      annotations = NULL,
+      shape = 3,
+      size = 0.1,
+      y_label = y_label,
+      x_label = "Rank",
+      legend_position = "none"
+    )
+    
+    if (with_annotations) {
+      # Add specific annotations for plots with annotations
+      plot_config$annotations <- list(
+        list(
+          x = median(df[[rank_var]], na.rm = TRUE),
+          y = max(df[[zscore_var]], na.rm = TRUE) * 0.9,
+          label = paste("Deletion Enhancers =", num_enhancers)
+        ),
         list(
-          x = mean(range(df_ranked[[x_var]], na.rm = TRUE)),
-          y = mean(range(df_ranked[[y_var]], na.rm = TRUE)),
-          label = paste("R-squared =", round(r_squared, 2)),
-          hjust = 0.5,
-          vjust = 1,
-          size = 5
+          x = median(df[[rank_var]], na.rm = TRUE),
+          y = min(df[[zscore_var]], na.rm = TRUE) * 0.9,
+          label = paste("Deletion Suppressors =", num_suppressors)
         )
       )
+    }
 
-      rectangles <- if (plot_type == "Avg Zscore vs lm") {
-        list(list(xmin = -2, xmax = 2, ymin = -2, ymax = 2, fill = NA, color = "grey20", alpha = 0.1))
-      } else {
-        NULL
-      }
+    return(plot_config)
+  }
 
-      configs[[length(configs) + 1]] <- list(
-        df = df_ranked,
-        x_var = x_var,
-        y_var = y_var,
-        plot_type = "scatter",
-        title = title,
-        annotations = annotations,
-        shape = 3,
-        size = 0.25,
-        smooth = TRUE,
-        smooth_color = "black",
-        lm_line = list(intercept = intercept, slope = slope),
-        legend_position = "right",
-        color_var = if (overlap_color) "Overlap" else NULL,
-        x_label = x_var,
-        y_label = y_var,
-        rectangles = rectangles
-      )
+  # Generate plots for each variable
+  for (variable in variables) {
+    rank_var <- if (is_lm) paste0("Rank_lm_", variable) else paste0("Rank_", variable)
+    zscore_var <- if (is_lm) paste0("Z_lm_", variable) else paste0("Avg_Zscore_", variable)
+    y_label <- if (is_lm) paste("Int Z score", variable) else paste("Avg Z score", variable)
+    
+    # Loop through SD bands
+    for (sd_band in sd_bands) {
+      # Create plot with annotations
+      configs[[length(configs) + 1]] <- create_plot_config(variable, rank_var, zscore_var, y_label, sd_band, with_annotations = TRUE)
+      
+      # Create plot without annotations
+      configs[[length(configs) + 1]] <- create_plot_config(variable, rank_var, zscore_var, y_label, sd_band, with_annotations = FALSE)
     }
   }