Cleanup plot inconsistincies

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -466,20 +466,21 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
 }
 
 generate_scatter_plot <- function(plot, config) {
-  
-  # Determine Shape, Size, and Position for geom_point
   shape <- if (!is.null(config$shape)) config$shape else 3
   size <- if (!is.null(config$size)) config$size else 0.1
-  position <- if (!is.null(config$position) && config$position == "jitter") "jitter" else "identity"
+    position <-
-  
+      if (!is.null(config$position) && config$position == "jitter") {
-  # Add geom_point with determined parameters
+        position_jitter(width = 0.1, height = 0)
+      } else {
+        "identity"
+      }
   plot <- plot + geom_point(
     shape = shape,
     size = size,
     position = position
   )
 
-  if (!is.null(config$cyan_points)) {
+  if (!is.null(config$cyan_points) && config$cyan_points) {
     plot <- plot + geom_point(
       aes(x = .data[[config$x_var]], y = .data[[config$y_var]]),
       color = "cyan",
@@ -514,19 +515,19 @@ generate_scatter_plot <- function(plot, config) {
         "rect",
         xmin = -Inf, xmax = Inf,
         ymin = config$sd_band, ymax = Inf,
-        fill = "#542788",
+        fill = ifelse(!is.null(config$fill_positive), config$fill_positive, "#542788"),
-        alpha = 0.3
+        alpha = ifelse(!is.null(config$alpha_positive), config$alpha_positive, 0.3)
       ) +
       annotate(
         "rect",
         xmin = -Inf, xmax = Inf,
         ymin = -config$sd_band, ymax = -Inf,
-        fill = "orange",
+        fill = ifelse(!is.null(config$fill_negative), config$fill_negative, "orange"),
-        alpha = 0.3
+        alpha = ifelse(!is.null(config$alpha_negative), config$alpha_negative, 0.3)
       ) +
       geom_hline(
         yintercept = c(-config$sd_band, config$sd_band),
-        color = "gray"
+        color = ifelse(!is.null(config$hl_color), config$hl_color, "gray")
       )
   }
 
@@ -590,7 +591,10 @@ generate_scatter_plot <- function(plot, config) {
           x = annotation$x,
           y = annotation$y,
           label = annotation$label,
-          na.rm = TRUE
+          hjust = ifelse(is.null(annotation$hjust), 0.5, annotation$hjust),
+          vjust = ifelse(is.null(annotation$vjust), 0.5, annotation$vjust),
+          size = ifelse(is.null(annotation$size), 4, annotation$size),
+          color = ifelse(is.null(annotation$color), "black", annotation$color)
         )
     }
   }
@@ -768,7 +772,7 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
   
   # SD-based plots for L and K
   for (variable in c("L", "K")) {
-
+    
     if (is_lm) {
       rank_var <- paste0("Rank_lm_", variable)
       zscore_var <- paste0("Z_lm_", variable)
@@ -778,9 +782,9 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
       zscore_var <- paste0("Avg_Zscore_", variable)
       y_label <- paste("Avg Z score", variable)
     }
-
+    
     for (sd_band in sd_bands) {
-
+      
       num_enhancers <- sum(df_filtered[[zscore_var]] >= sd_band, na.rm = TRUE)
       num_suppressors <- sum(df_filtered[[zscore_var]] <= -sd_band, na.rm = TRUE)
       
@@ -792,16 +796,24 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
         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_filtered[[rank_var]], na.rm = TRUE),
             y = 10,
-            label = paste("Deletion Enhancers =", num_enhancers)
+            label = paste("Deletion Enhancers =", num_enhancers),
+            hjust = 0.5,
+            vjust = 1
           ),
           list(
             x = median(df_filtered[[rank_var]], na.rm = TRUE),
             y = -10,
-            label = paste("Deletion Suppressors =", num_suppressors)
+            label = paste("Deletion Suppressors =", num_suppressors),
+            hjust = 0.5,
+            vjust = 0
           )
         ),
         shape = 3,
@@ -819,6 +831,10 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
         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,
@@ -868,9 +884,18 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
         title = title,
         annotations = list(
           list(
-            x = 0,
+            x = median(df_filtered[[rank_var]], na.rm = TRUE),
-            y = 0,
+            y = 10,
-            label = paste("R-squared =", round(lm_summary$r.squared, 2))
+            label = paste("Deletion Enhancers =", num_enhancers),
+            hjust = 0.5,
+            vjust = 1
+          ),
+          list(
+            x = median(df_filtered[[rank_var]], na.rm = TRUE),
+            y = -10,
+            label = paste("Deletion Suppressors =", num_suppressors),
+            hjust = 0.5,
+            vjust = 0
           )
         ),
         shape = 3,
@@ -916,7 +941,15 @@ generate_correlation_plot_configs <- function(df) {
       x_label = paste("z-score", gsub("Z_lm_", "", rel$x)),
       y_label = paste("z-score", gsub("Z_lm_", "", rel$y)),
       annotations = list(
-        list(x = 0, y = 0, label = paste("R-squared =", round(lm_summary$r.squared, 3)))
+        list(
+          x = Inf,
+          y = Inf,
+          label = paste("R-squared =", round(lm_summary$r.squared, 3)),
+          hjust = 1.1,
+          vjust = 2,
+          size = 4,
+          color = "black"
+        )
       ),
       add_smooth = TRUE,  # Add regression line
       lm_line = list(intercept = coef(lm_model)[1], slope = coef(lm_model)[2]),
@@ -1380,15 +1413,14 @@ main <- function() {
         )
 
       # Re-rank
-      zscores_interactions_filtered <- process_data(
+      zscores_interactions_filtered_ranked <- process_data(
         df = zscores_interactions_filtered,
         variables = interaction_vars,
-        filter_na = TRUE, # TODO what I'm currently having issues with
         rank = TRUE
       )
 
       rank_plot_filtered_configs <- generate_rank_plot_configs(
-        df = zscores_interactions_filtered,
+        df = zscores_interactions_filtered_ranked,
         variables = interaction_vars,
         is_lm = FALSE
       )
@@ -1402,7 +1434,7 @@ main <- function() {
 
       message("Generating filtered ranked linear model plots")
       rank_plot_lm_filtered_configs <- generate_rank_plot_configs(
-        df = zscores_interactions_filtered,
+        df = zscores_interactions_filtered_ranked,
         variables = interaction_vars,
         is_lm = TRUE
       )