Fix sd vars

workflow/apps/r/calculate_interaction_zscores5.R

@@ -192,29 +192,29 @@ calculate_summary_stats <- function(df, variables, group_vars = c("conc_num", "c
   summary_stats <- df %>%
     group_by(across(all_of(group_vars))) %>%
     summarise(across(all_of(variables), list(
-      N = ~length(.),
+      N = ~length(na.omit(.)),  # Exclude NA values from count
-      mean = ~mean(., na.rm = TRUE),
+      mean = ~mean(., na.rm = TRUE),  # Mean ignoring NAs
-      median = ~median(., na.rm = TRUE),
+      median = ~median(., na.rm = TRUE),  # Median ignoring NAs
-      max = ~max(., na.rm = TRUE),
+      max = ~ifelse(all(is.na(.)), NA, max(., na.rm = TRUE)),  # Handle groups where all values are NA
-      min = ~min(., na.rm = TRUE),
+      min = ~ifelse(all(is.na(.)), NA, min(., na.rm = TRUE)),  # Handle groups where all values are NA
-      sd = ~sd(., na.rm = TRUE)
+      sd = ~sd(., na.rm = TRUE)  # Standard deviation ignoring NAs
     ), .names = "{.fn}_{.col}")) %>%
     mutate(
-      se_L = sd_L / sqrt(N_L - 1),
+      se_L = ifelse(N_L > 1, sd_L / sqrt(N_L - 1), NA),  # Standard error with check for division by zero
-      se_K = sd_K / sqrt(N_K - 1),
+      se_K = ifelse(N_K > 1, sd_K / sqrt(N_K - 1), NA),
-      se_r = sd_r / sqrt(N_r - 1),
+      se_r = ifelse(N_r > 1, sd_r / sqrt(N_r - 1), NA),
-      se_AUC = sd_AUC / sqrt(N_AUC - 1),
+      se_AUC = ifelse(N_AUC > 1, sd_AUC / sqrt(N_AUC - 1), NA),
-      z_max_L = (max_L - mean_L) / sd_L,
+      z_max_L = ifelse(sd_L == 0, NA, (max_L - mean_L) / sd_L),  # Avoid division by zero for Z-scores
-      z_max_K = (max_K - mean_K) / sd_K,
+      z_max_K = ifelse(sd_K == 0, NA, (max_K - mean_K) / sd_K),
-      z_max_r = (max_r - mean_r) / sd_r,
+      z_max_r = ifelse(sd_r == 0, NA, (max_r - mean_r) / sd_r),
-      z_max_AUC = (max_AUC - mean_AUC) / sd_AUC
+      z_max_AUC = ifelse(sd_AUC == 0, NA, (max_AUC - mean_AUC) / sd_AUC)
     )
   
   return(summary_stats)
 }
 
 
-calculate_interaction_scores <- function(df_ref, df, max_conc, variables, group_vars = c("OrfRep", "Gene", "num")) {
+calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c("OrfRep", "Gene", "num")) {
 
   # Calculate total concentration variables
   total_conc_num <- length(unique(df$conc_num))
@@ -351,7 +351,7 @@ generate_plot <- function(df, x_var, y_var = NULL, plot_type, color_var = "conc_
     "scatter" = plot + geom_point() + geom_smooth(method = "lm", se = FALSE),
     "box" = plot + geom_boxplot(),
     "density" = plot + geom_density(),
-    "bar" = plot + geom_bar(stat = "identity"),
+    "bar" = plot + geom_bar(),
     plot  # Default: return the plot as is
   )
   
@@ -548,7 +548,7 @@ generate_plots <- function(df, x_var, y_vars, plot_type, color_var = "conc_num",
     } else if (plot_type == "density") {
       plot <- plot + geom_density()
     } else if (plot_type == "bar") {
-      plot <- plot + geom_bar(stat = "identity")
+      plot <- plot + geom_bar()
     }
     
     if (!is.null(x_label)) plot <- plot + xlab(x_label)
@@ -657,9 +657,9 @@ main <- function() {
 
     # Filter data within and outside 2SD
     within_2sd_k <- stats_joined %>%
-      filter(K >= (K_mean - 2 * K_sd) & K <= (K_mean + 2 * K_sd))
+      filter(K >= (mean_K - 2 * sd_K) & K <= (mean_K + 2 * sd_K))
     outside_2sd_k <- stats_joined %>%
-      filter(K < (K_mean - 2 * K_sd) | K > (K_mean + 2 * K_sd))
+      filter(K < (mean_K - 2 * sd_K) | K > (mean_K + 2 * sd_K))
 
     # Summary statistics for within and outside 2SD of K
     l_within_2sd_k <- calculate_summary_stats(within_2sd_k, "L", group_vars = c("conc_num", "conc_num_factor"))
@@ -730,8 +730,8 @@ main <- function() {
       # Calculate interactions
       variables <- c("L", "K", "r", "AUC")
       # We are recalculating some of the data here
-      reference_results <- calculate_interaction_scores(stats_joined, reference_strain, max_conc, variables)
+      reference_results <- calculate_interaction_scores(reference_strain, max_conc, variables)
-      deletion_results <- calculate_interaction_scores(stats_joined, deletion_strains, max_conc, variables)
+      deletion_results <- calculate_interaction_scores(deletion_strains, max_conc, variables)
       
       zscores_calculations_reference <- reference_results$zscores_calculations
       zscores_interactions_reference <- reference_results$zscores_interactions