diff --git a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R index e0208856..cd5ccf54 100644 --- a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R +++ b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R @@ -193,8 +193,7 @@ calculate_summary_stats <- function(df, variables, group_vars) { return(list(summary_stats = summary_stats, df_with_stats = df_joined)) } -calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", "r", "AUC"), - group_vars = c("OrfRep", "Gene", "num")) { +calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", "r", "AUC")) { # Calculate total concentration variables total_conc_num <- length(unique(df$conc_num)) @@ -221,7 +220,7 @@ calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", " )$df_with_stats calculations <- calculations %>% - group_by(across(all_of(group_vars))) %>% + group_by(OrfRep, Gene, num) %>% mutate( NG = sum(NG, na.rm = TRUE), DB = sum(DB, na.rm = TRUE), @@ -303,12 +302,8 @@ calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", " # Summarize some of the stats interactions <- calculations %>% - group_by(across(all_of(group_vars))) %>% + group_by(OrfRep, Gene, num) %>% mutate( - OrfRep = first(OrfRep), - Gene = first(Gene), - num = first(num), - # Calculate raw shifts Raw_Shift_L = first(Raw_Shift_L), Raw_Shift_K = first(Raw_Shift_K), @@ -355,7 +350,7 @@ calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", " interactions <- interactions %>% select( - "OrfRep", "Gene", "num", "NG", "DB", "SM", + "OrfRep", "Gene", "conc_num", "conc_num_factor", "num", "NG", "DB", "SM", "Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_r", "Raw_Shift_AUC", "Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC", "Sum_Z_Score_L", "Sum_Z_Score_K", "Sum_Z_Score_r", "Sum_Z_Score_AUC", @@ -364,21 +359,17 @@ calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", " "R_Squared_L", "R_Squared_K", "R_Squared_r", "R_Squared_AUC", "Z_lm_L", "Z_lm_K", "Z_lm_r", "Z_lm_AUC") - # cleaned_df <- df %>% - # select(-any_of(setdiff(intersect(names(df), names(calculations)), group_vars))) - - # calculations_joined <- left_join(cleaned_df, calculations, by = c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor")) - cleaned_df <- df %>% - select(-any_of(setdiff(intersect(names(df), names(interactions)), group_vars))) + select(-any_of( + setdiff(intersect(names(df), names(interactions)), + c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor")))) interactions_joined <- left_join(cleaned_df, interactions, by = c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor")) return(list( calculations = calculations, interactions = interactions, - interactions_joined = interactions_joined - )) + interactions_joined = interactions_joined)) } generate_and_save_plots <- function(out_dir, filename, plot_configs, grid_layout = NULL) {