From 9627bcc69bf5fb6f6ebadbed268dedb9c682636a Mon Sep 17 00:00:00 2001 From: Bryan Roessler Date: Sun, 1 Sep 2024 19:03:39 -0400 Subject: [PATCH] Add missing grouping var Gene --- .../apps/r/calculate_interaction_zscores5.R | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/workflow/apps/r/calculate_interaction_zscores5.R b/workflow/apps/r/calculate_interaction_zscores5.R index b97c6f34..c6880ed1 100644 --- a/workflow/apps/r/calculate_interaction_zscores5.R +++ b/workflow/apps/r/calculate_interaction_zscores5.R @@ -579,13 +579,13 @@ main <- function() { df_na %>% filter(if_all(c(L, r, AUC, K), is.finite)) } - # Generate QC PDFs and HTMLs - message("Generating QC plots") - variables <- c("L", "K", "r", "AUC", "delta_bg") - generate_and_save_plots(df, out_dir_qc, "Before_QC", variables, include_qc = TRUE) - generate_and_save_plots(df_above_tolerance, out_dir_qc, "Raw_L_vs_K_above_delta_bg_threshold", variables, include_qc = TRUE) - generate_and_save_plots(df_na_filtered, out_dir_qc, "After_QC", variables) - generate_and_save_plots(df_no_zeros, out_dir_qc, "No_Zeros", variables) + # # Generate QC PDFs and HTMLs + # message("Generating QC plots") + # variables <- c("L", "K", "r", "AUC", "delta_bg") + # generate_and_save_plots(df, out_dir_qc, "Before_QC", variables, include_qc = TRUE) + # generate_and_save_plots(df_above_tolerance, out_dir_qc, "Raw_L_vs_K_above_delta_bg_threshold", variables, include_qc = TRUE) + # generate_and_save_plots(df_na_filtered, out_dir_qc, "After_QC", variables) + # generate_and_save_plots(df_no_zeros, out_dir_qc, "No_Zeros", variables) rm(df, df_above_tolerance, df_no_zeros) @@ -622,9 +622,9 @@ main <- function() { # Recalculate summary statistics for the background strain message("Calculating summary statistics for background strain") stats_bg <- calculate_summary_stats(df_bg, variables, group_vars = c("OrfRep", "Gene", "conc_num", "conc_num_factor")) - stats_by_l_bg <- stats_bg %>% select(starts_with("L_"), "OrfRep", "conc_num", "conc_num_factor") - stats_by_k_bg <- stats_bg %>% select(starts_with("K_"), "OrfRep", "conc_num", "conc_num_factor") - stats_by_r_bg <- stats_bg %>% select(starts_with("r_"), "OrfRep", "conc_num", "conc_num_factor") + stats_by_l_bg <- stats_bg %>% select(starts_with("L_"), "OrfRep", "Gene", "conc_num", "conc_num_factor") + stats_by_k_bg <- stats_bg %>% select(starts_with("K_"), "OrfRep", "Gene", "conc_num", "conc_num_factor") + stats_by_r_bg <- stats_bg %>% select(starts_with("r_"), "OrfRep", "Gene", "conc_num", "conc_num_factor") stats_by_auc_bg <- stats_bg %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor") write.csv(stats_bg, file = file.path(out_dir, paste0("SummaryStats_BackgroundStrains_", strain, ".csv")),