From 403a7490ebc2c8267247f5ea14ab64ac66d60dba Mon Sep 17 00:00:00 2001 From: Bryan Roessler Date: Sun, 1 Sep 2024 16:31:04 -0400 Subject: [PATCH] Move plotting further down main() to work on df --- .../apps/r/calculate_interaction_zscores5.R | 20 ++++++++----------- 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/workflow/apps/r/calculate_interaction_zscores5.R b/workflow/apps/r/calculate_interaction_zscores5.R index c3f4422e..efa707b8 100644 --- a/workflow/apps/r/calculate_interaction_zscores5.R +++ b/workflow/apps/r/calculate_interaction_zscores5.R @@ -564,18 +564,7 @@ main <- function() { ) df_no_zeros <- df_na %>% filter(L > 0) - # Variables for QC analysis - variables <- c("L", "K", "r", "AUC", "delta_bg") - - # Generate QC PDFs and HTMLs - 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, out_dir_qc, "After_QC", variables) - generate_and_save_plots(df_no_zeros, out_dir_qc, "No_Zeros", variables) - - rm(df_no_zeros, df_above_tolerance) - - # Summary statistics + # Calculate summary statistics variables <- c("L", "K", "r", "AUC") summary_stats <- calculate_summary_stats(df_na, variables, group_vars = c("conc_num", "conc_num_factor")) write.csv(summary_stats, file = file.path(out_dir, "SummaryStats_ALLSTRAINS.csv"), row.names = FALSE) @@ -585,6 +574,13 @@ main <- function() { stats_by_k <- summary_stats %>% select(starts_with("K_"), "OrfRep", "conc_num", "conc_num_factor") stats_by_r <- summary_stats %>% select(starts_with("r_"), "OrfRep", "conc_num", "conc_num_factor") stats_by_auc <- summary_stats %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor") + + # Generate QC PDFs and HTMLs + 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, out_dir_qc, "After_QC", variables) + generate_and_save_plots(df_no_zeros, out_dir_qc, "No_Zeros", variables) # Process background strains background_strains <- c("YDL227C")