From f4c9985e40c233ab09077d1279ab21ad2a52a347 Mon Sep 17 00:00:00 2001 From: Bryan Roessler Date: Sun, 1 Sep 2024 17:54:08 -0400 Subject: [PATCH] Fix dataframe mutation order --- workflow/apps/r/calculate_interaction_zscores5.R | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/workflow/apps/r/calculate_interaction_zscores5.R b/workflow/apps/r/calculate_interaction_zscores5.R index 17a02ff5..bae8a882 100644 --- a/workflow/apps/r/calculate_interaction_zscores5.R +++ b/workflow/apps/r/calculate_interaction_zscores5.R @@ -561,11 +561,11 @@ main <- function() { max_conc <- max(df$conc_num_factor) # QC - # Filter the df above sd tolerance + # Filter the df above sd tolerance for raw L vs K plot df_above_tolerance <- df %>% filter(DB == 1) - # Exclude variables above delta bg tolerance - df_na <- df_above_tolerance %>% + # Set vars above the delta background tolerance to NA + df_na <- df %>% mutate( L = ifelse(DB == 1, NA, L), r = ifelse(DB == 1, NA, r), @@ -577,10 +577,12 @@ main <- function() { # 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, out_dir_qc, "After_QC", variables) - # generate_and_save_plots(df_no_zeros, out_dir_qc, "No_Zeros", variables) + 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, df_above_tolerance, df_no_zeros) # Calculate summary statistics message("Calculating summary statistics for all strains")