From f848a6087198d5c3dcb3fadf863acf67dcfdcacc Mon Sep 17 00:00:00 2001 From: Bryan Roessler Date: Sun, 15 Sep 2024 17:48:44 -0400 Subject: [PATCH] Add interaction vars to ranks --- .../apps/r/calculate_interaction_zscores.R | 21 +++++++++---------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R index 61111e01..16e2d416 100644 --- a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R +++ b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R @@ -883,7 +883,6 @@ main <- function() { write.csv(ss$summary_stats, file = file.path(out_dir, "max_observed_L_vals_for_spots_outside_2sd_K.csv"), row.names = FALSE) # Each plots list corresponds to a file - message("Generating quality control plot configurations") l_vs_k_plots <- list( list( df = df, @@ -1049,15 +1048,15 @@ main <- function() { ) message("Generating quality control plots") - generate_and_save_plots(out_dir_qc, "L_vs_K_before_quality_control", l_vs_k_plots) - generate_and_save_plots(out_dir_qc, "frequency_delta_background", frequency_delta_bg_plots) - generate_and_save_plots(out_dir_qc, "L_vs_K_above_threshold", above_threshold_plots) - generate_and_save_plots(out_dir_qc, "plate_analysis", plate_analysis_plots) - generate_and_save_plots(out_dir_qc, "plate_analysis_boxplots", plate_analysis_boxplots) - generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros", plate_analysis_no_zeros_plots) - generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros_boxplots", plate_analysis_no_zeros_boxplots) - generate_and_save_plots(out_dir_qc, "L_vs_K_for_strains_2SD_outside_mean_K", l_outside_2sd_k_plots) - generate_and_save_plots(out_dir_qc, "delta_background_vs_K_for_strains_2sd_outside_mean_K", delta_bg_outside_2sd_k_plots) + # generate_and_save_plots(out_dir_qc, "L_vs_K_before_quality_control", l_vs_k_plots) + # generate_and_save_plots(out_dir_qc, "frequency_delta_background", frequency_delta_bg_plots) + # generate_and_save_plots(out_dir_qc, "L_vs_K_above_threshold", above_threshold_plots) + # generate_and_save_plots(out_dir_qc, "plate_analysis", plate_analysis_plots) + # generate_and_save_plots(out_dir_qc, "plate_analysis_boxplots", plate_analysis_boxplots) + # generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros", plate_analysis_no_zeros_plots) + # generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros_boxplots", plate_analysis_no_zeros_boxplots) + # generate_and_save_plots(out_dir_qc, "L_vs_K_for_strains_2SD_outside_mean_K", l_outside_2sd_k_plots) + # generate_and_save_plots(out_dir_qc, "delta_background_vs_K_for_strains_2sd_outside_mean_K", delta_bg_outside_2sd_k_plots) # TODO: Originally this filtered L NA's # Let's try to avoid for now since stats have already been calculated @@ -1214,7 +1213,7 @@ main <- function() { file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K_lm.csv"), row.names = FALSE) # TODO needs explanation - zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions) + zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions, variables = interaction_vars) rank_plot_configs <- c( generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_L", "Avg_Zscore_L", "L"),