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@@ -883,7 +883,6 @@ main <- function() {
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write.csv(ss$summary_stats, file = file.path(out_dir, "max_observed_L_vals_for_spots_outside_2sd_K.csv"), row.names = FALSE)
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# Each plots list corresponds to a file
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- message("Generating quality control plot configurations")
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l_vs_k_plots <- list(
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list(
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df = df,
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@@ -1049,15 +1048,15 @@ main <- function() {
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)
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message("Generating quality control plots")
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- generate_and_save_plots(out_dir_qc, "L_vs_K_before_quality_control", l_vs_k_plots)
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- generate_and_save_plots(out_dir_qc, "frequency_delta_background", frequency_delta_bg_plots)
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- generate_and_save_plots(out_dir_qc, "L_vs_K_above_threshold", above_threshold_plots)
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- generate_and_save_plots(out_dir_qc, "plate_analysis", plate_analysis_plots)
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- generate_and_save_plots(out_dir_qc, "plate_analysis_boxplots", plate_analysis_boxplots)
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- generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros", plate_analysis_no_zeros_plots)
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- generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros_boxplots", plate_analysis_no_zeros_boxplots)
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- generate_and_save_plots(out_dir_qc, "L_vs_K_for_strains_2SD_outside_mean_K", l_outside_2sd_k_plots)
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- generate_and_save_plots(out_dir_qc, "delta_background_vs_K_for_strains_2sd_outside_mean_K", delta_bg_outside_2sd_k_plots)
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+ # generate_and_save_plots(out_dir_qc, "L_vs_K_before_quality_control", l_vs_k_plots)
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+ # generate_and_save_plots(out_dir_qc, "frequency_delta_background", frequency_delta_bg_plots)
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+ # generate_and_save_plots(out_dir_qc, "L_vs_K_above_threshold", above_threshold_plots)
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+ # generate_and_save_plots(out_dir_qc, "plate_analysis", plate_analysis_plots)
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+ # generate_and_save_plots(out_dir_qc, "plate_analysis_boxplots", plate_analysis_boxplots)
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+ # generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros", plate_analysis_no_zeros_plots)
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+ # generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros_boxplots", plate_analysis_no_zeros_boxplots)
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+ # generate_and_save_plots(out_dir_qc, "L_vs_K_for_strains_2SD_outside_mean_K", l_outside_2sd_k_plots)
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+ # generate_and_save_plots(out_dir_qc, "delta_background_vs_K_for_strains_2sd_outside_mean_K", delta_bg_outside_2sd_k_plots)
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# TODO: Originally this filtered L NA's
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# Let's try to avoid for now since stats have already been calculated
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@@ -1214,7 +1213,7 @@ main <- function() {
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file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K_lm.csv"), row.names = FALSE)
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# TODO needs explanation
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- zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions)
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+ zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions, variables = interaction_vars)
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rank_plot_configs <- c(
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generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_L", "Avg_Zscore_L", "L"),
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