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Add interaction vars to ranks

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Bryan Roessler
2024-09-15 17:48:44 -04:00
parent 549090b572
commit f848a60871
1 changed files with 10 additions and 11 deletions
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21
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -883,7 +883,6 @@ main <- function() {
write.csv(ss$summary_stats, file = file.path(out_dir, "max_observed_L_vals_for_spots_outside_2sd_K.csv"), row.names = FALSE) write.csv(ss$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 # Each plots list corresponds to a file
message("Generating quality control plot configurations")
l_vs_k_plots <- list( l_vs_k_plots <- list(
list( list(
df = df, df = df,
@@ -1049,15 +1048,15 @@ main <- function() {
) )
message("Generating quality control plots") 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, "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, "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, "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", 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_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", 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, "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, "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, "delta_background_vs_K_for_strains_2sd_outside_mean_K", delta_bg_outside_2sd_k_plots)
# TODO: Originally this filtered L NA's # TODO: Originally this filtered L NA's
# Let's try to avoid for now since stats have already been calculated # 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) file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K_lm.csv"), row.names = FALSE)
# TODO needs explanation # 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( rank_plot_configs <- c(
generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_L", "Avg_Zscore_L", "L"), generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_L", "Avg_Zscore_L", "L"),