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Add missing grouping var Gene

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Bryan Roessler
2024-09-01 19:03:39 -04:00
parent 3fbde2de24
commit 9627bcc69b
1 changed files with 10 additions and 10 deletions
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20
workflow/apps/r/calculate_interaction_zscores5.R
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@@ -579,13 +579,13 @@ main <- function() {
df_na %>% filter(if_all(c(L, r, AUC, K), is.finite)) df_na %>% filter(if_all(c(L, r, AUC, K), is.finite))
} }
# Generate QC PDFs and HTMLs # # Generate QC PDFs and HTMLs
message("Generating QC plots") # message("Generating QC plots")
variables <- c("L", "K", "r", "AUC", "delta_bg") # 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, 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_above_tolerance, out_dir_qc, "Raw_L_vs_K_above_delta_bg_threshold", variables, include_qc = TRUE)
generate_and_save_plots(df_na_filtered, out_dir_qc, "After_QC", variables) # generate_and_save_plots(df_na_filtered, out_dir_qc, "After_QC", variables)
generate_and_save_plots(df_no_zeros, out_dir_qc, "No_Zeros", variables) # generate_and_save_plots(df_no_zeros, out_dir_qc, "No_Zeros", variables)
rm(df, df_above_tolerance, df_no_zeros) rm(df, df_above_tolerance, df_no_zeros)
@@ -622,9 +622,9 @@ main <- function() {
# Recalculate summary statistics for the background strain # Recalculate summary statistics for the background strain
message("Calculating summary statistics for background strain") message("Calculating summary statistics for background strain")
stats_bg <- calculate_summary_stats(df_bg, variables, group_vars = c("OrfRep", "Gene", "conc_num", "conc_num_factor")) stats_bg <- calculate_summary_stats(df_bg, variables, group_vars = c("OrfRep", "Gene", "conc_num", "conc_num_factor"))
stats_by_l_bg <- stats_bg %>% select(starts_with("L_"), "OrfRep", "conc_num", "conc_num_factor") stats_by_l_bg <- stats_bg %>% select(starts_with("L_"), "OrfRep", "Gene", "conc_num", "conc_num_factor")
stats_by_k_bg <- stats_bg %>% select(starts_with("K_"), "OrfRep", "conc_num", "conc_num_factor") stats_by_k_bg <- stats_bg %>% select(starts_with("K_"), "OrfRep", "Gene", "conc_num", "conc_num_factor")
stats_by_r_bg <- stats_bg %>% select(starts_with("r_"), "OrfRep", "conc_num", "conc_num_factor") stats_by_r_bg <- stats_bg %>% select(starts_with("r_"), "OrfRep", "Gene", "conc_num", "conc_num_factor")
stats_by_auc_bg <- stats_bg %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor") stats_by_auc_bg <- stats_bg %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor")
write.csv(stats_bg, write.csv(stats_bg,
file = file.path(out_dir, paste0("SummaryStats_BackgroundStrains_", strain, ".csv")), file = file.path(out_dir, paste0("SummaryStats_BackgroundStrains_", strain, ".csv")),