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Move plotting further down main() to work on df

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Bryan Roessler
2024-09-01 16:31:04 -04:00
parent ddb7a98e50
commit 403a7490eb
1 changed files with 8 additions and 12 deletions
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20
workflow/apps/r/calculate_interaction_zscores5.R
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@@ -564,18 +564,7 @@ main <- function() {
) )
df_no_zeros <- df_na %>% filter(L > 0) df_no_zeros <- df_na %>% filter(L > 0)
# Variables for QC analysis # Calculate summary statistics
variables <- c("L", "K", "r", "AUC", "delta_bg")
# Generate QC PDFs and HTMLs
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_no_zeros, df_above_tolerance)
# Summary statistics
variables <- c("L", "K", "r", "AUC") variables <- c("L", "K", "r", "AUC")
summary_stats <- calculate_summary_stats(df_na, variables, group_vars = c("conc_num", "conc_num_factor")) summary_stats <- calculate_summary_stats(df_na, variables, group_vars = c("conc_num", "conc_num_factor"))
write.csv(summary_stats, file = file.path(out_dir, "SummaryStats_ALLSTRAINS.csv"), row.names = FALSE) write.csv(summary_stats, file = file.path(out_dir, "SummaryStats_ALLSTRAINS.csv"), row.names = FALSE)
@@ -586,6 +575,13 @@ main <- function() {
stats_by_r <- summary_stats %>% select(starts_with("r_"), "OrfRep", "conc_num", "conc_num_factor") stats_by_r <- summary_stats %>% select(starts_with("r_"), "OrfRep", "conc_num", "conc_num_factor")
stats_by_auc <- summary_stats %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor") stats_by_auc <- summary_stats %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor")
# Generate QC PDFs and HTMLs
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)
# Process background strains # Process background strains
background_strains <- c("YDL227C") background_strains <- c("YDL227C")
lapply(background_strains, function(strain) { lapply(background_strains, function(strain) {