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Fix dataframe mutation order

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This commit is contained in:
Bryan Roessler
2024-09-01 17:54:08 -04:00
parent e1f57ff7d7
commit f4c9985e40
1 changed files with 9 additions and 7 deletions
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16
workflow/apps/r/calculate_interaction_zscores5.R
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@@ -561,11 +561,11 @@ main <- function() {
max_conc <- max(df$conc_num_factor)
# QC
# Filter the df above sd tolerance
# Filter the df above sd tolerance for raw L vs K plot
df_above_tolerance <- df %>% filter(DB == 1)
# Exclude variables above delta bg tolerance
df_na <- df_above_tolerance %>%
# Set vars above the delta background tolerance to NA
df_na <- df %>%
mutate(
L = ifelse(DB == 1, NA, L),
r = ifelse(DB == 1, NA, r),
@@ -577,10 +577,12 @@ main <- function() {
# Generate QC PDFs and HTMLs
message("Generating QC plots")
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)
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, df_above_tolerance, df_no_zeros)
# Calculate summary statistics
message("Calculating summary statistics for all strains")