bryan/hartman-server
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Add more informative output

Browse Source
This commit is contained in:
Bryan Roessler
2024-09-01 17:33:40 -04:00
parent c6c4870d46
commit e1f57ff7d7
1 changed files with 59 additions and 56 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
workflow/apps/r/calculate_interaction_zscores5.R
View File

@@ -233,6 +233,10 @@ calculate_summary_stats <- function(df, variables, group_vars = c("conc_num", "c
summary_stats <- df %>% summary_stats <- df %>%
group_by(across(all_of(group_vars))) %>% group_by(across(all_of(group_vars))) %>%
summarise(across(all_of(variables), list( summarise(across(all_of(variables), list(
N = ~{
message("Calculating summary statistics for ", cur_column())
n()
},
mean = ~mean(.x, na.rm = TRUE), mean = ~mean(.x, na.rm = TRUE),
median = ~median(.x, na.rm = TRUE), median = ~median(.x, na.rm = TRUE),
max = ~max(.x, na.rm = TRUE), max = ~max(.x, na.rm = TRUE),
@@ -284,7 +288,6 @@ save_plots <- function(file_name, plot_list, output_dir) {
message("Error in plot: ", plot_name, "\n", e) message("Error in plot: ", plot_name, "\n", e)
return(NULL) return(NULL)
}) })
if (!is.null(pgg)) { if (!is.null(pgg)) {
saveWidget(pgg, saveWidget(pgg,
file = file.path(output_dir, file = file.path(output_dir,
@@ -329,8 +332,8 @@ process_strains <- function(df, l_within_2sd_k, strain, output_dir) {
return(df_strains) return(df_strains)
} }
calculate_interaction_scores <- function(df, df_stats_by_l, df_stats_by_k, calculate_interaction_scores <- function(df, df_stats_by_l, df_stats_by_k, df_stats_by_r, df_stats_by_auc,
df_stats_by_r, df_stats_by_auc, background_means, max_conc, variables, group_vars = c("OrfRep", "Gene", "num")) { background_means, max_conc, variables, group_vars = c("OrfRep", "Gene", "num")) {
# Calculate all necessary statistics and shifts in one step # Calculate all necessary statistics and shifts in one step
interaction_scores_all <- df %>% interaction_scores_all <- df %>%
@@ -574,10 +577,10 @@ main <- function() {
# 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, out_dir_qc, "After_QC", variables) # 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_no_zeros, out_dir_qc, "No_Zeros", variables)
# Calculate summary statistics # Calculate summary statistics
message("Calculating summary statistics for all strains") message("Calculating summary statistics for all strains")