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

Refactor out individual stats dataframes

Browse Source
This commit is contained in:
Bryan Roessler
2024-09-01 22:38:59 -04:00
parent e915e77504
commit d91a38004a
1 changed files with 32 additions and 38 deletions
Download Patch File Download Diff File Expand all files Collapse all files

70
workflow/apps/r/calculate_interaction_zscores5.R
View File

@@ -283,7 +283,7 @@ process_strains <- function(df, l_within_2sd_k, strain) {
if (concentration > 0) { if (concentration > 0) {
max_l_theoretical <- l_within_2sd_k %>% max_l_theoretical <- l_within_2sd_k %>%
filter(conc_num_factor == concentration) %>% filter(conc_num_factor == concentration) %>%
pull(max_L) pull(L_max)
df_temp <- df_temp %>% df_temp <- df_temp %>%
mutate( mutate(
L = ifelse(L == 0 & !is.na(L), max_l_theoretical, L), L = ifelse(L == 0 & !is.na(L), max_l_theoretical, L),
@@ -297,14 +297,13 @@ process_strains <- function(df, l_within_2sd_k, strain) {
return(df_strains) return(df_strains)
} }
calculate_interaction_scores <- function(df, df_stats_by_l, df_stats_by_k, df_stats_by_r, df_stats_by_auc, calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c("OrfRep", "Gene", "num")) {
max_conc, variables, group_vars = c("OrfRep", "Gene", "num")) {
# Calculate background means # Pull the background means
L_mean_bg <- df %>% filter(conc_num_factor == 0) %>% pull(L_mean) l_mean_bg <- df %>% filter(conc_num_factor == 0) %>% pull(L_mean)
K_mean_bg <- df %>% filter(conc_num_factor == 0) %>% pull(K_mean) k_mean_bg <- df %>% filter(conc_num_factor == 0) %>% pull(K_mean)
r_mean_bg <- df %>% filter(conc_num_factor == 0) %>% pull(r_mean) r_mean_bg <- df %>% filter(conc_num_factor == 0) %>% pull(r_mean)
AUC_mean_bg <- df %>% filter(conc_num_factor == 0) %>% pull(AUC_mean) auc_mean_bg <- df %>% filter(conc_num_factor == 0) %>% pull(AUC_mean)
# 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 %>%
@@ -314,26 +313,26 @@ calculate_interaction_scores <- function(df, df_stats_by_l, df_stats_by_k, df_st
across(all_of(variables), list(mean = mean, sd = sd), na.rm = TRUE), across(all_of(variables), list(mean = mean, sd = sd), na.rm = TRUE),
NG = sum(NG, na.rm = TRUE), NG = sum(NG, na.rm = TRUE),
SM = sum(SM, na.rm = TRUE), SM = sum(SM, na.rm = TRUE),
raw_shift_l = mean(L, na.rm = TRUE) - L_mean_bg, raw_shift_l = mean(L, na.rm = TRUE) - l_mean_bg,
raw_shift_k = mean(K, na.rm = TRUE) - K_mean_bg, raw_shift_k = mean(K, na.rm = TRUE) - k_mean_bg,
raw_shift_r = mean(r, na.rm = TRUE) - r_mean_bg, raw_shift_r = mean(r, na.rm = TRUE) - r_mean_bg,
raw_shift_auc = mean(AUC, na.rm = TRUE) - AUC_mean_bg, raw_shift_auc = mean(AUC, na.rm = TRUE) - auc_mean_bg,
z_shift_l = raw_shift_l / df_stats_by_l$L_sd[1], z_shift_l = raw_shift_l / L_sd[1],
z_shift_k = raw_shift_k / df_stats_by_k$K_sd[1], z_shift_k = raw_shift_k / K_sd[1],
z_shift_r = raw_shift_r / df_stats_by_r$r_sd[1], z_shift_r = raw_shift_r / r_sd[1],
z_shift_auc = raw_shift_auc / df_stats_by_auc$AUC_sd[1], z_shift_auc = raw_shift_auc / AUC_sd[1],
exp_l = L_mean_bg + raw_shift_l, exp_l = l_mean_bg + raw_shift_l,
exp_k = K_mean_bg + raw_shift_k, exp_k = k_mean_bg + raw_shift_k,
exp_r = r_mean_bg + raw_shift_r, exp_r = r_mean_bg + raw_shift_r,
exp_auc = AUC_mean_bg + raw_shift_auc, exp_auc = auc_mean_bg + raw_shift_auc,
delta_l = mean(L, na.rm = TRUE) - exp_l, delta_l = mean(L, na.rm = TRUE) - exp_l,
delta_k = mean(K, na.rm = TRUE) - exp_k, delta_k = mean(K, na.rm = TRUE) - exp_k,
delta_r = mean(r, na.rm = TRUE) - exp_r, delta_r = mean(r, na.rm = TRUE) - exp_r,
delta_auc = mean(AUC, na.rm = TRUE) - exp_auc, delta_auc = mean(AUC, na.rm = TRUE) - exp_auc,
zscore_l = delta_l / df_stats_by_l$L_sd, zscore_l = delta_l / L_sd,
zscore_k = delta_k / df_stats_by_k$K_sd, zscore_k = delta_k / K_sd,
zscore_r = delta_r / df_stats_by_r$r_sd, zscore_r = delta_r / r_sd,
zscore_auc = delta_auc / df_stats_by_auc$AUC_sd, zscore_auc = delta_auc / AUC_sd,
sum_z_score_l = sum(zscore_l, na.rm = TRUE), sum_z_score_l = sum(zscore_l, na.rm = TRUE),
avg_zscore_l = sum_z_score_l / (length(variables) - sum(NG, na.rm = TRUE)), avg_zscore_l = sum_z_score_l / (length(variables) - sum(NG, na.rm = TRUE)),
sum_z_score_k = sum(zscore_k, na.rm = TRUE), sum_z_score_k = sum(zscore_k, na.rm = TRUE),
@@ -574,24 +573,21 @@ main <- function() {
stats_joined <- left_join(df_na, stats, by = c("conc_num", "conc_num_factor")) stats_joined <- left_join(df_na, stats, by = c("conc_num", "conc_num_factor"))
# Create separate dataframes for each variable (we'll use later for plotting) # Create separate dataframes for each variable (we'll use later for plotting)
stats_by_l <- stats_joined %>% select(starts_with("L_"), "OrfRep", "conc_num", "conc_num_factor") # stats_by_l <- stats_joined %>% select(starts_with("L_"), "OrfRep", "conc_num", "conc_num_factor")
stats_by_k <- stats_joined %>% select(starts_with("K_"), "OrfRep", "conc_num", "conc_num_factor") # stats_by_k <- stats_joined %>% select(starts_with("K_"), "OrfRep", "conc_num", "conc_num_factor")
stats_by_r <- stats_joined %>% select(starts_with("r_"), "OrfRep", "conc_num", "conc_num_factor") # stats_by_r <- stats_joined %>% select(starts_with("r_"), "OrfRep", "conc_num", "conc_num_factor")
stats_by_auc <- stats_joined %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor") # stats_by_auc <- stats_joined %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor")
# Originally this filtered L NA's # Originally this filtered L NA's
# I've removed that filtering for now since it didn't seem right but may need to add it back in later # I've removed that filtering for now since it didn't seem right but may need to add it back in later
# str(stats_by_k) # str(stats_by_k)
stats_by_k_joined <- left_join(df_na, stats_by_k, by = c("conc_num", "conc_num_factor"))
str(stats_by_k_joined)
# Filter data within 2SD # Filter data within 2SD
within_2sd_k <- stats_by_k %>% within_2sd_k <- stats_joined %>%
filter(K >= (K_mean - 2 * K_sd) & K <= (K_mean + 2 * K_sd)) filter(K >= (K_mean - 2 * K_sd) & K <= (K_mean + 2 * K_sd))
# Filter data outside 2SD # Filter data outside 2SD
outside_2sd_k <- stats_by_k %>% outside_2sd_k <- stats_joined %>%
filter(K < (K_mean - 2 * K_sd) | K > (K_mean + 2 * K_sd)) filter(K < (K_mean - 2 * K_sd) | K > (K_mean + 2 * K_sd))
# Calculate summary statistics for L within and outside 2SD of K # Calculate summary statistics for L within and outside 2SD of K
@@ -627,10 +623,10 @@ 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", "Gene", "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", "Gene", "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", "Gene", "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", "Gene", "conc_num", "conc_num_factor") # stats_by_auc_bg <- stats_bg %>% select(starts_with("AUC_"), "OrfRep", "Gene", "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")),
row.names = FALSE) row.names = FALSE)
@@ -666,11 +662,9 @@ main <- function() {
# Calculate interactions # Calculate interactions
variables <- c("L", "K", "r", "AUC") variables <- c("L", "K", "r", "AUC")
message("Calculating reference interaction scores") message("Calculating reference interaction scores")
reference_results <- calculate_interaction_scores(reference_strain, stats_by_l, reference_results <- calculate_interaction_scores(reference_strain, max_conc, variables)
stats_by_k, stats_by_r, stats_by_auc, max_conc, variables)
message("Calculating deletion interaction scores") message("Calculating deletion interaction scores")
deletion_results <- calculate_interaction_scores(deletion_strains, stats_by_l, deletion_results <- calculate_interaction_scores(deletion_strains, max_conc, variables)
stats_by_k, stats_by_r, stats_by_auc, max_conc, variables)
zscores_calculations_reference <- reference_results$zscores_calculations zscores_calculations_reference <- reference_results$zscores_calculations
zscores_interactions_reference <- reference_results$zscores_interactions zscores_interactions_reference <- reference_results$zscores_interactions