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Fix interaction calculation grouping

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This commit is contained in:
Bryan Roessler
2024-09-13 00:37:06 -04:00
parent e469ed532f
commit 30c03f87cb
1 changed files with 10 additions and 12 deletions
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22
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -229,11 +229,9 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
sd = ~sd(., na.rm = TRUE), sd = ~sd(., na.rm = TRUE),
se = ~ifelse(sum(!is.na(.)) > 1, sd(., na.rm = TRUE) / sqrt(sum(!is.na(.)) - 1), NA) se = ~ifelse(sum(!is.na(.)) > 1, sd(., na.rm = TRUE) / sqrt(sum(!is.na(.)) - 1), NA)
), .names = "{.fn}_{.col}") ), .names = "{.fn}_{.col}")
) %>% )
ungroup()
stats <- stats %>% stats <- stats %>%
group_by(across(all_of(group_vars))) %>%
mutate( mutate(
Raw_Shift_L = mean_L[[1]] - bg_means$L, Raw_Shift_L = mean_L[[1]] - bg_means$L,
Raw_Shift_K = mean_K[[1]] - bg_means$K, Raw_Shift_K = mean_K[[1]] - bg_means$K,
@@ -272,7 +270,8 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
Zscore_K = Delta_K / WT_sd_K, Zscore_K = Delta_K / WT_sd_K,
Zscore_r = Delta_r / WT_sd_r, Zscore_r = Delta_r / WT_sd_r,
Zscore_AUC = Delta_AUC / WT_sd_AUC Zscore_AUC = Delta_AUC / WT_sd_AUC
) ) %>%
ungroup()
# Create linear models with error handling for missing/insufficient data # Create linear models with error handling for missing/insufficient data
# This part is a PITA so best to contain it in its own function # This part is a PITA so best to contain it in its own function
@@ -345,7 +344,8 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
Z_lm_K = (lm_Score_K - mean(lm_Score_K, na.rm = TRUE)) / sd(lm_Score_K, na.rm = TRUE), Z_lm_K = (lm_Score_K - mean(lm_Score_K, na.rm = TRUE)) / sd(lm_Score_K, na.rm = TRUE),
Z_lm_r = (lm_Score_r - mean(lm_Score_r, na.rm = TRUE)) / sd(lm_Score_r, na.rm = TRUE), Z_lm_r = (lm_Score_r - mean(lm_Score_r, na.rm = TRUE)) / sd(lm_Score_r, na.rm = TRUE),
Z_lm_AUC = (lm_Score_AUC - mean(lm_Score_AUC, na.rm = TRUE)) / sd(lm_Score_AUC, na.rm = TRUE) Z_lm_AUC = (lm_Score_AUC - mean(lm_Score_AUC, na.rm = TRUE)) / sd(lm_Score_AUC, na.rm = TRUE)
) ) %>%
ungroup()
# Declare column order for output # Declare column order for output
calculations <- stats %>% calculations <- stats %>%
@@ -361,9 +361,8 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
"Exp_L", "Exp_K", "Exp_r", "Exp_AUC", "Exp_L", "Exp_K", "Exp_r", "Exp_AUC",
"Delta_L", "Delta_K", "Delta_r", "Delta_AUC", "Delta_L", "Delta_K", "Delta_r", "Delta_AUC",
"Zscore_L", "Zscore_K", "Zscore_r", "Zscore_AUC", "Zscore_L", "Zscore_K", "Zscore_r", "Zscore_AUC",
"NG", "SM", "DB") %>% "NG", "SM", "DB")
ungroup()
interactions <- stats %>% interactions <- stats %>%
select("OrfRep", "Gene", "num", "Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_AUC", "Raw_Shift_r", select("OrfRep", "Gene", "num", "Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_AUC", "Raw_Shift_r",
"Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC", "Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC",
@@ -374,13 +373,12 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
"Z_lm_L", "Z_lm_K", "Z_lm_r", "Z_lm_AUC", "Z_lm_L", "Z_lm_K", "Z_lm_r", "Z_lm_AUC",
"NG", "SM", "DB") %>% "NG", "SM", "DB") %>%
arrange(desc(lm_Score_L)) %>% arrange(desc(lm_Score_L)) %>%
arrange(desc(NG)) %>% arrange(desc(NG))
ungroup()
df <- df %>% select(-any_of(setdiff(names(calculations), group_vars))) df <- df %>% select(-any_of(setdiff(names(calculations), group_vars)))
df <- left_join(df, calculations, by = group_vars) df <- left_join(df, calculations, by = group_vars)
df <- df %>% select(-any_of(setdiff(names(interactions), group_vars))) # df <- df %>% select(-any_of(setdiff(names(interactions), group_vars)))
df <- left_join(df, interactions, by = group_vars) # df <- left_join(df, interactions, by = group_vars)
return(list(calculations = calculations, interactions = interactions, joined = df)) return(list(calculations = calculations, interactions = interactions, joined = df))
} }