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

Preserve conc cols for later

Browse Source
This commit is contained in:
Bryan Roessler
2024-09-24 20:40:09 -04:00
parent 89b32de29c
commit eaf75f8892
1 changed files with 8 additions and 17 deletions
Download Patch File Download Diff File Expand all files Collapse all files

25
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
View File

@@ -193,8 +193,7 @@ calculate_summary_stats <- function(df, variables, group_vars) {
return(list(summary_stats = summary_stats, df_with_stats = df_joined)) return(list(summary_stats = summary_stats, df_with_stats = df_joined))
} }
calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", "r", "AUC"), calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", "r", "AUC")) {
group_vars = c("OrfRep", "Gene", "num")) {
# Calculate total concentration variables # Calculate total concentration variables
total_conc_num <- length(unique(df$conc_num)) total_conc_num <- length(unique(df$conc_num))
@@ -221,7 +220,7 @@ calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", "
)$df_with_stats )$df_with_stats
calculations <- calculations %>% calculations <- calculations %>%
group_by(across(all_of(group_vars))) %>% group_by(OrfRep, Gene, num) %>%
mutate( mutate(
NG = sum(NG, na.rm = TRUE), NG = sum(NG, na.rm = TRUE),
DB = sum(DB, na.rm = TRUE), DB = sum(DB, na.rm = TRUE),
@@ -303,12 +302,8 @@ calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", "
# Summarize some of the stats # Summarize some of the stats
interactions <- calculations %>% interactions <- calculations %>%
group_by(across(all_of(group_vars))) %>% group_by(OrfRep, Gene, num) %>%
mutate( mutate(
OrfRep = first(OrfRep),
Gene = first(Gene),
num = first(num),
# Calculate raw shifts # Calculate raw shifts
Raw_Shift_L = first(Raw_Shift_L), Raw_Shift_L = first(Raw_Shift_L),
Raw_Shift_K = first(Raw_Shift_K), Raw_Shift_K = first(Raw_Shift_K),
@@ -355,7 +350,7 @@ calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", "
interactions <- interactions %>% interactions <- interactions %>%
select( select(
"OrfRep", "Gene", "num", "NG", "DB", "SM", "OrfRep", "Gene", "conc_num", "conc_num_factor", "num", "NG", "DB", "SM",
"Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_r", "Raw_Shift_AUC", "Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_r", "Raw_Shift_AUC",
"Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC", "Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC",
"Sum_Z_Score_L", "Sum_Z_Score_K", "Sum_Z_Score_r", "Sum_Z_Score_AUC", "Sum_Z_Score_L", "Sum_Z_Score_K", "Sum_Z_Score_r", "Sum_Z_Score_AUC",
@@ -364,21 +359,17 @@ calculate_interaction_scores <- function(df, max_conc, variables = c("L", "K", "
"R_Squared_L", "R_Squared_K", "R_Squared_r", "R_Squared_AUC", "R_Squared_L", "R_Squared_K", "R_Squared_r", "R_Squared_AUC",
"Z_lm_L", "Z_lm_K", "Z_lm_r", "Z_lm_AUC") "Z_lm_L", "Z_lm_K", "Z_lm_r", "Z_lm_AUC")
# cleaned_df <- df %>%
# select(-any_of(setdiff(intersect(names(df), names(calculations)), group_vars)))
# calculations_joined <- left_join(cleaned_df, calculations, by = c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor"))
cleaned_df <- df %>% cleaned_df <- df %>%
select(-any_of(setdiff(intersect(names(df), names(interactions)), group_vars))) select(-any_of(
setdiff(intersect(names(df), names(interactions)),
c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor"))))
interactions_joined <- left_join(cleaned_df, interactions, by = c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor")) interactions_joined <- left_join(cleaned_df, interactions, by = c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor"))
return(list( return(list(
calculations = calculations, calculations = calculations,
interactions = interactions, interactions = interactions,
interactions_joined = interactions_joined interactions_joined = interactions_joined))
))
} }
generate_and_save_plots <- function(out_dir, filename, plot_configs, grid_layout = NULL) { generate_and_save_plots <- function(out_dir, filename, plot_configs, grid_layout = NULL) {