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Standardize output filenames

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This commit is contained in:
Bryan Roessler
2024-09-25 15:15:48 -04:00
parent b35966cb88
commit 1661f913d8
3 changed files with 54 additions and 53 deletions
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98
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -1295,9 +1295,9 @@ main <- function() {
group_vars = c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor") group_vars = c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor")
)$df_with_stats )$df_with_stats
reference_results <- calculate_interaction_scores(df_reference_stats, max_conc, bg_stats, group_vars = c("OrfRep", "Gene", "num")) reference_results <- calculate_interaction_scores(df_reference_stats, max_conc, bg_stats, group_vars = c("OrfRep", "Gene", "num"))
zscores_calculations_reference <- reference_results$calculations zscore_calculations_reference <- reference_results$calculations
zscores_interactions_reference <- reference_results$interactions zscore_interactions_reference <- reference_results$interactions
zscores_interactions_reference_joined <- reference_results$interactions_joined zscore_interactions_reference_joined <- reference_results$interactions_joined
message("Calculating deletion strain(s) interactions scores") message("Calculating deletion strain(s) interactions scores")
df_deletion_stats <- calculate_summary_stats( df_deletion_stats <- calculate_summary_stats(
@@ -1306,97 +1306,97 @@ main <- function() {
group_vars = c("OrfRep", "Gene", "conc_num", "conc_num_factor") group_vars = c("OrfRep", "Gene", "conc_num", "conc_num_factor")
)$df_with_stats )$df_with_stats
deletion_results <- calculate_interaction_scores(df_deletion_stats, max_conc, bg_stats, group_vars = c("OrfRep")) deletion_results <- calculate_interaction_scores(df_deletion_stats, max_conc, bg_stats, group_vars = c("OrfRep"))
zscores_calculations <- deletion_results$calculations zscore_calculations <- deletion_results$calculations
zscores_interactions <- deletion_results$interactions zscore_interactions <- deletion_results$interactions
zscores_interactions_joined <- deletion_results$interactions_joined zscore_interactions_joined <- deletion_results$interactions_joined
# Writing Z-Scores to file # Writing Z-Scores to file
write.csv(zscores_calculations_reference, file = file.path(out_dir, "RF_ZScores_Calculations.csv"), row.names = FALSE) write.csv(zscore_calculations_reference, file = file.path(out_dir, "zscore_calculations_reference.csv"), row.names = FALSE)
write.csv(zscores_calculations, file = file.path(out_dir, "ZScores_Calculations.csv"), row.names = FALSE) write.csv(zscore_calculations, file = file.path(out_dir, "zscore_calculations.csv"), row.names = FALSE)
write.csv(zscores_interactions_reference, file = file.path(out_dir, "RF_ZScores_Interaction.csv"), row.names = FALSE) write.csv(zscore_interactions_reference, file = file.path(out_dir, "zscore_interactions_reference.csv"), row.names = FALSE)
write.csv(zscores_interactions, file = file.path(out_dir, "ZScores_Interaction.csv"), row.names = FALSE) write.csv(zscore_interactions, file = file.path(out_dir, "zscore_interactions.csv"), row.names = FALSE)
# Create interaction plots # Create interaction plots
message("Generating reference interaction plots") message("Generating reference interaction plots")
reference_plot_configs <- generate_interaction_plot_configs(zscores_interactions_reference_joined, interaction_vars) reference_plot_configs <- generate_interaction_plot_configs(zscore_interactions_reference_joined, interaction_vars)
generate_and_save_plots(out_dir, "RF_interactionPlots", reference_plot_configs, grid_layout = list(ncol = 4, nrow = 3)) generate_and_save_plots(out_dir, "interaction_plots_reference", reference_plot_configs, grid_layout = list(ncol = 4, nrow = 3))
message("Generating deletion interaction plots") message("Generating deletion interaction plots")
deletion_plot_configs <- generate_interaction_plot_configs(zscores_interactions_joined, interaction_vars) deletion_plot_configs <- generate_interaction_plot_configs(zscore_interactions_joined, interaction_vars)
generate_and_save_plots(out_dir, "InteractionPlots", deletion_plot_configs, grid_layout = list(ncol = 4, nrow = 3)) generate_and_save_plots(out_dir, "interaction_plots", deletion_plot_configs, grid_layout = list(ncol = 4, nrow = 3))
# Define conditions for enhancers and suppressors # Define conditions for enhancers and suppressors
# TODO Add to study config? # TODO Add to study config?
threshold <- 2 threshold <- 2
enhancer_condition_L <- zscores_interactions$Avg_Zscore_L >= threshold enhancer_condition_L <- zscore_interactions$Avg_Zscore_L >= threshold
suppressor_condition_L <- zscores_interactions$Avg_Zscore_L <= -threshold suppressor_condition_L <- zscore_interactions$Avg_Zscore_L <= -threshold
enhancer_condition_K <- zscores_interactions$Avg_Zscore_K >= threshold enhancer_condition_K <- zscore_interactions$Avg_Zscore_K >= threshold
suppressor_condition_K <- zscores_interactions$Avg_Zscore_K <= -threshold suppressor_condition_K <- zscore_interactions$Avg_Zscore_K <= -threshold
# Subset data # Subset data
enhancers_L <- zscores_interactions[enhancer_condition_L, ] enhancers_L <- zscore_interactions[enhancer_condition_L, ]
suppressors_L <- zscores_interactions[suppressor_condition_L, ] suppressors_L <- zscore_interactions[suppressor_condition_L, ]
enhancers_K <- zscores_interactions[enhancer_condition_K, ] enhancers_K <- zscore_interactions[enhancer_condition_K, ]
suppressors_K <- zscores_interactions[suppressor_condition_K, ] suppressors_K <- zscore_interactions[suppressor_condition_K, ]
# Save enhancers and suppressors # Save enhancers and suppressors
message("Writing enhancer/suppressor csv files") message("Writing enhancer/suppressor csv files")
write.csv(enhancers_L, file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_L.csv"), row.names = FALSE) write.csv(enhancers_L, file = file.path(out_dir, "zscore_interactions_deletion_enhancers_L.csv"), row.names = FALSE)
write.csv(suppressors_L, file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_L.csv"), row.names = FALSE) write.csv(suppressors_L, file = file.path(out_dir, "zscore_interactions_deletion_suppressors_L.csv"), row.names = FALSE)
write.csv(enhancers_K, file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_K.csv"), row.names = FALSE) write.csv(enhancers_K, file = file.path(out_dir, "zscore_interactions_deletion_enhancers_K.csv"), row.names = FALSE)
write.csv(suppressors_K, file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K.csv"), row.names = FALSE) write.csv(suppressors_K, file = file.path(out_dir, "zscore_interactions_deletion_suppressors_K.csv"), row.names = FALSE)
# Combine conditions for enhancers and suppressors # Combine conditions for enhancers and suppressors
enhancers_and_suppressors_L <- zscores_interactions[enhancer_condition_L | suppressor_condition_L, ] enhancers_and_suppressors_L <- zscore_interactions[enhancer_condition_L | suppressor_condition_L, ]
enhancers_and_suppressors_K <- zscores_interactions[enhancer_condition_K | suppressor_condition_K, ] enhancers_and_suppressors_K <- zscore_interactions[enhancer_condition_K | suppressor_condition_K, ]
# Save combined enhancers and suppressors # Save combined enhancers and suppressors
write.csv(enhancers_and_suppressors_L, write.csv(enhancers_and_suppressors_L,
file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_and_Suppressors_L.csv"), row.names = FALSE) file = file.path(out_dir, "zscore_interactions_deletion_enhancers_and_suppressors_L.csv"), row.names = FALSE)
write.csv(enhancers_and_suppressors_K, write.csv(enhancers_and_suppressors_K,
file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_and_Suppressors_K.csv"), row.names = FALSE) file = file.path(out_dir, "zscore_interaction_deletion_enhancers_and_suppressors_K.csv"), row.names = FALSE)
# Handle linear model based enhancers and suppressors # Handle linear model based enhancers and suppressors
lm_threshold <- 2 lm_threshold <- 2
enhancers_lm_L <- zscores_interactions[zscores_interactions$Z_lm_L >= lm_threshold, ] enhancers_lm_L <- zscore_interactions[zscore_interactions$Z_lm_L >= lm_threshold, ]
suppressors_lm_L <- zscores_interactions[zscores_interactions$Z_lm_L <= -lm_threshold, ] suppressors_lm_L <- zscore_interactions[zscore_interactions$Z_lm_L <= -lm_threshold, ]
enhancers_lm_K <- zscores_interactions[zscores_interactions$Z_lm_K >= lm_threshold, ] enhancers_lm_K <- zscore_interactions[zscore_interactions$Z_lm_K >= lm_threshold, ]
suppressors_lm_K <- zscores_interactions[zscores_interactions$Z_lm_K <= -lm_threshold, ] suppressors_lm_K <- zscore_interactions[zscore_interactions$Z_lm_K <= -lm_threshold, ]
# Save linear model based enhancers and suppressors # Save linear model based enhancers and suppressors
message("Writing linear model enhancer/suppressor csv files") message("Writing linear model enhancer/suppressor csv files")
write.csv(enhancers_lm_L, write.csv(enhancers_lm_L,
file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_L_lm.csv"), row.names = FALSE) file = file.path(out_dir, "zscore_interactions_deletion_enhancers_lm_L.csv"), row.names = FALSE)
write.csv(suppressors_lm_L, write.csv(suppressors_lm_L,
file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_L_lm.csv"), row.names = FALSE) file = file.path(out_dir, "zscore_interactions_deletion_suppressors_lm_L.csv"), row.names = FALSE)
write.csv(enhancers_lm_K, write.csv(enhancers_lm_K,
file = file.path(out_dir, "ZScores_Interaction_Deletion_Enhancers_K_lm.csv"), row.names = FALSE) file = file.path(out_dir, "zscore_interactions_deletion_enhancers_lm_K.csv"), row.names = FALSE)
write.csv(suppressors_lm_K, write.csv(suppressors_lm_K,
file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K_lm.csv"), row.names = FALSE) file = file.path(out_dir, "zscore_interactions_deletion_suppressors_lm_K.csv"), row.names = FALSE)
message("Generating rank plots") message("Generating rank plots")
rank_plot_configs <- generate_rank_plot_configs( rank_plot_configs <- generate_rank_plot_configs(
df = zscores_interactions_joined, df = zscore_interactions_joined,
variables = interaction_vars, variables = interaction_vars,
is_lm = FALSE, is_lm = FALSE,
adjust = TRUE adjust = TRUE
) )
generate_and_save_plots(out_dir = out_dir, filename = "RankPlots", generate_and_save_plots(out_dir = out_dir, filename = "rank_plots",
plot_configs = rank_plot_configs, grid_layout = list(ncol = 3, nrow = 2)) plot_configs = rank_plot_configs, grid_layout = list(ncol = 3, nrow = 2))
message("Generating ranked linear model plots") message("Generating ranked linear model plots")
rank_lm_plot_configs <- generate_rank_plot_configs( rank_lm_plot_configs <- generate_rank_plot_configs(
df = zscores_interactions_joined, df = zscore_interactions_joined,
variables = interaction_vars, variables = interaction_vars,
is_lm = TRUE, is_lm = TRUE,
adjust = TRUE adjust = TRUE
) )
generate_and_save_plots(out_dir = out_dir, filename = "RankPlots_lm", generate_and_save_plots(out_dir = out_dir, filename = "rank_plots_lm",
plot_configs = rank_lm_plot_configs, grid_layout = list(ncol = 3, nrow = 2)) plot_configs = rank_lm_plot_configs, grid_layout = list(ncol = 3, nrow = 2))
message("Filtering and reranking plots") message("Filtering and reranking plots")
# Formerly X_NArm # Formerly X_NArm
zscores_interactions_filtered <- zscores_interactions_joined %>% zscore_interactions_filtered <- zscore_interactions_joined %>%
filter(!is.na(Z_lm_L) & !is.na(Avg_Zscore_L)) %>% filter(!is.na(Z_lm_L) & !is.na(Avg_Zscore_L)) %>%
mutate( mutate(
Overlap = case_when( Overlap = case_when(
@@ -1418,7 +1418,7 @@ main <- function() {
message("Generating filtered ranked plots") message("Generating filtered ranked plots")
rank_plot_filtered_configs <- generate_rank_plot_configs( rank_plot_filtered_configs <- generate_rank_plot_configs(
df = zscores_interactions_filtered, df = zscore_interactions_filtered,
variables = interaction_vars, variables = interaction_vars,
is_lm = FALSE, is_lm = FALSE,
adjust = FALSE, adjust = FALSE,
@@ -1433,7 +1433,7 @@ main <- function() {
message("Generating filtered ranked linear model plots") message("Generating filtered ranked linear model plots")
rank_plot_lm_filtered_configs <- generate_rank_plot_configs( rank_plot_lm_filtered_configs <- generate_rank_plot_configs(
df = zscores_interactions_filtered, df = zscore_interactions_filtered,
variables = interaction_vars, variables = interaction_vars,
is_lm = TRUE, is_lm = TRUE,
adjust = FALSE, adjust = FALSE,
@@ -1441,15 +1441,15 @@ main <- function() {
) )
generate_and_save_plots( generate_and_save_plots(
out_dir = out_dir, out_dir = out_dir,
filename = "RankPlots_lm_na_rm", filename = "rank_plots_lm_na_rm",
plot_configs = rank_plot_lm_filtered_configs, plot_configs = rank_plot_lm_filtered_configs,
grid_layout = list(ncol = 3, nrow = 2)) grid_layout = list(ncol = 3, nrow = 2))
message("Generating correlation plots") message("Generating correlation curve parameter pair plots")
correlation_plot_configs <- generate_correlation_plot_configs(zscores_interactions_filtered) correlation_plot_configs <- generate_correlation_plot_configs(zscore_interactions_filtered)
generate_and_save_plots( generate_and_save_plots(
out_dir = out_dir, out_dir = out_dir,
filename = "Correlation_CPPs", filename = "correlation_cpps",
plot_configs = correlation_plot_configs, plot_configs = correlation_plot_configs,
grid_layout = list(ncol = 2, nrow = 2)) grid_layout = list(ncol = 2, nrow = 2))
}) })

8
qhtcp-workflow/apps/r/join_interaction_zscores.R
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@@ -9,11 +9,11 @@ suppressMessages({
parse_arguments <- function() { parse_arguments <- function() {
if (interactive()) { if (interactive()) {
args <- c( args <- c(
"/home/bryan/documents/develop/scripts/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD", "/home/bryan/documents/develop/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD",
3, # sd value 3, # sd value
"/home/bryan/documents/develop/scripts/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD/20240822_jhartman2_DoxoHLD/exp1", "/home/bryan/documents/develop/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD/20240822_jhartman2_DoxoHLD/exp1",
"Experiment 1: Doxo versus HLD", "Experiment 1: Doxo versus HLD",
"/home/bryan/documents/develop/scripts/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD/20240822_jhartman2_DoxoHLD/exp2", "/home/bryan/documents/develop/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD/20240822_jhartman2_DoxoHLD/exp2",
"Experiment 2: HLD versus Doxo" "Experiment 2: HLD versus Doxo"
) )
} else { } else {
@@ -42,7 +42,7 @@ dir.create(args$out_dir, showWarnings = FALSE, recursive = TRUE)
combine_zscores <- function(experiments, out_dir) { combine_zscores <- function(experiments, out_dir) {
combined_data <- lapply(names(experiments), function(exp_name) { combined_data <- lapply(names(experiments), function(exp_name) {
exp_dir <- experiments[[exp_name]] exp_dir <- experiments[[exp_name]]
zscore_file <- file.path(exp_dir, "zscores", "zscores_interaction.csv") zscore_file <- file.path(exp_dir, "zscores", "zscore_interactions.csv")
if (!file.exists(zscore_file)) { if (!file.exists(zscore_file)) {
stop("Z-score file does not exist for ", exp_name, " at ", zscore_file) stop("Z-score file does not exist for ", exp_name, " at ", zscore_file)

1
qhtcp-workflow/qhtcp-workflow
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@@ -1432,6 +1432,7 @@ wrapper calculate_interaction_zscores
# * More variables can be read in from the config file to allow more configuration # * More variables can be read in from the config file to allow more configuration
# * Add gene names, other threshold values, etc. # * Add gene names, other threshold values, etc.
# * Dataframe columns and output file columns should be standardized in calculate_interactions() # * Dataframe columns and output file columns should be standardized in calculate_interactions()
# * Need to decide if conc_num_factor is numeric or factor
# #
# INPUT # INPUT
# #