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Add rank plot annotations

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Bryan Roessler
2024-09-10 14:01:29 -04:00
parent 01752d20e3
commit 9986d138b3
1 changed files with 17 additions and 5 deletions
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22
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -180,7 +180,6 @@ calculate_summary_stats <- function(df, variables, group_vars = c("conc_num", "c
return(list(summary_stats = summary_stats, df_with_stats = df_with_stats)) return(list(summary_stats = summary_stats, df_with_stats = df_with_stats))
} }
calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c("OrfRep", "Gene", "num")) { calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c("OrfRep", "Gene", "num")) {
# Calculate total concentration variables # Calculate total concentration variables
@@ -515,11 +514,11 @@ generate_interaction_plot_configs <- function(df, variables) {
return(plot_configs) return(plot_configs)
} }
generate_rank_plot_configs <- function(df, rank_var, zscore_var, label_prefix) { generate_rank_plot_config <- function(df, rank_var, zscore_var, label_prefix) {
configs <- list() configs <- list()
for (sd_band in c(1, 2, 3)) { for (sd_band in c(1, 2, 3)) {
# Annotated version # Annotated version (with text)
configs[[length(configs) + 1]] <- list( configs[[length(configs) + 1]] <- list(
df = df, df = df,
x_var = rank_var, x_var = rank_var,
@@ -537,20 +536,33 @@ generate_rank_plot_configs <- function(df, rank_var, zscore_var, label_prefix) {
) )
) )
# Non-annotated version # Non-annotated version (_notext)
configs[[length(configs) + 1]] <- list( configs[[length(configs) + 1]] <- list(
df = df, df = df,
x_var = rank_var, x_var = rank_var,
y_var = zscore_var, y_var = zscore_var,
plot_type = "rank", plot_type = "rank",
title = paste("Average Z score vs. Rank for", label_prefix, "above", sd_band, "SD"), title = paste("Average Z score vs. Rank for", label_prefix, "above", sd_band, "SD"),
sd_band = sd_band sd_band = sd_band,
enhancer_label = NULL, # Remove annotations for _notext
suppressor_label = NULL # Remove annotations for _notext
) )
} }
return(configs) return(configs)
} }
# Generate all rank plot configurations for L and K (annotated and _notext)
rank_plot_config <- c(
create_rank_plot_config(zscores_interactions_adjusted, "L_Rank", "Avg_Zscore_L", "L"),
create_rank_plot_config(zscores_interactions_adjusted, "K_Rank", "Avg_Zscore_K", "K")
)
# Generate and save rank plots
generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots",
plot_configs = rank_plot_config, grid_layout = list(ncol = 3, nrow = 2))
generate_correlation_plot_configs <- function(df, lm_list, lm_summaries) { generate_correlation_plot_configs <- function(df, lm_list, lm_summaries) {
lapply(seq_along(lm_list), function(i) { lapply(seq_along(lm_list), function(i) {
r_squared <- round(lm_summaries[[i]]$r.squared, 3) r_squared <- round(lm_summaries[[i]]$r.squared, 3)