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Include interaction results in plot df

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Bryan Roessler
2024-09-13 00:14:41 -04:00
parent a018656f7f
commit e469ed532f
1 changed files with 29 additions and 13 deletions
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42
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -377,7 +377,12 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
arrange(desc(NG)) %>% arrange(desc(NG)) %>%
ungroup() ungroup()
return(list(calculations = calculations, interactions = interactions)) df <- df %>% select(-any_of(setdiff(names(calculations), group_vars)))
df <- left_join(df, calculations, by = group_vars)
df <- df %>% select(-any_of(setdiff(names(interactions), group_vars)))
df <- left_join(df, interactions, by = group_vars)
return(list(calculations = calculations, interactions = interactions, joined = df))
} }
generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_layout = NULL) { generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_layout = NULL) {
@@ -391,11 +396,20 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
# "delta_bg_tolerance", "delta_bg", "Gene", "L", "K", "r", "AUC", "NG", "DB"))), n = 5) # "delta_bg_tolerance", "delta_bg", "Gene", "L", "K", "r", "AUC", "NG", "DB"))), n = 5)
# Plots are testy about missing aesthetics, so handle them here # Plots are testy about missing aesthetics, so handle them here
aes_mapping <- aes( aes_mapping <-
x = !!sym(config$x_var), if (is.null(config$color_var)) {
y = if (!is.null(config$y_var)) !!sym(config$y_var) else NULL, if (is.null(config$y_var)) {
color = if (!is.null(config$color_var)) as.factor(!!sym(config$color_var)) else NULL aes(x = !!sym(config$x_var))
) } else {
aes(x = !!sym(config$x_var), y = !!sym(config$y_var))
}
} else {
if (is.null(config$y_var)) {
aes(x = !!sym(config$x_var), color = as.factor(!!sym(config$color_var)))
} else {
aes(x = !!sym(config$x_var), y = !!sym(config$y_var), color = as.factor(!!sym(config$color_var)))
}
}
# Start building the plot # Start building the plot
plot <- ggplot(df, aes_mapping) plot <- ggplot(df, aes_mapping)
@@ -553,10 +567,10 @@ generate_interaction_plot_configs <- function(df, variables) {
# Define annotation positions based on the variable being plotted # Define annotation positions based on the variable being plotted
annotation_positions <- list( annotation_positions <- list(
L = list(ZShift = 45, lm_ZScore = 25, NG = -25, DB = -35, SM = -45), L = list(Z_Shift_L = 45, lm_ZScore = 25, NG = -25, DB = -35, SM = -45),
K = list(ZShift = 45, lm_ZScore = 25, NG = -25, DB = -35, SM = -45), K = list(Z_Shift_K = 45, lm_ZScore = 25, NG = -25, DB = -35, SM = -45),
r = list(ZShift = 0.45, lm_ZScore = 0.25, NG = -0.25, DB = -0.35, SM = -0.45), r = list(Z_Shift_r = 0.45, lm_ZScore = 0.25, NG = -0.25, DB = -0.35, SM = -0.45),
AUC = list(ZShift = 4500, lm_ZScore = 2500, NG = -2500, DB = -3500, SM = -4500) AUC = list(Z_Shift_AUC = 4500, lm_ZScore = 2500, NG = -2500, DB = -3500, SM = -4500)
) )
# Define which annotations to include for each plot # Define which annotations to include for each plot
@@ -586,7 +600,7 @@ generate_interaction_plot_configs <- function(df, variables) {
# Dynamically generate the names of the columns # Dynamically generate the names of the columns
var_info <- list( var_info <- list(
ylim = limits_map[[variable]], ylim = limits_map[[variable]],
lm_model = df[[paste0("lm_", variable)]][[1]], # Access the precomputed linear model lm_model = df[[paste0("lm_", variable)]][[1]],
sd_col = paste0("WT_sd_", variable), sd_col = paste0("WT_sd_", variable),
delta_var = paste0("Delta_", variable) delta_var = paste0("Delta_", variable)
) )
@@ -1086,8 +1100,10 @@ main <- function() {
zscores_calculations_reference <- reference_results$calculations zscores_calculations_reference <- reference_results$calculations
zscores_interactions_reference <- reference_results$interactions zscores_interactions_reference <- reference_results$interactions
zscores_joined_reference <- reference_results$joined
zscores_calculations <- deletion_results$calculations zscores_calculations <- deletion_results$calculations
zscores_interactions <- deletion_results$interactions zscores_interactions <- deletion_results$interactions
zscores_joined <- deletion_results$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(zscores_calculations_reference, file = file.path(out_dir, "RF_ZScores_Calculations.csv"), row.names = FALSE)
@@ -1097,8 +1113,8 @@ main <- function() {
# Create interaction plots # Create interaction plots
message("Generating interaction plot configurations") message("Generating interaction plot configurations")
reference_plot_configs <- generate_interaction_plot_configs(df_reference, interaction_vars) reference_plot_configs <- generate_interaction_plot_configs(zscores_joined_reference, interaction_vars)
deletion_plot_configs <- generate_interaction_plot_configs(df_deletion, interaction_vars) deletion_plot_configs <- generate_interaction_plot_configs(zscores_joined, interaction_vars)
message("Generating interaction plots") message("Generating interaction plots")
generate_and_save_plots(out_dir, "RF_interactionPlots", reference_plot_configs, grid_layout = list(ncol = 4, nrow = 3)) generate_and_save_plots(out_dir, "RF_interactionPlots", reference_plot_configs, grid_layout = list(ncol = 4, nrow = 3))
generate_and_save_plots(out_dir, "InteractionPlots", deletion_plot_configs, grid_layout = list(ncol = 4, nrow = 3)) generate_and_save_plots(out_dir, "InteractionPlots", deletion_plot_configs, grid_layout = list(ncol = 4, nrow = 3))