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Allow missing y_var for some plot types

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Bryan Roessler
2024-09-10 23:04:24 -04:00
parent d8eb162fb5
commit 2eccb30b31
1 changed files with 53 additions and 52 deletions
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103
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -336,58 +336,58 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
}
generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_layout = NULL) {
plots <- lapply(plot_configs, function(config) {
df <- config$df
# Helper function for plot type logic
apply_plot_type <- function(plot, config) {
switch(config$plot_type,
"rank" = {
plot <- plot + geom_point(size = 0.1, shape = 3)
if (!is.null(config$sd_band)) {
for (i in seq_len(config$sd_band)) {
plot <- plot +
annotate("rect", xmin = -Inf, xmax = Inf, ymin = i, ymax = Inf, fill = "#542788", alpha = 0.3) +
annotate("rect", xmin = -Inf, xmax = Inf, ymin = -i, ymax = -Inf, fill = "orange", alpha = 0.3) +
geom_hline(yintercept = c(-i, i), color = "gray")
}
# Check if y_var is NULL and adjust the aes mapping
aes_mapping <- 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)))
}
plot <- ggplot(df, aes_mapping)
# Handle plot types like "rank", "correlation", and default scatter/box/density
if (config$plot_type == "rank") {
plot <- plot + geom_point(size = 0.1, shape = 3)
if (!is.null(config$sd_band)) {
for (i in seq_len(config$sd_band)) {
plot <- plot +
annotate("rect", xmin = -Inf, xmax = Inf, ymin = i, ymax = Inf, fill = "#542788", alpha = 0.3) +
annotate("rect", xmin = -Inf, xmax = Inf, ymin = -i, ymax = -Inf, fill = "orange", alpha = 0.3) +
geom_hline(yintercept = c(-i, i), color = "gray")
}
plot
},
"correlation" = {
plot + geom_point(shape = 3, color = "gray70") + geom_smooth(method = "lm", color = "tomato3") +
annotate("text", x = 0, y = 0, label = config$correlation_text)
},
"box" = plot + geom_boxplot(),
"density" = plot + geom_density(),
"bar" = plot + geom_bar(stat = "identity"),
plot + geom_point(shape = 3) + geom_smooth(method = "lm", se = FALSE) # Default scatter plot
)
}
}
if (!is.null(config$enhancer_label)) {
plot <- plot + annotate("text", x = config$enhancer_label$x, y = config$enhancer_label$y,
label = config$enhancer_label$label) +
annotate("text", x = config$suppressor_label$x, y = config$suppressor_label$y, label = config$suppressor_label$label)
}
} else if (config$plot_type == "correlation") {
plot <- plot + geom_point(shape = 3, color = "gray70") + geom_smooth(method = "lm", color = "tomato3") +
annotate("text", x = 0, y = 0, label = config$correlation_text)
} else {
# Adjust based on plot types that may or may not need y_var
if (config$plot_type == "box") {
plot <- plot + geom_boxplot()
} else if (config$plot_type == "density") {
plot <- plot + geom_density()
} else if (config$plot_type == "bar") {
plot <- plot + geom_bar(stat = "identity")
} else {
plot <- plot + geom_point(shape = 3) + geom_smooth(method = "lm", se = FALSE)
}
}
# Helper function for error bars
apply_error_bars <- function(plot, config) {
# Add error bars for "delta_bg" or general cases
if (!is.null(config$error_bar) && config$error_bar) {
y_mean_col <- paste0("mean_", config$y_var)
y_sd_col <- paste0("sd_", config$y_var)
plot <- plot + geom_errorbar(aes(ymin = !!sym(y_mean_col) - !!sym(y_sd_col),
ymax = !!sym(y_mean_col) + !!sym(y_sd_col)), width = 0.1) +
ymax = !!sym(y_mean_col) + !!sym(y_sd_col)), width = 0.1) +
geom_point(aes(y = !!sym(y_mean_col)), size = 0.6)
}
plot
}
# Helper function for annotations
apply_annotations <- function(plot, config) {
if (!is.null(config$annotations)) {
plot <- plot + geom_text(aes(x = config$annotations$x, y = config$annotations$y, label = config$annotations$label))
}
plot
}
# Generate each plot
plots <- lapply(plot_configs, function(config) {
plot <- ggplot(config$df, aes(x = !!sym(config$x_var), y = !!sym(config$y_var), color = as.factor(!!sym(config$color_var))))
plot <- apply_plot_type(plot, config)
plot <- apply_error_bars(plot, config)
# Apply y-limits if provided
if (!is.null(config$ylim_vals)) {
@@ -399,17 +399,19 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
theme_publication(legend_position = if (!is.null(config$legend_position)) config$legend_position else "bottom") +
xlab(config$x_label %||% "") + ylab(config$y_label %||% "")
plot <- apply_annotations(plot, config)
# Add annotations if available
if (!is.null(config$annotations)) {
plot <- plot + geom_text(aes(x = config$annotations$x, y = config$annotations$y, label = config$annotations$label))
}
return(plot)
})
# Save plots to PDF
# Save the plots
pdf(file.path(output_dir, paste0(file_name, ".pdf")), width = 14, height = 9)
lapply(plots, print)
dev.off()
# Generate Plotly versions for interactive HTML
plotly_plots <- lapply(plots, function(plot) suppressWarnings(ggplotly(plot) %>% layout(legend = list(orientation = "h"))))
# Handle grid layout
@@ -417,6 +419,7 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
saveWidget(combined_plot, file = file.path(output_dir, paste0(file_name, ".html")), selfcontained = TRUE)
}
generate_interaction_plot_configs <- function(df, variables) {
configs <- list()
@@ -661,11 +664,9 @@ main <- function() {
title = paste("Raw L vs K for strains above delta background threshold of", df_above_tolerance$delta_bg_tolerance[[1]], "or above"),
color_var = "conc_num",
annotations = list(
list(
x = L_half_median,
y = K_half_median,
label = paste("Strains above delta background tolerance =", nrow(df_above_tolerance))
)
x = L_half_median,
y = K_half_median,
label = paste("Strains above delta background tolerance =", nrow(df_above_tolerance))
),
error_bar = FALSE,
legend_position = "right"