Skip empty plots to fix grid.arrange() error
This commit is contained in:
@@ -509,30 +509,23 @@ calculate_interaction_scores <- function(df, df_bg, type, overlap_threshold = 2)
|
||||
generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width = 12, page_height = 8) {
|
||||
message("Generating ", filename, ".pdf and ", filename, ".html")
|
||||
|
||||
# Check if we're dealing with multiple plot groups
|
||||
plot_groups <- if ("plots" %in% names(plot_configs)) {
|
||||
list(plot_configs) # Single group
|
||||
} else {
|
||||
plot_configs # Multiple groups
|
||||
}
|
||||
|
||||
# Open the PDF device once for all plots
|
||||
pdf(file.path(out_dir, paste0(filename, ".pdf")), width = page_width, height = page_height)
|
||||
|
||||
# Loop through each plot group
|
||||
for (group in plot_groups) {
|
||||
static_plots <- list()
|
||||
plotly_plots <- list()
|
||||
|
||||
# Retrieve grid layout if it exists, otherwise skip
|
||||
grid_layout <- group$grid_layout
|
||||
plots <- group$plots
|
||||
|
||||
for (i in seq_along(plots)) {
|
||||
config <- plots[[i]]
|
||||
for (i in seq_along(group$plots)) {
|
||||
config <- group$plots[[i]]
|
||||
df <- config$df
|
||||
|
||||
# Filter points outside of y-limits if specified
|
||||
# Filter and debug out-of-bounds data
|
||||
if (!is.null(config$ylim_vals)) {
|
||||
out_of_bounds <- df %>%
|
||||
filter(
|
||||
@@ -540,14 +533,11 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
|
||||
.data[[config$y_var]] < config$ylim_vals[1] |
|
||||
.data[[config$y_var]] > config$ylim_vals[2]
|
||||
)
|
||||
|
||||
# Print rows being filtered out
|
||||
if (nrow(out_of_bounds) > 0) {
|
||||
message("Filtered ", nrow(out_of_bounds), " row(s) from '", config$title, "' because ", config$y_var,
|
||||
" is outside of y-limits: [", config$ylim_vals[1], ", ", config$ylim_vals[2], "]:")
|
||||
print(out_of_bounds %>% select(OrfRep, Gene, num, Drug, scan, Plate, Row, Col, conc_num, all_of(config$y_var)), width = 1000)
|
||||
# print(out_of_bounds %>% select(OrfRep, Gene, num, Drug, scan, Plate, Row, Col, conc_num, all_of(config$y_var)), width = 1000)
|
||||
}
|
||||
|
||||
df <- df %>%
|
||||
filter(
|
||||
!is.na(.data[[config$y_var]]) &
|
||||
@@ -556,13 +546,17 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
|
||||
)
|
||||
}
|
||||
|
||||
# Filter NAs if specified
|
||||
# Filter NAs
|
||||
if (!is.null(config$filter_na) && config$filter_na) {
|
||||
df <- df %>%
|
||||
filter(!is.na(.data[[config$y_var]]))
|
||||
}
|
||||
|
||||
# Set up aes mapping based on plot type
|
||||
if (nrow(df) == 0) {
|
||||
message("No data available after filtering for plot ", config$title)
|
||||
next # Skip this plot if no data is available
|
||||
}
|
||||
|
||||
aes_mapping <- if (config$plot_type == "bar") {
|
||||
if (!is.null(config$color_var)) {
|
||||
aes(x = .data[[config$x_var]], fill = .data[[config$color_var]], color = .data[[config$color_var]])
|
||||
@@ -587,16 +581,14 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
|
||||
|
||||
plot <- ggplot(df, aes_mapping) + theme_publication(legend_position = config$legend_position)
|
||||
|
||||
# Add appropriate plot layer or helper function based on plot type
|
||||
plot <- switch(config$plot_type,
|
||||
"scatter" = generate_scatter_plot(plot, config),
|
||||
"box" = generate_boxplot(plot, config),
|
||||
"density" = plot + geom_density(),
|
||||
"bar" = plot + geom_bar(),
|
||||
plot # default (unused)
|
||||
plot # default
|
||||
)
|
||||
|
||||
# Add labels and title
|
||||
if (!is.null(config$title)) {
|
||||
plot <- plot + ggtitle(config$title)
|
||||
if (!is.null(config$title_size)) {
|
||||
@@ -607,44 +599,21 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
|
||||
if (!is.null(config$y_label)) plot <- plot + ylab(config$y_label)
|
||||
if (!is.null(config$coord_cartesian)) plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
|
||||
|
||||
# Add annotations if specified
|
||||
if (!is.null(config$annotations)) {
|
||||
for (annotation in config$annotations) {
|
||||
plot <- plot +
|
||||
annotate(
|
||||
"text",
|
||||
x = ifelse(is.null(annotation$x), 0, annotation$x),
|
||||
y = ifelse(is.null(annotation$y), Inf, annotation$y),
|
||||
label = annotation$label,
|
||||
hjust = ifelse(is.null(annotation$hjust), 0.5, annotation$hjust),
|
||||
vjust = ifelse(is.null(annotation$vjust), 1, annotation$vjust),
|
||||
size = ifelse(is.null(annotation$size), 3, annotation$size),
|
||||
color = ifelse(is.null(annotation$color), "black", annotation$color)
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
# Convert ggplot to plotly for interactive version
|
||||
plotly_plot <- suppressWarnings(plotly::ggplotly(plot))
|
||||
|
||||
# Store both static and interactive versions
|
||||
static_plots[[i]] <- plot
|
||||
plotly_plots[[i]] <- plotly_plot
|
||||
}
|
||||
|
||||
# Print the plots in the current group to the PDF
|
||||
grid_layout <- group$grid_layout
|
||||
if (!is.null(grid_layout)) {
|
||||
# Set grid_ncol to 1 if not specified
|
||||
if (is.null(grid_layout$ncol)) {
|
||||
grid_layout$ncol <- 1
|
||||
}
|
||||
|
||||
# If ncol is set but nrow is not, calculate nrow dynamically based on num_plots
|
||||
if (!is.null(grid_layout$ncol) && is.null(grid_layout$nrow)) {
|
||||
num_plots <- length(static_plots)
|
||||
nrow <- ceiling(num_plots / grid_layout$ncol)
|
||||
# message("No nrow provided, automatically using nrow = ", nrow)
|
||||
grid_layout$nrow <- nrow
|
||||
grid_layout$nrow <- ceiling(num_plots / grid_layout$ncol)
|
||||
}
|
||||
|
||||
total_spots <- grid_layout$nrow * grid_layout$ncol
|
||||
@@ -655,24 +624,26 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
|
||||
static_plots <- c(static_plots, replicate(total_spots - num_plots, nullGrob(), simplify = FALSE))
|
||||
}
|
||||
|
||||
# Print a page of gridded plots
|
||||
tryCatch({
|
||||
grid.arrange(
|
||||
grobs = static_plots,
|
||||
ncol = grid_layout$ncol,
|
||||
nrow = grid_layout$nrow)
|
||||
nrow = grid_layout$nrow
|
||||
)
|
||||
}, error = function(e) {
|
||||
message("Error in grid.arrange: ", e$message)
|
||||
print(static_plots)
|
||||
})
|
||||
|
||||
} else {
|
||||
# Print individual plots on separate pages if no grid layout
|
||||
for (plot in static_plots) {
|
||||
print(plot)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
# Close the PDF device after all plots are done
|
||||
dev.off()
|
||||
|
||||
# Save HTML file with interactive plots if needed
|
||||
out_html_file <- file.path(out_dir, paste0(filename, ".html"))
|
||||
message("Saving combined HTML file: ", out_html_file)
|
||||
htmltools::save_html(
|
||||
@@ -681,6 +652,7 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
generate_scatter_plot <- function(plot, config) {
|
||||
|
||||
# Define the points
|
||||
@@ -1118,7 +1090,7 @@ generate_interaction_plot_configs <- function(df_summary, df_interactions, type)
|
||||
x_breaks = unique(group_data$conc_num_factor_factor),
|
||||
x_labels = as.character(unique(group_data$conc_num)),
|
||||
ylim_vals = y_limits,
|
||||
filter_na = TRUE,
|
||||
# filter_na = TRUE,
|
||||
lm_line = list(
|
||||
intercept = lm_intercept_value,
|
||||
slope = lm_slope_value,
|
||||
|
||||
Reference in New Issue
Block a user