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Rework plotting code, add auto-grid layout

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Tento commit je obsažen v:
Bryan Roessler
2024-09-18 03:34:16 -04:00
rodič 7bfe5c337e
revize 3251c8f879
1 změnil soubory, kde provedl 36 přidání a 66 odebrání
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102
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -370,68 +370,18 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
config <- plot_configs[[i]]
df <- config$df
# Initialize tooltip_text
tooltip_text <- NULL
# Define aes_mapping based on plot type
if (config$plot_type == "scatter") {
# Check if y_var is provided
aes_mapping <- if (is.null(config$color_var)) {
if (is.null(config$y_var)) {
warning(paste("Plot", i, "of type 'scatter' is missing 'y_var'. Skipping this plot."))
next
}
# Construct tooltip_text based on configuration flags
if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
# Ensure 'delta_bg' exists
if (!"delta_bg" %in% names(df)) {
warning(paste("Plot", i, "requires 'delta_bg' column for tooltip, but it's missing."))
tooltip_text <- paste("OrfRep:", df$OrfRep, "<br>Gene:", df$Gene)
} else {
tooltip_text <- paste("OrfRep:", df$OrfRep, "<br>Gene:", df$Gene, "<br>delta_bg:", df$delta_bg)
}
} else if (!is.null(config$gene_point) && config$gene_point) {
tooltip_text <- paste("OrfRep:", df$OrfRep, "<br>Gene:", df$Gene)
aes(x = .data[[config$x_var]])
} else {
tooltip_text <- paste("x:", df[[config$x_var]], "<br>y:", df[[config$y_var]])
}
# Define aesthetic mapping with or without color_var
aes_mapping <- if (is.null(config$color_var)) {
aes(x = .data[[config$x_var]], y = .data[[config$y_var]], text = tooltip_text)
} else {
aes(x = .data[[config$x_var]], y = .data[[config$y_var]],
color = as.factor(.data[[config$color_var]]), text = tooltip_text)
aes(x = .data[[config$x_var]], y = .data[[config$y_var]])
}
} else {
# Handle other plot types
# For 'box' plots, y_var is required
if (config$plot_type == "box") {
if (is.null(config$y_var)) {
warning(paste("Plot", i, "of type 'box' is missing 'y_var'. Skipping this plot."))
next
}
}
# Define aes_mapping for non-scatter plots
aes_mapping <- if (is.null(config$color_var)) {
if (config$plot_type %in% c("density", "bar")) {
aes(x = .data[[config$x_var]])
} else {
aes(x = .data[[config$x_var]], y = .data[[config$y_var]])
}
if (is.null(config$y_var)) {
aes(x = .data[[config$x_var]], color = as.factor(.data[[config$color_var]]))
} else {
if (config$plot_type %in% c("density", "bar")) {
aes(x = .data[[config$x_var]],
color = as.factor(.data[[config$color_var]]))
} else {
aes(x = .data[[config$x_var]], y = .data[[config$y_var]],
color = as.factor(.data[[config$color_var]]))
}
aes(x = .data[[config$x_var]], y = .data[[config$y_var]], color = as.factor(.data[[config$color_var]]))
}
# No tooltip for non-scatter plots
tooltip_text <- NULL
}
# Start building the plot with aes_mapping
@@ -443,10 +393,7 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
"box" = generate_box_plot(plot_base, config),
"density" = plot_base + geom_density(),
"bar" = plot_base + geom_bar(),
{
warning(paste("Unknown plot_type:", config$plot_type, "- using base plot"))
plot_base
}
plot_base # default case if no type matches
)
# Apply additional settings if provided
@@ -465,11 +412,27 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
plot <- plot + ylab(config$y_label)
}
# Convert to plotly object
# Apply scale_color_discrete(guide = FALSE) when color_var is NULL
if (is.null(config$color_var)) {
plot <- plot + scale_color_discrete(guide = FALSE)
}
# Add interactive tooltips for plotly
tooltip_vars <- c()
if (config$plot_type == "scatter") {
plotly_plot <- ggplotly(plot, tooltip = "text")
if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
tooltip_vars <- c(tooltip_vars, "OrfRep", "Gene", "delta_bg")
} else if (!is.null(config$gene_point) && config$gene_point) {
tooltip_vars <- c(tooltip_vars, "OrfRep", "Gene")
} else if (!is.null(config$y_var) && !is.null(config$x_var)) {
tooltip_vars <- c(config$x_var, config$y_var)
}
}
# Convert to plotly object
if (length(tooltip_vars) > 0) {
plotly_plot <- ggplotly(plot, tooltip = tooltip_vars)
} else {
# For non-scatter plots, decide if tooltips are needed
plotly_plot <- ggplotly(plot, tooltip = "none")
}
@@ -489,9 +452,16 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
dev.off()
# Combine and save interactive HTML plots
combined_plot <- subplot(plotly_plots,
nrows = ifelse(is.null(grid_layout$nrow), length(plotly_plots), grid_layout$nrow),
margin = 0.05)
combined_plot <- subplot(
plotly_plots,
nrows = if (!is.null(grid_layout) && !is.null(grid_layout$nrow)) {
grid_layout$nrow
} else {
# Calculate nrow based on the length of plotly_plots (default 1 row if only one plot)
ceiling(length(plotly_plots) / ifelse(!is.null(grid_layout) && !is.null(grid_layout$ncol), grid_layout$ncol, 1))
},
margin = 0.05
)
saveWidget(combined_plot, file = file.path(out_dir, paste0(file_name, ".html")), selfcontained = TRUE)
}