--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_plot_bar.R	Tue Dec 03 17:45:23 2024 +0000
@@ -0,0 +1,74 @@
+#!/usr/bin/env Rscript
+
+# Load libraries
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("phyloseq"))
+suppressPackageStartupMessages(library("ggplot2"))
+
+# Define options
+option_list <- list(
+    make_option(c("--input"),
+        action = "store", dest = "input",
+        help = "Input file containing a phyloseq object"
+    ),
+    make_option(c("--x"),
+        action = "store", dest = "x",
+        help = "Variable for x-axis (e.g., 'Sample', 'Phylum')"
+    ),
+    make_option(c("--fill"),
+        action = "store", dest = "fill", default = NULL,
+        help = "Variable for fill color (e.g., 'Genus', 'Order') (optional)"
+    ),
+    make_option(c("--facet"),
+        action = "store", dest = "facet", default = NULL,
+        help = "Facet by variable (optional)"
+    ),
+    make_option(c("--output"),
+        action = "store", dest = "output",
+        help = "Output file (PDF)"
+    )
+)
+
+# Parse arguments
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args <- parse_args(parser, positional_arguments = TRUE)
+opt <- args$options
+
+# Validate required options
+if (is.null(opt$input) || opt$input == "") {
+    stop("Error: Input file is required.")
+}
+if (is.null(opt$x) || opt$x == "") {
+    stop("Error: X-axis variable is required.")
+}
+if (is.null(opt$output) || opt$output == "") {
+    stop("Error: Output file is required.")
+}
+
+# Load phyloseq object
+print(paste("Trying to read:", opt$input))
+physeq <- readRDS(opt$input)
+
+# Check if the 'x' and 'fill' variables are valid
+sample_vars <- colnames(sample_data(physeq))
+if (!opt$x %in% sample_vars) {
+    stop(paste("Error: X-axis variable", opt$x, "does not exist in the sample data."))
+}
+
+# Generate bar plot
+p <- plot_bar(physeq, x = opt$x, fill = opt$fill)
+
+# Only facet if the facet variable is provided and exists in the sample data
+if (!is.null(opt$facet) && opt$facet != "") {
+    if (opt$facet %in% sample_vars) {
+        p <- p + facet_wrap(as.formula(paste("~", opt$facet)))
+    } else {
+        warning(paste("Facet variable", opt$facet, "does not exist in the sample data. Faceting will be skipped."))
+    }
+}
+
+# Save to output file using PDF device
+print(paste("Saving plot to:", opt$output))
+pdf(file = opt$output, width = 10, height = 8)
+print(p)
+dev.off()