--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_plot_ordination.R	Thu Mar 03 13:28:04 2022 +0000
@@ -0,0 +1,30 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("phyloseq"))
+
+option_list <- list(
+    make_option(c("--input"), action = "store", dest = "input", help = "Input file containing a phyloseq object"),
+    make_option(c("--method"), action = "store", dest = "method", help = "Ordination method"),
+    make_option(c("--distance"), action = "store", dest = "distance", help = "Distance method"),
+    make_option(c("--type"), action = "store", dest = "type", help = "Plot type"),
+    make_option(c("--output"), action = "store", dest = "output", help = "Output")
+)
+
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list);
+args <- parse_args(parser, positional_arguments = TRUE);
+opt <- args$options;
+
+# Construct a phyloseq object.
+phyloseq_obj <- readRDS(opt$input);
+
+# Transform data to proportions as appropriate for
+# Bray-Curtis distances.
+proportions_obj <- transform_sample_counts(phyloseq_obj, function(otu) otu / sum(otu));
+ordination_obj <- ordinate(proportions_obj, method = opt$method, distance = opt$distance);
+
+# Start PDF device driver and generate the plot.
+dev.new();
+pdf(file = opt$output);
+plot_ordination(proportions_obj, ordination_obj, type = opt$type);
+dev.off();