Mercurial > repos > iuc > phyloseq_plot_ordination
diff phyloseq_plot_ordination.R @ 0:11d43fa12aab draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
author | iuc |
---|---|
date | Thu, 03 Mar 2022 13:28:30 +0000 |
parents | |
children | 92e77800ef2c |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_plot_ordination.R Thu Mar 03 13:28:30 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();