Mercurial > repos > iuc > phyloseq_plot_bar

comparison phyloseq_plot_ordination.R @ 0:ad81e112f4d9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
author iuc
date Tue, 03 Dec 2024 17:45:48 +0000
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-1:000000000000 0:ad81e112f4d9
1 #!/usr/bin/env Rscript
2
3 suppressPackageStartupMessages(library("optparse"))
4 suppressPackageStartupMessages(library("phyloseq"))
5
6 option_list <- list(
7 make_option(c("--input"), action = "store", dest = "input", help = "Input file containing a phyloseq object"),
8 make_option(c("--method"), action = "store", dest = "method", help = "Ordination method"),
9 make_option(c("--distance"), action = "store", dest = "distance", help = "Distance method"),
10 make_option(c("--type"), action = "store", dest = "type", help = "Plot type"),
11 make_option(c("--output"), action = "store", dest = "output", help = "Output")
12 )
13
14 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
15 args <- parse_args(parser, positional_arguments = TRUE)
16 opt <- args$options
17 # Construct a phyloseq object.
18 phyloseq_obj <- readRDS(opt$input)
19 # Transform data to proportions as appropriate for
20 # Bray-Curtis distances.
21 proportions_obj <- transform_sample_counts(phyloseq_obj, function(otu) otu / sum(otu))
22 ordination_obj <- ordinate(proportions_obj, method = opt$method, distance = opt$distance)
23 # Start PDF device driver and generate the plot.
24 dev.new()
25 pdf(file = opt$output)
26 plot_ordination(proportions_obj, ordination_obj, type = opt$type)
27 dev.off()