Mercurial > repos > iuc > phyloseq_plot_richness

comparison phyloseq_plot_ordination.R @ 0:92b82deaaed1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
author iuc
date Thu, 03 Mar 2022 13:28:55 +0000
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children 1ff178d1757e
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-1:000000000000 0:92b82deaaed1
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$options;
17
18 # Construct a phyloseq object.
19 phyloseq_obj <- readRDS(opt$input);
20
21 # Transform data to proportions as appropriate for
22 # Bray-Curtis distances.
23 proportions_obj <- transform_sample_counts(phyloseq_obj, function(otu) otu / sum(otu));
24 ordination_obj <- ordinate(proportions_obj, method = opt$method, distance = opt$distance);
25
26 # Start PDF device driver and generate the plot.
27 dev.new();
28 pdf(file = opt$output);
29 plot_ordination(proportions_obj, ordination_obj, type = opt$type);
30 dev.off();