Mercurial > repos > iuc > phyloseq_plot_richness

annotate phyloseq_plot_ordination.R @ 1:1ff178d1757e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
author iuc
date Fri, 09 Feb 2024 21:42:16 +0000
parents 92b82deaaed1
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92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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1 #!/usr/bin/env Rscript
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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3 suppressPackageStartupMessages(library("optparse"))
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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4 suppressPackageStartupMessages(library("phyloseq"))
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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6 option_list <- list(
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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7 make_option(c("--input"), action = "store", dest = "input", help = "Input file containing a phyloseq object"),
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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8 make_option(c("--method"), action = "store", dest = "method", help = "Ordination method"),
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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9 make_option(c("--distance"), action = "store", dest = "distance", help = "Distance method"),
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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10 make_option(c("--type"), action = "store", dest = "type", help = "Plot type"),
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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11 make_option(c("--output"), action = "store", dest = "output", help = "Output")
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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12 )
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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14 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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15 args <- parse_args(parser, positional_arguments = TRUE)
1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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16 opt <- args$options
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92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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17 # Construct a phyloseq object.
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1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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18 phyloseq_obj <- readRDS(opt$input)
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19 # Transform data to proportions as appropriate for
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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20 # Bray-Curtis distances.
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1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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21 proportions_obj <- transform_sample_counts(phyloseq_obj, function(otu) otu / sum(otu))
1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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22 ordination_obj <- ordinate(proportions_obj, method = opt$method, distance = opt$distance)
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92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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23 # Start PDF device driver and generate the plot.
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1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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24 dev.new()
1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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25 pdf(file = opt$output)
1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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26 plot_ordination(proportions_obj, ordination_obj, type = opt$type)
1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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27 dev.off()