Mercurial > repos > iuc > phyloseq_plot_richness

annotate phyloseq_from_dada2.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
children fb7c4bbe8994
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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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5 suppressPackageStartupMessages(library("tidyverse"))
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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7 option_list <- list(
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("--sequence_table"), action = "store", dest = "sequence_table", help = "Input sequence table"),
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("--taxonomy_table"), action = "store", dest = "taxonomy_table", help = "Input taxonomy table"),
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("--output"), action = "store", dest = "output", help = "RDS output")
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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11 )
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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13 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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14 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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15 opt <- args$options
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92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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16 # The input sequence_table is an integer matrix
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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17 # stored as tabular (rows = samples, columns = ASVs).
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1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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18 seq_table_numeric_matrix <- data.matrix(read.table(opt$sequence_table, sep = "\t"))
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19 # The input taxonomy_table is a table containing
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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20 # the assigned taxonomies exceeding the minBoot
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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21 # level of bootstrapping confidence. Rows correspond
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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22 # to sequences, columns to taxonomic levels. NA
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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23 # indicates that the sequence was not consistently
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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24 # classified at that level at the minBoot threshold.
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25 tax_table_matrix <- as.matrix(read.table(opt$taxonomy_table, header = FALSE, sep = "\t"))
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26 # Construct a tax_table object. The rownames of
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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27 # tax_tab must match the OTU names (taxa_names)
92b82deaaed1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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28 # of the otu_table defined below.
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29 tax_tab <- tax_table(tax_table_matrix)
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30 # Construct an otu_table 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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31 otu_tab <- otu_table(seq_table_numeric_matrix, taxa_are_rows = TRUE)
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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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32 # 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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33 phyloseq_obj <- phyloseq(otu_tab, tax_tab)
1ff178d1757e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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34 saveRDS(phyloseq_obj, file = opt$output, compress = TRUE)