Mercurial > repos > iuc > phyloseq_plot_ordination

annotate phyloseq_plot_bar.R @ 4:5007bc8a3d90 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 4dba8c02f5b33b425d4ecd9c9f0d0eaa0a74f9bf
author iuc
date Thu, 26 Dec 2024 18:34:41 +0000
parents c35e0075c7a2
children
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c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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1 #!/usr/bin/env Rscript
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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3 # Load libraries
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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4 suppressPackageStartupMessages(library("optparse"))
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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5 suppressPackageStartupMessages(library("phyloseq"))
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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6 suppressPackageStartupMessages(library("ggplot2"))
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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8 # Define options
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9 option_list <- list(
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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10 make_option(c("--input"),
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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11 action = "store", dest = "input",
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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12 help = "Input file containing a phyloseq object"
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13 ),
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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14 make_option(c("--x"),
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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15 action = "store", dest = "x",
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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16 help = "Variable for x-axis (e.g., 'Sample', 'Phylum')"
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17 ),
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18 make_option(c("--fill"),
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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19 action = "store", dest = "fill", default = NULL,
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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20 help = "Variable for fill color (e.g., 'Genus', 'Order') (optional)"
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21 ),
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22 make_option(c("--facet"),
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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23 action = "store", dest = "facet", default = NULL,
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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24 help = "Facet by variable (optional)"
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25 ),
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26 make_option(c("--output"),
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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27 action = "store", dest = "output",
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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28 help = "Output file (PDF)"
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29 )
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30 )
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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32 # Parse arguments
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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33 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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34 args <- parse_args(parser, positional_arguments = TRUE)
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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35 opt <- args$options
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37 # Validate required options
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38 if (is.null(opt$input) || opt$input == "") {
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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39 stop("Error: Input file is required.")
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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40 }
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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41 if (is.null(opt$x) || opt$x == "") {
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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42 stop("Error: X-axis variable is required.")
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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43 }
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44 if (is.null(opt$output) || opt$output == "") {
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45 stop("Error: Output file is required.")
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46 }
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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47
c35e0075c7a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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48 # Load phyloseq object
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49 print(paste("Trying to read:", opt$input))
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50 physeq <- readRDS(opt$input)
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51
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52 # Check if the 'x' and 'fill' variables are valid
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53 sample_vars <- colnames(sample_data(physeq))
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54 if (!opt$x %in% sample_vars) {
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55 stop(paste("Error: X-axis variable", opt$x, "does not exist in the sample data."))
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56 }
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57
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58 # Generate bar plot
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59 p <- plot_bar(physeq, x = opt$x, fill = opt$fill)
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60
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61 # Only facet if the facet variable is provided and exists in the sample data
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62 if (!is.null(opt$facet) && opt$facet != "") {
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63 if (opt$facet %in% sample_vars) {
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64 p <- p + facet_wrap(as.formula(paste("~", opt$facet)))
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65 } else {
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66 warning(paste("Facet variable", opt$facet, "does not exist in the sample data. Faceting will be skipped."))
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67 }
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68 }
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69
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70 # Save to output file using PDF device
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71 print(paste("Saving plot to:", opt$output))
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72 pdf(file = opt$output, width = 10, height = 8)
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73 print(p)
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74 dev.off()