Mercurial > repos > iuc > phyloseq_plot_richness

comparison phyloseq_plot_bar.R @ 3:1a6c2cc92c6e 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 17:45:16 +0000
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children a20bc31f2821
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2:fb7c4bbe8994 3:1a6c2cc92c6e
1 #!/usr/bin/env Rscript
2
3 # Load libraries
4 suppressPackageStartupMessages(library("optparse"))
5 suppressPackageStartupMessages(library("phyloseq"))
6 suppressPackageStartupMessages(library("ggplot2"))
7
8 # Define options
9 option_list <- list(
10 make_option(c("--input"),
11 action = "store", dest = "input",
12 help = "Input file containing a phyloseq object"
13 ),
14 make_option(c("--x"),
15 action = "store", dest = "x",
16 help = "Variable for x-axis (e.g., 'Sample', 'Phylum')"
17 ),
18 make_option(c("--fill"),
19 action = "store", dest = "fill", default = NULL,
20 help = "Variable for fill color (e.g., 'Genus', 'Order') (optional)"
21 ),
22 make_option(c("--facet"),
23 action = "store", dest = "facet", default = NULL,
24 help = "Facet by variable (optional)"
25 ),
26 make_option(c("--output"),
27 action = "store", dest = "output",
28 help = "Output file (PDF)"
29 )
30 )
31
32 # Parse arguments
33 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
34 args <- parse_args(parser, positional_arguments = TRUE)
35 opt <- args$options
36
37 # Validate required options
38 if (is.null(opt$input) || opt$input == "") {
39 stop("Error: Input file is required.")
40 }
41 if (is.null(opt$x) || opt$x == "") {
42 stop("Error: X-axis variable is required.")
43 }
44 if (is.null(opt$output) || opt$output == "") {
45 stop("Error: Output file is required.")
46 }
47
48 # Load phyloseq object
49 print(paste("Trying to read:", opt$input))
50 physeq <- readRDS(opt$input)
51
52 # Check if the 'x' and 'fill' variables are valid
53 sample_vars <- colnames(sample_data(physeq))
54 if (!opt$x %in% sample_vars) {
55 stop(paste("Error: X-axis variable", opt$x, "does not exist in the sample data."))
56 }
57
58 # Generate bar plot
59 p <- plot_bar(physeq, x = opt$x, fill = opt$fill)
60
61 # Only facet if the facet variable is provided and exists in the sample data
62 if (!is.null(opt$facet) && opt$facet != "") {
63 if (opt$facet %in% sample_vars) {
64 p <- p + facet_wrap(as.formula(paste("~", opt$facet)))
65 } else {
66 warning(paste("Facet variable", opt$facet, "does not exist in the sample data. Faceting will be skipped."))
67 }
68 }
69
70 # Save to output file using PDF device
71 print(paste("Saving plot to:", opt$output))
72 pdf(file = opt$output, width = 10, height = 8)
73 print(p)
74 dev.off()