| Previous changeset 2:dfe800a3faaf (2024-03-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9 |
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added:
phyloseq_plot_bar.R |
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| diff -r dfe800a3faaf -r c35e0075c7a2 phyloseq_plot_bar.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_plot_bar.R Tue Dec 03 17:45:23 2024 +0000 |
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| @@ -0,0 +1,74 @@ +#!/usr/bin/env Rscript + +# Load libraries +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("phyloseq")) +suppressPackageStartupMessages(library("ggplot2")) + +# Define options +option_list <- list( + make_option(c("--input"), + action = "store", dest = "input", + help = "Input file containing a phyloseq object" + ), + make_option(c("--x"), + action = "store", dest = "x", + help = "Variable for x-axis (e.g., 'Sample', 'Phylum')" + ), + make_option(c("--fill"), + action = "store", dest = "fill", default = NULL, + help = "Variable for fill color (e.g., 'Genus', 'Order') (optional)" + ), + make_option(c("--facet"), + action = "store", dest = "facet", default = NULL, + help = "Facet by variable (optional)" + ), + make_option(c("--output"), + action = "store", dest = "output", + help = "Output file (PDF)" + ) +) + +# Parse arguments +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) +args <- parse_args(parser, positional_arguments = TRUE) +opt <- args$options + +# Validate required options +if (is.null(opt$input) || opt$input == "") { + stop("Error: Input file is required.") +} +if (is.null(opt$x) || opt$x == "") { + stop("Error: X-axis variable is required.") +} +if (is.null(opt$output) || opt$output == "") { + stop("Error: Output file is required.") +} + +# Load phyloseq object +print(paste("Trying to read:", opt$input)) +physeq <- readRDS(opt$input) + +# Check if the 'x' and 'fill' variables are valid +sample_vars <- colnames(sample_data(physeq)) +if (!opt$x %in% sample_vars) { + stop(paste("Error: X-axis variable", opt$x, "does not exist in the sample data.")) +} + +# Generate bar plot +p <- plot_bar(physeq, x = opt$x, fill = opt$fill) + +# Only facet if the facet variable is provided and exists in the sample data +if (!is.null(opt$facet) && opt$facet != "") { + if (opt$facet %in% sample_vars) { + p <- p + facet_wrap(as.formula(paste("~", opt$facet))) + } else { + warning(paste("Facet variable", opt$facet, "does not exist in the sample data. Faceting will be skipped.")) + } +} + +# Save to output file using PDF device +print(paste("Saving plot to:", opt$output)) +pdf(file = opt$output, width = 10, height = 8) +print(p) +dev.off() |