annotate phyloseq_plot_bar.R @ 3:1a6c2cc92c6e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9

#!/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()