Mercurial > repos > iuc > phyloseq_plot_bar
comparison phyloseq_plot_richness.R @ 0:ad81e112f4d9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
| author | iuc |
|---|---|
| date | Tue, 03 Dec 2024 17:45:48 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:ad81e112f4d9 |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 suppressPackageStartupMessages(library("optparse")) | |
| 4 suppressPackageStartupMessages(library("phyloseq")) | |
| 5 | |
| 6 option_list <- list( | |
| 7 make_option(c("--input"), action = "store", dest = "input", help = "Input RDS file containing a phyloseq object"), | |
| 8 make_option(c("--output"), action = "store", dest = "output", help = "Output PDF") | |
| 9 ) | |
| 10 | |
| 11 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) | |
| 12 args <- parse_args(parser, positional_arguments = TRUE) | |
| 13 opt <- args$options | |
| 14 phyloseq_obj <- readRDS(opt$input) | |
| 15 # Start PDF device driver and generate the plot. | |
| 16 dev.new() | |
| 17 pdf(file = opt$output) | |
| 18 plot_richness(phyloseq_obj, x = "samples", color = "samples") | |
| 19 dev.off() |