Mercurial > repos > iuc > phyloseq_plot_richness
comparison phyloseq_plot_richness.R @ 0:92b82deaaed1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
| author | iuc |
|---|---|
| date | Thu, 03 Mar 2022 13:28:55 +0000 |
| parents | |
| children | 1ff178d1757e |
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| -1:000000000000 | 0:92b82deaaed1 |
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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$options; | |
| 14 | |
| 15 phyloseq_obj <- readRDS(opt$input); | |
| 16 | |
| 17 # Start PDF device driver and generate the plot. | |
| 18 dev.new(); | |
| 19 pdf(file = opt$output); | |
| 20 plot_richness(phyloseq_obj, x = "samples", color = "samples"); | |
| 21 dev.off() |