Mercurial > repos > iuc > phyloseq_plot_richness

comparison phyloseq_plot_richness.R @ 1:1ff178d1757e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
author iuc
date Fri, 09 Feb 2024 21:42:16 +0000
parents 92b82deaaed1
children
comparison
equal deleted inserted replaced
0:92b82deaaed1 1:1ff178d1757e
6 option_list <- list( 6 option_list <- list(
7 make_option(c("--input"), action = "store", dest = "input", help = "Input RDS file containing a phyloseq object"), 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") 8 make_option(c("--output"), action = "store", dest = "output", help = "Output PDF")
9 ) 9 )
10 10
11 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list); 11 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
12 args <- parse_args(parser, positional_arguments = TRUE); 12 args <- parse_args(parser, positional_arguments = TRUE)
13 opt <- args$options; 13 opt <- args$options
14 14 phyloseq_obj <- readRDS(opt$input)
15 phyloseq_obj <- readRDS(opt$input);
16
17 # Start PDF device driver and generate the plot. 15 # Start PDF device driver and generate the plot.
18 dev.new(); 16 dev.new()
19 pdf(file = opt$output); 17 pdf(file = opt$output)
20 plot_richness(phyloseq_obj, x = "samples", color = "samples"); 18 plot_richness(phyloseq_obj, x = "samples", color = "samples")
21 dev.off() 19 dev.off()