Mercurial > repos > iuc > phyloseq_from_dada2

annotate phyloseq_plot_richness.R @ 0:46a99bd1f10e 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 d1004c06207be773c278e12745aada276b63172e"
author iuc
date Thu, 03 Mar 2022 13:28:04 +0000
parents
children b85ba18a8f36
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
1 #!/usr/bin/env Rscript
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
2
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
3 suppressPackageStartupMessages(library("optparse"))
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
4 suppressPackageStartupMessages(library("phyloseq"))
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
5
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
6 option_list <- list(
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
7 make_option(c("--input"), action = "store", dest = "input", help = "Input RDS file containing a phyloseq object"),
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
8 make_option(c("--output"), action = "store", dest = "output", help = "Output PDF")
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
9 )
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
10
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
11 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list);
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
12 args <- parse_args(parser, positional_arguments = TRUE);
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
13 opt <- args$options;
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
14
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
15 phyloseq_obj <- readRDS(opt$input);
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
16
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
17 # Start PDF device driver and generate the plot.
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
18 dev.new();
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
19 pdf(file = opt$output);
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
20 plot_richness(phyloseq_obj, x = "samples", color = "samples");
46a99bd1f10e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
21 dev.off()