Mercurial > repos > iuc > ampvis2_subset_samples

diff test-data/generate.R @ 0:03b77eb5ed68 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
author iuc
date Mon, 04 Apr 2022 10:25:42 +0000
parents
children 14b38ec15fe9
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/generate.R	Mon Apr 04 10:25:42 2022 +0000
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+library(ampvis2)
+
+# subset taxa using 200 random OTUs
+aalborgwwtps <- amp_subset_taxa(AalborgWWTPs, tax_vector = sample(AalborgWWTPs$tax$OTU, 200))
+
+ape::write.tree(aalborgwwtps$tree, "AalborgWWTPs.nwk")
+amp_export_fasta(aalborgwwtps, "AalborgWWTPs.fa", tax = F)
+amp_export_otutable(aalborgwwtps, "AalborgWWTPs.otu")
+write.table(aalborgwwtps$tax, file = "AalborgWWTPs.tax", quote = F, sep = "\t", row.names = F)
+write.table(aalborgwwtps$metadata, file = "AalborgWWTPs.tsv", quote = F, sep = "\t")