Mercurial > repos > iuc > ampvis2_boxplot

comparison test-data/generate.R @ 0:797603efc62d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
author iuc
date Fri, 16 Aug 2024 08:50:10 +0000
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-1:000000000000 0:797603efc62d
1 library(ampvis2)
2
3 # subset taxa using 200 random OTUs
4 aalborgwwtps <- amp_subset_taxa(AalborgWWTPs, tax_vector = sample(AalborgWWTPs$tax$OTU, 200))
5
6 ape::write.tree(aalborgwwtps$tree, "AalborgWWTPs.nwk")
7 amp_export_fasta(aalborgwwtps, "AalborgWWTPs.fa", tax = F)
8 amp_export_otutable(aalborgwwtps, "AalborgWWTPs.otu")
9 write.table(aalborgwwtps$tax, file = "AalborgWWTPs.tax", quote = F, sep = "\t", row.names = F)
10 write.table(aalborgwwtps$metadata, file = "AalborgWWTPs.tsv", quote = F, sep = "\t")
11
12 # construct data for merge_ampvis2
13 t <- amp_load(otutable = "AalborgWWTPs.otu.csv", metadata = "AalborgWWTPs.tsv", taxonomy = "AalborgWWTPs.tax.tsv", fasta = "AalborgWWTPs.fa", tree = "AalborgWWTPs.nwk")
14 d_2010 <- amp_subset_samples(t, Period %in% "2010")
15 # 60 samples and 109 OTUs have been filtered
16 # Before: 67 samples and 200 OTUs
17 # After: 7 samples and 91 OTUs
18 d_2011 <- amp_subset_samples(t, Period %in% "2011")
19 # 61 samples and 94 OTUs have been filtered
20 # Before: 67 samples and 200 OTUs
21 # After: 6 samples and 106 OTUs
22
23 saveRDS(d_2010, "AalborgWWTPs.2010.rds")
24 saveRDS(d_2011, "AalborgWWTPs.2011.rds")
25
26 # => merging should give 13 samples