Mercurial > repos > iuc > ampvis2_export_otu
comparison test-data/generate.R @ 0:8e6d236aab1c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit f32c3d9a92dca8a60504824fc7bcee290c30a211
| author | iuc |
|---|---|
| date | Tue, 01 Apr 2025 10:00:46 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:8e6d236aab1c |
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| 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 |