Mercurial > repos > iuc > ampvis2_timeseries
view test-data/generate.R @ 5:6121b061418a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
author | iuc |
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date | Fri, 16 Aug 2024 09:00:26 +0000 |
parents | 77d2f88d8716 |
children |
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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") # construct data for merge_ampvis2 t <- amp_load(otutable = "AalborgWWTPs.otu.csv", metadata = "AalborgWWTPs.tsv", taxonomy = "AalborgWWTPs.tax.tsv", fasta = "AalborgWWTPs.fa", tree = "AalborgWWTPs.nwk") d_2010 <- amp_subset_samples(t, Period %in% "2010") # 60 samples and 109 OTUs have been filtered # Before: 67 samples and 200 OTUs # After: 7 samples and 91 OTUs d_2011 <- amp_subset_samples(t, Period %in% "2011") # 61 samples and 94 OTUs have been filtered # Before: 67 samples and 200 OTUs # After: 6 samples and 106 OTUs saveRDS(d_2010, "AalborgWWTPs.2010.rds") saveRDS(d_2011, "AalborgWWTPs.2011.rds") # => merging should give 13 samples