Mercurial > repos > iuc > ampvis2_frequency
diff test-data/generate.R @ 1:0feab98f9577 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
| author | iuc |
|---|---|
| date | Thu, 07 Apr 2022 13:59:35 +0000 |
| parents | f77f7c426d6f |
| children |
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--- a/test-data/generate.R Mon Apr 04 10:18:21 2022 +0000 +++ b/test-data/generate.R Thu Apr 07 13:59:35 2022 +0000 @@ -8,3 +8,19 @@ 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