Mercurial > repos > iuc > ampvis2_venn
annotate test-data/generate.R @ 6:bbb4a531d80b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb30e4b8d695e096753fe7cb5056b118b25a87fd
author | iuc |
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date | Mon, 26 Aug 2024 16:19:29 +0000 |
parents | 62c6d4c55190 |
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rev | line source |
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36d4584a5ceb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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1 library(ampvis2) |
36d4584a5ceb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff
changeset
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2 |
36d4584a5ceb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff
changeset
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3 # subset taxa using 200 random OTUs |
36d4584a5ceb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff
changeset
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4 aalborgwwtps <- amp_subset_taxa(AalborgWWTPs, tax_vector = sample(AalborgWWTPs$tax$OTU, 200)) |
36d4584a5ceb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff
changeset
|
5 |
36d4584a5ceb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff
changeset
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6 ape::write.tree(aalborgwwtps$tree, "AalborgWWTPs.nwk") |
36d4584a5ceb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff
changeset
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7 amp_export_fasta(aalborgwwtps, "AalborgWWTPs.fa", tax = F) |
36d4584a5ceb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff
changeset
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8 amp_export_otutable(aalborgwwtps, "AalborgWWTPs.otu") |
36d4584a5ceb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff
changeset
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9 write.table(aalborgwwtps$tax, file = "AalborgWWTPs.tax", quote = F, sep = "\t", row.names = F) |
36d4584a5ceb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff
changeset
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10 write.table(aalborgwwtps$metadata, file = "AalborgWWTPs.tsv", quote = F, sep = "\t") |
1
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
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11 |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
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12 # construct data for merge_ampvis2 |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
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13 t <- amp_load(otutable = "AalborgWWTPs.otu.csv", metadata = "AalborgWWTPs.tsv", taxonomy = "AalborgWWTPs.tax.tsv", fasta = "AalborgWWTPs.fa", tree = "AalborgWWTPs.nwk") |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
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14 d_2010 <- amp_subset_samples(t, Period %in% "2010") |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
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changeset
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15 # 60 samples and 109 OTUs have been filtered |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
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16 # Before: 67 samples and 200 OTUs |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
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changeset
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17 # After: 7 samples and 91 OTUs |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
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changeset
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18 d_2011 <- amp_subset_samples(t, Period %in% "2011") |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
diff
changeset
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19 # 61 samples and 94 OTUs have been filtered |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
diff
changeset
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20 # Before: 67 samples and 200 OTUs |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
diff
changeset
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21 # After: 6 samples and 106 OTUs |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
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changeset
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22 |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
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23 saveRDS(d_2010, "AalborgWWTPs.2010.rds") |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
diff
changeset
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24 saveRDS(d_2011, "AalborgWWTPs.2011.rds") |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
diff
changeset
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25 |
62c6d4c55190
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
0
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26 # => merging should give 13 samples |