Mercurial > repos > iuc > ampvis2_alpha_diversity

diff test-data/generate.R @ 1:6b8580e02e99 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
author iuc
date Thu, 07 Apr 2022 14:09:25 +0000
parents b54f72135f58
children
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--- a/test-data/generate.R	Mon Apr 04 10:26:31 2022 +0000
+++ b/test-data/generate.R	Thu Apr 07 14:09:25 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