Paul J. McMurdie joey711
joey711
/ Phyloseq Issue 213
Last active
December 17, 2015 13:18
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| library("phyloseq") | |
| data("GlobalPatterns") | |
| x10 = prune_taxa(tail(names(sort(taxa_sums(GlobalPatterns))), 10), GlobalPatterns) | |
| # Fix the node labels for the sake of the tree at the end: | |
| phy_tree(x10)$node.label <- gsub("\\.[[:alnum:]]+$", "", phy_tree(x10)$node.label) | |
| # Add a new rank, Strain, with the OTU ids | |
| tax_table(x10) <- cbind(tax_table(x10), Strain=taxa_names(x10)) | |
| # Define the ranks you want to include | |
| myranks = c("Genus", "Species", "Strain") | |
| mylabels = apply(tax_table(x10)[, myranks], 1, paste, sep="", collapse="_") |