sort_taxa_from_tree: Get sorted supertaxon list based on a rooted taxonomy tree
In trvinh/test: PhyloProfile

Description Usage Arguments Value Author(s) See Also Examples

Get sorted supertaxon list based on a rooted taxonomy tree

1	sort_taxa_from_tree(tree)

tree

rooted taxonomy tree

list of taxa sorted according to the taxonomy tree

Vinh Tran tran@bio.uni-frankfurt.de

pp_taxonomy_matrix for a demo taxonomy matrix data

data("pp_taxonomy_matrix", package = "phyloprofile")
# prepare matrix for calculating distances
distDf <- subset(pp_taxonomy_matrix, select = -c(ncbiID, fullName))
row.names(distDf) <- distDf$abbrName
distDf <- distDf[, -1]
# create taxonomy tree rooted by ncbi10090
rooted_tree <- create_rooted_tree(distDf, "ncbi10090")
# get taxon list sorted from tree
sort_taxa_from_tree(rooted_tree)