sort_input_taxa: Sort list of (super)taxa based on a selected reference...
In trvinh/test: PhyloProfile

Description Usage Arguments Value Author(s) See Also Examples

Sort list of (super)taxa based on a selected reference (super)taxon

1	sort_input_taxa(taxon_IDs, taxon_names, rank_name, ref_taxon, taxa_tree)

`taxon_IDs`	list of taxon IDs (e.g.: ncbi1234, ncbi9999, ...)
`taxon_names`	list of taxon names and their corresponding taxonomy ranks, IDs,...
`rank_name`	working taxonomy rank (e.g. "species", "phylum",...)
`ref_taxon`	selected reference taxon
`taxa_tree`	input taxonomy tree (optional)

Taxonomy matrix for the input taxa ordered by the selected reference taxon. This matrix is sorted either based on the NCBI taxonomy info, or based on an user-defined taxonomy tree (if provided).

Vinh Tran tran@bio.uni-frankfurt.de

get_name_list, get_taxonomy_matrix, create_rooted_tree, sort_taxa_from_tree, get_input_taxa_name, get_input_taxa_id, create_long_matrix

taxon_IDs <- c(
    "ncbi272557", "ncbi176299", "ncbi3702", "ncbi876142", "ncbi9606"
)
taxon_names <- get_input_taxa_name("species", taxon_IDs)
sort_input_taxa(taxon_IDs, taxon_names, "species", "Homo sapiens", NULL)