searchTxnyms | R Documentation |
Return names of each node in tree based on searching tip labels through Global Names Resolver http://resolver.globalnames.org/ in NCBI.
searchTxnyms(tree, cache = FALSE, parent = NULL, clean = TRUE, infer = TRUE)
tree |
TreeMan object |
cache |
T/F, create a local cache of downloaded names? |
parent |
specify parent of all names to prevent false names |
clean |
T/F, ensure returned names contain no special characters? |
infer |
T/F, infer taxonyms for unfound nodes? |
For each node, all the descendants are searched, the taxonomic lineages returned and then searched to find the lowest shared name. All the tip labels are searched against a specified taxonomic database through the GNR and NCBI. (So far only tested with NCBI database.) Use the infer argument to ensure a taxonym is returned for all nodes. If infer is true, all nodes without an identifed taxonym adopt the taxonym of their parent. Will raise a warning if connection fails and will return NULL.
taxaResolve
, setTxnyms
, getNdsFrmTxnyms
tree <- randTree(8)
new_tids <- c(
"Gallus_gallus", "Aileuropoda_melanoleucha", "Ailurus_fulgens",
"Rattus_rattus", "Mus_musculus", "Gorilla_gorilla", "Pan_trogoldytes", "Homo_sapiens"
)
tree <- setNdsID(tree, tree["tips"], new_tids)
nd_labels <- searchTxnyms(tree)
print(nd_labels)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.