readTree {treeman} | R Documentation |
Return a TreeMan
or TreeMen
object from a Newick treefile
readTree(file = NULL, text = NULL, spcl_slt_nm = "Unknown", wndmtrx = FALSE, parallel = FALSE, progress = "none")
file |
file path |
text |
Newick character string |
spcl_slt_nm |
name of special slot for internal node labels, default 'Unknown'. |
wndmtrx |
T/F add node matrix? Default FALSE. |
parallel |
logical, make parallel? |
progress |
name of the progress bar to use, see |
Read a single or multiple trees from a file, or a text string. Parallelizable
when reading multiple trees.
The function will add any internal node labels in the Newick tree as a user-defined data slots.
The name of this slot is defined with the spcl_slt_nm
.
These data can be accessed/manipulated with the `getNdsSlt()`
function.
Trees are always read as rooted. (Unrooted trees have polytomous root nodes.)
https://en.wikipedia.org/wiki/Newick_format,
addNdmtrx
, writeTree
,
randTree
, readTrmn
, writeTrmn
,
saveTreeMan
, loadTreeMan
library(treeman) # tree string with internal node labels as bootstrap results tree <- readTree(text="((A:1.0,B:1.0)0.9:1.0,(C:1.0,D:1.0)0.8:1.0)0.7:1.0;", spcl_slt_nm='bootstrap') # retrieve bootstrap values by node tree['bootstrap']