writeTreesJSON: 'writeTreesJSON' Experimental. Write trees in AIRR format

In dowser: B Cell Receptor Phylogenetics Toolkit

writeTreesJSON Experimental. Write trees in AIRR format

Description

writeTreesJSON Experimental. Write trees in AIRR format

Usage

writeTreesJSON(
  object,
  file,
  repertoire_id = "sample",
  check = TRUE,
  verbose = TRUE,
  edge_tol = 1e-08,
  cell = "cell_id",
  heavy = "IGH",
  light = c("IGK", "IGL"),
  dowser_fields = TRUE,
  nproc = 1
)

Arguments

object	Dowser object from getTrees
file	name of .json file
repertoire_id	repertoire_id to use
check	verify object is equivalent on reloading
verbose	print out more info
edge_tol	tolerance for branch length checks (if check=TRUE)
cell	cell id column name in Dowser object
heavy	name of heavy chain locus
light	names of light chain loci
dowser_fields	include dowser-specific information? (recommended)
nproc	number of cores to use (parallelizes by clone)

Details

Works with trees built by any of getTrees's build options ("pratchet", "pml", "igphyml", "raxml"). getTrees(..., build="pml") trees store the full phangorn::optim.pml fit in tree$parameters; since that object isn't JSON-serializable (and isn't meaningful to reconstruct from a file), it's reduced to a flat list of fitted model parameters via pmlParamsToList before being written out. See that function's documentation for what is kept and why.

dowser documentation built on Aug. 20, 2026, 5:06 p.m.