View source: R/AntibodyForests_phylo.R
AntibodyForests_phylo | R Documentation |
Will automatically convert the minimum spanning trees in a given AntibodyForests object into a phylogenetic tree as a phylo object. This new object will be added into the phylo slot of the AntibodyForests object.
AntibodyForests_phylo(trees, output.format, solve.multichotomies, parallel)
trees |
nested list of AntibodyForests objects or single object, as obtained from the AntibodyForests function. |
output.format |
string - 'treedata' will output the phylogenetic tree as a tidytree treedata object, 'phylo' as an ape::phylo object. |
solve.multichotomies |
boolean - whether to remove multichotomies in the resulting phylogenetic tree using ape::multi2di |
parallel |
boolean - whether to execute the main subroutine in parallel or not. Requires the 'parallel' R package to be installed. |
nested list of AntibodyForests objects for each clonotype and each sample/timepoint or a single object, with a new phylo slot for the phylogenetic tree.
## Not run: AntibodyForests_phylo(trees, output.format = 'phylo') ## End(Not run)
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