getTrees - Estimate lineage tree topologies, branch lengths, and internal node states if desired
Description¶
getTrees
Tree building function.
Usage¶
getTrees(
clones,
trait = NULL,
id = NULL,
dir = NULL,
modelfile = NULL,
build = "pratchet",
exec = NULL,
igphyml = NULL,
fixtrees = FALSE,
nproc = 1,
quiet = 0,
rm_temp = TRUE,
palette = NULL,
seq = NULL,
collapse = FALSE,
...
)
Arguments¶
- clones
- a tibble of
airrClone
objects, the output of formatClones - trait
- trait to use for parsimony models (required if
igphyml
specified) - id
- unique identifer for this analysis (required if
igphyml
ordnapars
specified) - dir
- directory where temporary files will be placed.
- modelfile
- file specifying parsimony model to use
- build
- program to use for tree building (pratchet, pml, dnapars, dnaml, igphyml, raxml)
- exec
- location of desired phylogenetic executable
- igphyml
- optional location of igphyml executible for parsimony
- fixtrees
- if TRUE, use supplied tree topologies
- nproc
- number of cores to parallelize computations
- quiet
- amount of rubbish to print to console
- rm_temp
- remove temporary files (default=TRUE)
- palette
- deprecated
- seq
- column name containing sequence information
- collapse
- Collapse internal nodes with identical sequences?
- …
- Additional arguments passed to tree building programs
Value¶
A list of phylo
objects in the same order as data
.
Details¶
Estimates phylogenetic tree topologies and branch lengths for a list of
airrClone
objects. By default, it will use phangnorn::pratchet to
estimate maximum parsimony tree topologies, and ape::acctran to estimate
branch lengths. If igpyhml
is specified, internal node trait
values will be predicted by maximum parsimony. In this case, dir
will
need to be specified as a temporary directory to place all the intermediate
files (will be created if not available). Further, id
will need to
specified to serve as a unique identifier for the temporary files. This
should be chosen to ensure that multiple getTrees
calls using the same
dir
do not overwrite each others files.
modelfile
is written automatically if not specified, but doesn’t
include any constraints. Intermediate files are deleted by default. This can
be toggled using (rm_files
).
For examples and vignettes, see https://dowser.readthedocs.io
Examples¶
data(ExampleClones)
trees <- getTrees(ExampleClones[10,])
plotTrees(trees)[[1]]
### Not run:
data(ExampleClones)
#
# trees <- getTrees(ExampleClones[10,],igphyml="/path/to/igphyml",
# id="temp",dir="temp", trait="sample_id")
# plotTrees(trees)[[1]]
See also¶
formatClones, findSwitches, buildPhylo, buildPratchet, buildPML, buildIgphyml, buildRAxML