plotBS: Plotting trees with bootstrap values

In phangorn: Phylogenetic Reconstruction and Analysis

Plotting trees with bootstrap values

Description

plotBS plots a phylogenetic tree with the bootstrap values assigned to the (internal) edges. It can also used to assign bootstrap values to a phylogenetic tree. add_support adds support values to a plot.

Usage

plotBS(tree, trees, type = "phylogram", method = "FBP", bs.col = "black",
  bs.adj = NULL, digits = 3, p = 0, frame = "none", tol = 1e-06,
  sep = "/", ...)

add_support(tree, trees, method = "FBP", tol = 1e-08, scale = TRUE,
  frame = "none", digits = 3, sep = "/", ...)

Arguments

tree	The tree on which edges the bootstrap values are plotted.
trees	a list of trees (object of class "multiPhylo").
type	the type of tree to plot, one of "phylogram", "cladogram", "fan", "unrooted", "radial" or "none". If type is "none" the tree is returned with the bootstrap values assigned to the node labels.
method	either "FBP" the classical bootstrap (default), "TBE" (transfer bootstrap) or "MCC" for assigning clade credibilities. In case of "MCC" all trees need to be rooted.
bs.col	color of bootstrap support labels.
bs.adj	one or two numeric values specifying the horizontal and vertical justification of the bootstrap labels.
digits	integer indicating the number of decimal places.
p	only plot support values higher than this percentage number (default is 0).
frame	a character string specifying the kind of frame to be printed around the bootstrap values. This must be one of "none" (the default), "rect" or "circle".
tol	a numeric value giving the tolerance to consider a branch length significantly greater than zero.
sep	seperator between the different methods.
...	further parameters used by plot.phylo.
scale	return ratio or percentage.

Details

The functions can either assign the classical Felsenstein’s bootstrap proportions (FBP) (Felsenstein (1985), Hendy & Penny (1985)) or the transfer bootstrap expectation (TBE) of Lemoine et al. (2018). Using the option type=="n" just assigns the bootstrap values and return the tree without plotting it.

Value

plotBS returns silently a tree, i.e. an object of class phylo with the bootstrap values as node labels. The argument trees is optional and if not supplied the labels supplied in the node.label slot will be used.

Author(s)

Klaus Schliep [e-mail]

References

Felsenstein J. (1985) Confidence limits on phylogenies. An approach using the bootstrap. Evolution 39, 783–791

Lemoine, F., Entfellner, J. B. D., Wilkinson, E., Correia, D., Felipe, M. D., De Oliveira, T., & Gascuel, O. (2018). Renewing Felsenstein’s phylogenetic bootstrap in the era of big data. Nature, 556(7702), 452–456.

Penny D. and Hendy M.D. (1985) Testing methods evolutionary tree construction. Cladistics 1, 266–278

Penny D. and Hendy M.D. (1986) Estimating the reliability of evolutionary trees. Molecular Biology and Evolution 3, 403–417

See Also

plot.phylo, add_ci, nodelabels, prop.clades, maxCladeCred, transferBootstrap, consensus, consensusNet

Examples

fdir <- system.file("extdata/trees", package = "phangorn")
# RAxML best-known tree with bipartition support (from previous analysis)
raxml.tree <- read.tree(file.path(fdir,"RAxML_bipartitions.woodmouse"))
# RAxML bootstrap trees (from previous analysis)
raxml.bootstrap <- read.tree(file.path(fdir,"RAxML_bootstrap.woodmouse"))
par(mfrow=c(1,2))
plotBS(raxml.tree,  raxml.bootstrap, "p")
plotBS(raxml.tree,  raxml.bootstrap, "p", "TBE")

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.