ggsplitnet

drawing phylogenetic tree from phylo object

Usage

ggsplitnet(tr, mapping = NULL, layout = "slanted", mrsd = NULL,
  as.Date = FALSE, yscale = "none", yscale_mapping = NULL,
  ladderize = FALSE, right = FALSE, branch.length = "branch.length",
  ndigits = NULL, ...)

Arguments

tr: a networx object
mapping: aes mapping
layout: so far only 'slanted' is supported.
mrsd: most recent sampling date
as.Date: logical whether using Date class in time tree
yscale: y scale
yscale_mapping: yscale mapping for category variable
ladderize: logical
right: logical
branch.length: variable for scaling branch, if 'none' draw cladogram
ndigits: number of digits to round numerical annotation variable
...: additional parameter

Value

tree

References

Schliep, K., Potts, A. J., Morrison, D. A. and Grimm, G. W. (2017), Intertwining phylogenetic trees and networks. Methods Ecol Evol. 8, 1212–1220. doi:10.1111/2041-210X.12760

Dress, A.W.M. and Huson, D.H. (2004) Constructing Splits Graphs IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 1(3), 109–115

Bagci, C., Bryant, D., Cetinkaya, B. and Huson, D.H. (2021), Microbial Phylogenetic Context Using Phylogenetic Outlines. Genome Biology and Evolution. Volume 13. Issue 9. evab213

Author

Klaus Schliep

Examples

data(yeast, package='phangorn')
dm <- phangorn::dist.ml(yeast)
nnet <- phangorn::neighborNet(dm)
ggsplitnet(nnet) + geom_tiplab2()