[R-sig-phylo] Plot phylogeny with "increasing" or "decreasing" node ages?

[Nick Matzke]

Hi all,

In FigTree, there is an option (Left menu->Trees->Order nodes->increasing,
or decreasing) to plot trees and order them such that the higher nodes/tips
in the tree plot at the top or bottom of the plot.

Does anything like this exist for plotting trees in R? Or do I have to
hunt-n-peck and manually rotate nodes 1-by-1 until it looks right?

(yes, I could save the tree out from FigTree and use that, but I want to
automate this plotting function without a FigTree step)

Cheers!
Nick

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[Liam J. Revell]

Hi Nick.

I'm not sure if this is what you mean, but have you tried the function
ladderize from the ape package?

All the best, Liam

Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: ***@umb.edu
blog: http://blog.phytools.org

Post by Nick Matzke
Hi all,
In FigTree, there is an option (Left menu->Trees->Order nodes->increasing,
or decreasing) to plot trees and order them such that the higher nodes/tips
in the tree plot at the top or bottom of the plot.
Does anything like this exist for plotting trees in R? Or do I have to
hunt-n-peck and manually rotate nodes 1-by-1 until it looks right?
(yes, I could save the tree out from FigTree and use that, but I want to
automate this plotting function without a FigTree step)
Cheers!
Nick
[[alternative HTML version deleted]]
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[Nick Matzke]

Yep, that's it exactly. Thanks guys!
Nick

Post by Liam J. Revell
Hi Nick.
I'm not sure if this is what you mean, but have you tried the function
ladderize from the ape package?
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
blog: http://blog.phytools.org

Post by Nick Matzke
Hi all,
In FigTree, there is an option (Left menu->Trees->Order nodes->increasing,
or decreasing) to plot trees and order them such that the higher
nodes/tips
in the tree plot at the top or bottom of the plot.
Does anything like this exist for plotting trees in R? Or do I have to
hunt-n-peck and manually rotate nodes 1-by-1 until it looks right?
(yes, I could save the tree out from FigTree and use that, but I want to
automate this plotting function without a FigTree step)
Cheers!
Nick
[[alternative HTML version deleted]]
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https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at

_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at

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