Hi David,
Have you tried ggtree? It is very powerful, as it interfaces nicely with the
ggplot2 package functions.
I tried to sketch an example, see this link or below signature.
https://gist.github.com/kopperud/ae8cca0c29927d1d51fe08fd74cdb90a
There are probably better ways of doing this, but it should work. Need a few
packages, though?
Cheers,
Bj�rn Tore Kopperud
```
library(ape)
library(ggtree) ## Ggtree is on github,
devtools::install_github("GuangchuangYu/ggtree")
library(ggplot2)
library(gridExtra)
## Random tree
set.seed(5)
phy <- rtree(15)
## No transformation
p1 <- ggtree(phy, ladderize = TRUE) + theme_tree2() + geom_tiplab() +
ggtitle("No transform")
## Manipulate the plotting coordinates, square transform
p2 <- ggtree(phy, ladderize = TRUE) +
theme_tree2() +
geom_tiplab() + scale_x_continuous(labels = function(x) sqrt(x), breaks =
seq(0, 4)^2) + ## Backtransform the axis labels, and add appropriate breaks
ggtitle("Square transform")
p2$data$x <- p2$data$x ^2
## Exponential instead
p3 <- ggtree(phy, ladderize = TRUE) +
theme_tree2() +
geom_tiplab() +
scale_x_continuous(labels = function(x) log(x), breaks = exp(seq(0, 4))) +
ggtitle("Exponential transform")
p3$data$x <- exp(p3$data$x)
grid.arrange(p1, p2, p3)
```
From: R-sig-phylo on behalf of David Bapst
Sent: 02 January 2019 21:15
To: R Sig Phylo Listserv
Subject: [R-sig-phylo] Logarithmic Scales for Plotting Dated Phyogenies (e.g.
Log of Time Axis?)
Hi all,
I've been dealing with a tree with one very deep divergence and many
very shallow divergences recently, and I was curious if there was an R
plotting capability that allows for the depth axis of the tree to be
non-linear or logarithmic - helpful if there can be a time axis bar as
well, as with axisPhylo(). Logging the axis directly with par seems to
break plot.phylo, presumably because its trying to plot something at a
negative coordinate.
It seems like a simple thing, but oddly I haven't come upon anything
yet that can do this. Any thoughts?
Cheers,
-Dave
PS: Tangential to that, is there a ladderize function that also takes
into account the edge length on non-ultrametric trees? I just noticed
that ladderize doesn't do much for a tree with a large polytomy
consisting of branches of very different length.
PPS: Happy New Years, all! I just checked and its now been nine years
I've been following this listserv...
--
David W. Bapst, PhD
Asst Research Professor, Geology & Geophysics, Texas A & M University
Postdoc, Ecology & Evolutionary Biology, Univ of Tenn Knoxville
https://github.com/dwbapst/paleotree
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