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 <r-sig-phylo-boun...@r-project.org> on behalf of David Bapst <dwba...@tamu.edu> 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 _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]]
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