Hi Liam, Would there be a way to modify this so that annotations like node labels and axes could be applied to both 1/2s of a split tree at the same time? I’ve been struggling with a similar problem using plot.phylo() and we can get our tree to look like what we want on one page, but splitting it up while keeping node and branch annotations etc is problematic.
For example, I am trying to plot a tree and annotate with the following function calls. #from ape plot.phylo(timetree, cex=0.315, label.offset=0.35, edge.width=1.25, edge.color=color) #from phyloch - adds a geologic time scale axisGeo(GTS = strat2012, unit = c("epoch", "period"), cex = 0.7, col = c("grey80", "white"), texcol = "black", gridty = 2, gridcol = "red", ages=TRUE) #then additional annotations with: nodelabels() axis() I want to cut my tree in 1/2 and plot each 1/2 on a separate page, but maintain the axes and annotations. Splitting a tree is great but it’s not super useful unless you can call other functions on the pieces. It would be great to be able to generate axes for each piece of a split tree independently and then annotate each one as if they were a separate plot. Jake > On Mar 5, 2015, at 11:46 AM, Jonas Eberle <eberle.jo...@gmail.com> wrote: > > Hi Liam, > > perfect! Your right, I didn't realize that some species were duplicated. > Great to have the option in phytools! > > All the best, > Jonas > > > 2015-03-05 17:16 GMT+01:00 Liam J. Revell <liam.rev...@umb.edu>: > >> Hi Jonas. >> >> I thought of the same thing. Unfortunately, one thing that I discovered is >> that because R automatically adds 4% or so to the plotting range, you will >> find that species & edges near the bottom of one page will also appear at >> the top of the next page. If you test your code & look for species or edges >> near the bottom or top of each page, you may find what I did. >> >> I have posted a solution to this here: http://blog.phytools.org/2015/ >> 03/splitting-tree-over-mutiple-plotting.html. It uses plotTree from >> phytools internally, but it could fairly easily be modified to use other >> tree plotters such as plot.phylo or plotSimmap. >> >> All the best, Liam >> >> Liam J. Revell, Assistant Professor of Biology >> University of Massachusetts Boston >> web: http://faculty.umb.edu/liam.revell/ >> email: liam.rev...@umb.edu >> blog: http://blog.phytools.org >> >> On 3/5/2015 5:19 AM, Jonas Eberle wrote: >> >>> MultipagePhyloPlot <- function (tree, npages = 5) { >>> ntips <- length(tree$tip.label) >>> tips.per.page <- ntips / npages >>> y1 <- ntips - tips.per.page >>> y2 <- ntips >>> for (i in 1:npages) { >>> plot.phylo(tree, y.lim = c(y1, y2)) >>> y1 <- y1 - tips.per.page >>> y2 <- y2 - tips.per.page >>> } >>> } >>> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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/ Jacob Berv Ph.D. Student Lovette Lab Cornell Laboratory of Ornithology _______________________________________________ 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/