Mind=Blown. Amazing. Thank you.
Jake > On Mar 5, 2015, at 2:55 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > > Hi Jacob. > > This is surprising easy. Check out the solution here: > http://blog.phytools.org/2015/03/splitting-tree-across-multiple-pages.html. > > You may find that, as in this example, some things like node & edge labels > are split across pages - in which case you can fiddle with the split > positions & replot the tree until it is the way you want it. > > 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 2:24 PM, Jacob Berv wrote: >> 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 >> 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/
