Sorry,my previous example for taxo.fonts was incomplete. Here is another example of the problem that I am having trying to align tips with taxo.fonts: The error ir produces is: Error in text.default(xx[-id], yy[-id], tax[-id], font = 3, adj = c(0, : zero length 'labels'
Here is the code that produces the error: library(ape) library(phyloch) read.tree(text="((JC0034:0.56193117703558859155,((JC0032:0.26417452948039871208,(JC0039:0.00000198431968445117,(JC0040:0.04090238861482920624,(JC0036:0.00000198431968445117,(JC0035:0.00278594072123998721,JC0043:0.00000198431968445117)98:0.00839151437796370123)81:0.00271501071388845780)37:0.00284385118684500095)99:0.27548176713181982134)99:0.19955357589693831222,(JC0042:0.16727054495452559069,((JC0044:0.20745840487731395663,(JC0045:0.03317407925666514962,JC0041:0.05169361744053992125)100:0.17820118129244821858)96:0.02713741920299188315,((JC0038:0.00000198431968445117,JC0046t:0.00000198431968445117)99:0.00837767044457797365,JC0037:0.00000198431968445117)100:0.14356932073243436343)100:0.17940764911877768450)100:0.44467488567142149369)75:0.04619993402434956209):0.52905368142148145871,7421_desC:0.52905368142148145871);")->ttt plot(ttt) plot.phylo(ttt, tip.color = 0, x.lim = c(0, 1.3)) taxo.fonts(ttt, align = TRUE, offset = 0.1) On Thu, Oct 28, 2010 at 1:16 PM, John Cumbers <johncumb...@gmail.com> wrote: > Hi Christoph et al. > > Thanks for the help, I've been trying to use ?taxo.fonts in the pyloch > package on my tree but I keep getting this error: > > Error in text.default(xx[-id], yy[-id], tax[-id], font = 3, adj = c(0, : > zero length 'labels' > > I can't understand why. I do have some zero length labels "", but > even when I add some arbitrary values to them I still get the error, > and even the vipera example has some "" (which I take to be zero > length) labels and that plots fine. I can repeat the problem with > the woodmouse dataset from Ape: > > data(woodmouse) > plot.phylo(woodmouse.nj, tip.color = 0, ) > taxo.fonts(woodmouse.nj, align = TRUE, offset = 0.1) > #produces the above error > > But this works fine: > data(vipera) > plot.phylo(vipera, tip.color = 0, x.lim = c(0, 1.3)) > taxo.fonts(vipera, align = TRUE, offset = 0.1) > > Any help appreciated. > > John > > > > On Wed, Oct 27, 2010 at 3:12 AM, Christoph Heibl > <christoph.he...@gmx.net> wrote: >> Hi, >> >> >> On Oct 27, 2010, at 1:03 AM, Andy Rominger wrote: >> >>> Hi John, >>> >>> This is the default plotting style in package ade4 (using an object of class >>> phylog to store your tree, and plot.phylog(...) for plotting). >>> >>> You can convert between an object of class `phylo' from ape to `phylog' in >>> ade4 with a two-step method: >>> # phylo to newick: >>> my.newick <- write.tree(my.phylo) >>> # newick to phylog >>> my.phylog <- newick2phylog(my.newick) >>> # you could do it in one line if you like that kind of thing... >>> >>> Your other option if you want to keep it all in package ape is to use >>> dist.nodes(...) to get the distance of each tip from the root and then use >>> this distance to add a line segment at the end of each tip. You can use >>> this command to get information about where all the various edges have been >>> drawn: >>> get("last_plot.phylo", envir = .PlotPhyloEnv) >> >> If you want use ape, Andy´s second approach is implemented in taxo.fonts in >> the phyloch package[1]. >> See the last example in ?taxo.fonts >> >> Best, >> Christoph >> >> [1] http://www.christophheibl.de/Rpackages.html >> >>> >>> Hope that helps, good luck! >>> Andy >>> >>> >>> On Tue, Oct 26, 2010 at 3:57 AM, John Cumbers <johncumb...@gmail.com> wrote: >>> >>>> Hi all, >>>> >>>> I'm trying to align or justify the tip labels of a tree on the right >>>> with the plot function in Ape. I want to keep the branch lengths, >>>> but have dotted lines reaching out to the tip labels. If this can't >>>> be done in Ape or R, what other tools would you suggest for preparing >>>> trees for publication. >>>> >>>> Thanks, >>>> John >>>> >>>> _______________________________________________ >>>> R-sig-phylo mailing list >>>> R-sig-phylo@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> R-sig-phylo mailing list >>> R-sig-phylo@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> >> > _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo