Hello Marina, the problem seems with the alpha parameter. It seems it does not work for smaller than 1/500, just set it to a small value, e.g. 0.01. I will include a check into the function for further releases. The alpha value and the edge weight are nice parameters to play with the appearance of the plot.
Regards, Klaus On Sat, Aug 22, 2015 at 1:51 PM, Marina Strelin <marina.streli...@gmail.com> wrote: > Dear all, > > > I want to plot superimposed trees from a posterior distribution using the > densiTree function of the R package phangorn. I’m using the R vesion 3.1.3 > (I understand that this package was written under that version). The > function works well when I use no more than 500 trees from the posterior > distribution, but once I reach that limit the function densiTree runs in > the R console (no error message pops up) but no plot is retrieved. I > believe my computer has no memory problems, since 1/3 of the C disc is > still empty. > > > trees<-read.nexus(file=file.choose()) > > consensus<-read.nexus(file=file.choose()) > > x<-sample(trees, 500) > > densiTree(x, type = "cladogram", alpha = 1/length(x), consensus = > consensus, optim = FALSE, > > scaleX = FALSE, col = 1, width = 1, cex = 0.8) > > > (THIS WORKS) > > > x<-sample(trees, 550) > > densiTree(x, type = "cladogram", alpha = 1/length(x), consensus = > consensus, optim = FALSE, > > scaleX = FALSE, col = 1, width = 1, cex = 0.8) > > > (THIS DOES NOT WORK!) > > > Thanks in advance for helping me with this! > > > Marina > > [[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/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston [[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/
