Hi all, I have a (almost certainly trivial) question about plotting a rooted tree with bootstrap values using ape and phangorn. I am using a simple script that looks like this:
dist <- daisy(matrix,metric="gower") nrooted <- root(nj(dist),outgroup=x) plot(nrooted) ## this plots the tree with the correct root, just the way I want it # now I would like to put some bootstrap values on this tree f <- function (xx) root(nj(daisy(xx,metric="gower")),outgroup=x) b <- boot.phylo(nrooted,matrix,FUN = f, B=1000, trees=T) tree <- plotBS(nrooted,b$trees,type="phylogram”) The tree that is produced by plotBS has lost the root I assigned it. I would be really grateful is somebody could point out to me how to do this right! Thanks so much. Kamila The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ 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/
