Hi Klaus. Thanks for the fix. In ape now.
Cheers, Emmanuel Le 30/07/2015 22:45, Klaus Schliep a écrit :
Dear Julia, this function should fix your problem and Emmanuel may can include it into edgelables function: edgeLabelsFan <- function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, thermo = NULL, pie = NULL, piecol = NULL, col = "black", bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, date = NULL, ...) { lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv) if (missing(edge)) { sel <- 1:dim(lastPP$edge)[1] subedge <- lastPP$edge } else { sel <- edge subedge <- lastPP$edge[sel, , drop = FALSE] } r <- sqrt(lastPP$xx^2 + lastPP$yy^2) XX <- lastPP$xx[subedge[,2]] * (r[subedge[,2]] + r[subedge[,1]]) / (r[subedge[,2]] * 2) YY <- lastPP$yy[subedge[,2]] * (r[subedge[,2]] + r[subedge[,1]]) / (r[subedge[,2]] * 2) if (!is.null(date)) XX[] <- max(lastPP$xx) - date BOTHlabels(text, sel, XX, YY, adj, frame, pch, thermo, pie, piecol, col, bg, horiz, width, height, ...) } Kind regards, Klaus On Thu, Jul 30, 2015 at 1:10 PM, Julia Dupin <julia.du...@gmail.com <mailto:julia.du...@gmail.com>> wrote: Dear all, I'm trying to plot a tree with some branches marked using edgelabels() but the function is misplacing the labels (it misses the actual branches) when I use it in a "fan" type tree. Here is an example tree<-pbtree(n=10,scale=10) plot(tree,type="fan") edgelabels() The phylogeny I am working on is pretty big so "fan" is the best option for me to visualize it. Has anyone had this issue before? Is there a way to fix it? Or maybe an alternative to edgelabels? Thanks in advance!! Julia -- Julia Dupin PhD candidate Smith lab Dept. Ecology and Evolutionary Biology, Ramaley Hall C127A University of Colorado - Boulder email: julia.du...@colorado.edu <mailto:julia.du...@colorado.edu> website: http://www.colorado.edu/smithlab/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org <mailto: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
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