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> 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
> website: http://www.colorado.edu/smithlab/
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
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>
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
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