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 <[email protected]
<mailto:[email protected]>> 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: [email protected] <mailto:[email protected]>
website: http://www.colorado.edu/smithlab/
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--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
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