Re: [R-sig-phylo] Plotting error edgelabels in phylogeny type=fan
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/
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--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
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Re: [R-sig-phylo] Plotting error edgelabels in phylogeny type=fan
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]]
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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]]
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Re: [R-sig-phylo] Plotting error edgelabels in phylogeny type=fan
Hi Klaus,
thank you so much for your quick reply! I will give it a try. I ended up
color coding the branches using edge.color for now.
Thanks again!
Julia
On Thu, Jul 30, 2015 at 1:45 PM, Klaus Schliep klaus.schl...@gmail.com
wrote:
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
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
--
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]]
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Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] Plotting error edgelabels in phylogeny type=fan
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 https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
