Hi Kamila,
The vectors x and y extracted by Liam are ordered in the same way than
the tip labels of the tree (say its names is 'phy'); for instance, the
followings should do the same output than plot(phy):
plot(phy, show.tip.label = FALSE)
obj <- get("last_plot.phylo", envir = .PlotPhyloEnv)
x <- obj$xx[1:obj$Ntip]
y <- obj$yy[1:obj$Ntip]
text(x, y, phy$tip.label)
Another R function that may be useful in your case is locator if you
plot the tree interactively (i.e., this will not work if using pdf(),
png(), ...). This may use in different ways, for instance:
text(locator(1), NULL, "Label to be placed interactively")
You then click on the graphical window where you want to add the text.
Best,
Emmanuel
Le 01/07/2016 05:47, Kamila Naxerova a écrit :
Thanks so much for your reply, Liam.
Most of the tip labels plotted by plot.phylo are in an optimal place, but while
plotting a large number of trees, I have observed some “outliers" where the tip
label is mispositioned and overlaps with the edge. Therefore, I would like to move
some of those “bad” labels.
I am afraid my grasp of R’s underbelly is not profound enough to understand how
to implement your last suggestion. It seems that you are extracting the tip
label xy coordinates from the last tree that was plotted, but how do you then
assign the new, modified coordinates to a new plot?
Thanks again for helping with this, it’s much appreciated.
Kamila
On Jun 29, 2016, at 10:32 PM, Liam J. Revell <liam.rev...@umb.edu> wrote:
Dear Kamila.
In what way would you like to adjust the tip labels? The most useful adjustment that I have
found is the argument lab4ut="axial" which plots the labels with the angle of the
corresponding terminal edge. It is also possible to offset the tip labels using
label.offset>0.
We can also get the positions of the tips in the coordinates of our plotting
device as follows:
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
x<-obj$xx[1:obj$Ntip]
y<-obj$yy[1:obj$Ntip]
You can then use these coordinates to plot your labels any way you choose!
- Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 6/29/2016 5:11 PM, Kamila Naxerova wrote:
Dear all,
is there a way to adjust the position of tip labels when plotted an unrooted
tree with plot.phylo?
Many thanks,
Kamila
The information in this e-mail is intended only for t...{{dropped:24}}
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