Thank you so very much for helping me with this! This is the perfect solution.
Kamila
> On Jul 1, 2016, at 3:37 AM, Emmanuel Paradis <emmanuel.para...@ird.fr> wrote:
>
> 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$tip.label)
>
> Another R function that may be useful in your case is locator if you plot the
> tree interactively (i.e., this will not work if using pdf(), png(), ...).
> This may use in different ways, for instance:
>
> text(locator(1), NULL, "Label to be placed interactively")
>
> You then click on the graphical window where you want to add the text.
>
> Best,
>
> Emmanuel
>
> Le 01/07/2016 05:47, Kamila Naxerova a �crit :
>> Thanks so much for your reply, Liam.
>>
>> Most of the tip labels plotted by plot.phylo are in an optimal place, but
>> while plotting a large number of trees, I have observed some �outliers"
>> where the tip label is mispositioned and overlaps with the edge. Therefore,
>> I would like to move some of those �bad� labels.
>>
>> I am afraid my grasp of R�s underbelly is not profound enough to understand
>> how to implement your last suggestion. It seems that you are extracting the
>> tip label xy coordinates from the last tree that was plotted, but how do you
>> then assign the new, modified coordinates to a new plot?
>>
>> Thanks again for helping with this, it�s much appreciated.
>>
>> Kamila
>>
>>> On Jun 29, 2016, at 10:32 PM, Liam J. Revell <liam.rev...@umb.edu> wrote:
>>>
>>> Dear Kamila.
>>>
>>> In what way would you like to adjust the tip labels? The most useful
>>> adjustment that I have found is the argument lab4ut="axial" which plots the
>>> labels with the angle of the corresponding terminal edge. It is also
>>> possible to offset the tip labels using label.offset>0.
>>>
>>> We can also get the positions of the tips in the coordinates of our
>>> plotting device as follows:
>>>
>>> obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
>>> x<-obj$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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