Hi Liam,
Would there be a way to modify this so that annotations like node labels and
axes could be applied to both 1/2s of a split tree at the same time? I’ve been
struggling with a similar problem using plot.phylo() and we can get our tree to
look like what we want on one page, but splitting it up while keeping node and
branch annotations etc is problematic.
For example, I am trying to plot a tree and annotate with the following
function calls.
#from ape
plot.phylo(timetree, cex=0.315, label.offset=0.35, edge.width=1.25,
edge.color=color)
#from phyloch - adds a geologic time scale
axisGeo(GTS = strat2012, unit = c("epoch", "period"), cex = 0.7, col =
c("grey80", "white"), texcol = "black", gridty = 2, gridcol = "red", ages=TRUE)
#then additional annotations with:
nodelabels()
axis()
I want to cut my tree in 1/2 and plot each 1/2 on a separate page, but maintain
the axes and annotations. Splitting a tree is great but it’s not super useful
unless you can call other functions on the pieces. It would be great to be able
to generate axes for each piece of a split tree independently and then annotate
each one as if they were a separate plot.
Jake
> On Mar 5, 2015, at 11:46 AM, Jonas Eberle <eberle.jo...@gmail.com> wrote:
>
> Hi Liam,
>
> perfect! Your right, I didn't realize that some species were duplicated.
> Great to have the option in phytools!
>
> All the best,
> Jonas
>
>
> 2015-03-05 17:16 GMT+01:00 Liam J. Revell <liam.rev...@umb.edu>:
>
>> Hi Jonas.
>>
>> I thought of the same thing. Unfortunately, one thing that I discovered is
>> that because R automatically adds 4% or so to the plotting range, you will
>> find that species & edges near the bottom of one page will also appear at
>> the top of the next page. If you test your code & look for species or edges
>> near the bottom or top of each page, you may find what I did.
>>
>> I have posted a solution to this here: http://blog.phytools.org/2015/
>> 03/splitting-tree-over-mutiple-plotting.html. It uses plotTree from
>> phytools internally, but it could fairly easily be modified to use other
>> tree plotters such as plot.phylo or plotSimmap.
>>
>> All the best, Liam
>>
>> Liam J. Revell, Assistant 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 3/5/2015 5:19 AM, Jonas Eberle wrote:
>>
>>> MultipagePhyloPlot <- function (tree, npages = 5) {
>>> ntips <- length(tree$tip.label)
>>> tips.per.page <- ntips / npages
>>> y1 <- ntips - tips.per.page
>>> y2 <- ntips
>>> for (i in 1:npages) {
>>> plot.phylo(tree, y.lim = c(y1, y2))
>>> y1 <- y1 - tips.per.page
>>> y2 <- y2 - tips.per.page
>>> }
>>> }
>>>
>>
>
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>
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Jacob Berv
Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology
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