Just to throw out another quick suggestion - for a tree with "only" 220
tips you could try a "fan" style plot which plots the tip labels
radially leaving you with a bit more chance of being able to read them.
This is implemented in the plot method for the object class, but also in
phytools::plotTree. For instance:
plotTree(tree,lwd=1,type="fan",fsize=0.7)
Of course, as Brian suggested you can wrap that it in pdf(...) //
dev.off() to use a PDF as your plotting device:
pdf(file="mytree.pdf",width=10,height=10)
plot(tree,lwd=1,type="fan",fsize=0.8)
dev.off()
All the best, 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 8/31/2016 8:03 AM, Brian O'Meara wrote:
A similar solution is to create a pdf:
pdf(file="AwesomeTree.pdf", width=10, height=10)
plot(phy)
dev.off()
As you increase the width and height, the labels become proportionally
smaller. You can probably mess around with cex options, too, but this is
the approach I normally use.
Best,
Brian
_______________________________________________________________________
Brian O'Meara, http://www.brianomeara.info, especially Calendar
<http://brianomeara.info/calendars/omeara/>, CV
<http://brianomeara.info/cv/>, and Feedback
<http://brianomeara.info/teaching/feedback/>
Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Director for Postdoctoral Activities, National Institute for
Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS)
Communication Director, Society of Systematic Biologists
On Wed, Aug 31, 2016 at 5:25 AM, Vojtěch Zeisek <vo...@trapa.cz> wrote:
Hello,
if onlythe readibility of the labels is the issue, what about using svg()
function? It produces a SVG file which You can open in almost any vector
editor (like Inkscape) andmove the labels around. Chech ?svg for possible
settings and play with them little bit. They vary among operating systems.
So You can do something like
svg(...) # Any parameters inside, at least output file name
# All the tree ploting commands...
dev.off() # To save the SVG file to the disc
Check also parameters of function tip.labels() - You can specify font size
or replace the text with some symbol.
(Sorry for being so brief, I don't have exact examples handy)
Yours,
V.
31. srpna 2016 11:11:33 CEST, "Bhuller, Ravneet" <
ravneet.bhulle...@imperial.ac.uk> napsal:
Dear All,
I am trying to construct a phylogenetic tree (neighbour joining) using
either APE or PHANGORN in R. But, since I have got 220 strains of
bacteria in my data, the resulted tree is not very clear. The branch
labels are so much overlapping that they cannot be read at all. Is
there any way, I can get a neat tree with clearly read labels? Any
guidance will be very much appreciated.
Regards,
Rav
--
Vojtěch Zeisek
http://trapa.cz/cs
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