Hi Saleh & Will,
I'm not sure whether phytools::cophylo does the same thing than
ape::comparePhylo (maybe rather ape::cophyloplot).
comparePhylo() is actually aimed for data exploration/summary rather
than for producing publication-ready graphs. That said, there is a
trick to play with the character sizes when you write the plot into a
PDF file, eg:
pdf("plot.pdf", w = 10, h = 10)
par(xpd = TRUE) # could be useful if w and h are small
comparePhylo(..... plot = TRUE)
dev.off()
You can change the values of 'w' and 'h' in the call to pdf() to
change the size of the characters (the smaller the values, the larger
the characters). Of course, this will affect all characters which may
not be what you want. You can have total control by plotting the trees
separately, typically after layout(matrix(1:2, 1)), and using the
option 'edge.width' in plot.phylo (or edge.col if you want to use
colours). If you go to this solution, you may find the branch numbers
(indices) of your trees with:
plot(tree)
edgelabels()
This will help you to create the vectors given to edge.width/edge.col.
HTH
Best,
Emmanuel
Thu, 13 Jun 2019 09:30:02 -0700 William Gearty <wgea...@stanford.edu>:
Hi Saleh,
Try using phytools::cophylo() instead. It has far more options for
plotting. Documentation is here:
https://www.rdocumentation.org/packages/phytools/versions/0.6-60/topics/cophylo
.
Best,
Will
On Thu, Jun 13, 2019 at 6:38 AM Saleh Rahimlouye Barabi <
saleh.rahim...@ut.ee> wrote:
Hello,
I'm using comparePhylo() function from APE package in R. I want to
know is
there anyway to change the tip labels size when plotting it?
Arguments like 'cex' does not work in this case.
Best
Saleh Rahimlou
Ph.D. Candidate
Department of Botany and Ecology
University of Tartu
14A Ravila, 50411 Tartu
Estonia
Email: saleh.rahim...@ut.ee<mailto:saleh.rahim...@ut.ee>
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--
William Gearty
PhD Candidate, Paleobiology
Department of Geological Sciences
Stanford School of Earth, Energy & Environmental Sciences
williamgearty.com
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