Hi Zech.

Regarding point (1), this is indeed a bug in plot.phylo, however there is a work-around. Try the following:

library(ape)
data(bird.orders)
plot(bird.orders,direction="downwards")
axis(2)
plot(bird.orders,direction="downwards",y.lim=c(-15,30))

Regarding point (2), plot.phylo(...,no.margin=TRUE) *does* plot without margins; however there is some space within a plotted graph between the (invisible) plot axes and plotted points and lines. If we want our edges to butt right up against the plot window, we can also accomplish this with the arguments y.lim and x.lim. For instance, I found via trial & error that:

plot(bird.orders,x.lim=c(1.3,35.5),y.lim=c(1.5,22.4),no.margin=T)

got me pretty darn close.

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 3/5/2013 2:32 AM, Not To Miss wrote:
Hi,

When plotting the phylo tree downwards, the tip labels are truncated:
library(ape)
data(bird.orders)
plot(bird.orders, direction='downwards')

I found the problem on the website:
http://www.mail-archive.com/r-sig-phylo@r-project.org/msg00298.html. It
seems still not solved? It's kind of annoying.

Another annoying thing is that, when setting the margins to zero, the
plot.phylo still plot some margins around the tree, which is totally
inconsistent to the general plotting convention. Is it possible to be
changed?

Thanks,
Zech

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