Thanks a lot for your reply, Liam. I'll use y.lim as a work-around. Best, Zech
On Tue, Mar 5, 2013 at 9:21 AM, Liam J. Revell <[email protected]> wrote: > 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/<http://faculty.umb.edu/liam.revell/> > email: [email protected] > 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-**[email protected]/**msg00298.html<http://www.mail-archive.com/[email protected]/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 >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> R-sig-phylo mailing list - [email protected] >> https://stat.ethz.ch/mailman/**listinfo/r-sig-phylo<https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> Searchable archive at http://www.mail-archive.com/r-** >> [email protected]/<http://www.mail-archive.com/[email protected]/> >> >> > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
