Hi Emmanuel A good compromise!
Initial tests work as expected. Thanks! Sam > Date: Mon, 7 Sep 2009 18:16:44 +0200 > From: [email protected] > To: [email protected] > CC: [email protected] > Subject: Re: [R-sig-phylo] plot.phylo downwards/leftwards > > Hi Sam & others, > > It's indeed difficult to have something nice with multichotomies, so I > have decided to leave the current behaviour in this case (e.g., if all > edges are red the vertical lines representing the node will be red, > otherwise black). For dichotomous nodes, the requested behaviour has > been implemented. For those interested to try the new version, it can be > downloaded here: > > http://ape.mpl.ird.fr/misc/plot.phylo.R > > I welcome any test because a number of changes has been done, so I'm > still waiting to put it on SVN. > > Cheers, > > Emmanuel > > Emmanuel Paradis wrote on 05/08/2009 12:13: > > Hi Sam, > > > > The problem is with (hard) multichotomies, eg: > > > > library(ape) > > tr <- read.tree(text = "(a,b,c);") > > plot(tr, edge.col = c("blue", "red", "green"), edge.width=5) > > > > What should be the colour of the vertical line? > > > > Emmanuel > > > > Sam Brown wrote: > >> Hi Emmanuel > >> > >>> I'll try to improve this and take the opportunity to clean-up the > >>> code of plot.phylo, so if you have suggestions or reports of little > >>> annoyances, please share them. > >>> > >>> EP > >> > >> My little annoyance: > >> When colouring edge lengths using plot.phylo(x, edge.colour=<vector of > >> colours>), if edges of two different colours meet at a node, the > >> colour of the vertical "edge" remains black. It is only a little > >> annoyance, but it'd be cool if it were possible to get the colours > >> consistent through to the nodes, as it does when edges of the same > >> colour meet. > >> Run this code a few times to see the current effect. > >> > >> tr<-rtree(10) > >> br.col<-c(rep("red",3),rep("blue",4), rep("yellow",5), rep("purple",6)) > >> > >> plot(tr, edge.color=br.col, use.edge.length=FALSE) > >> > >> Thanks! > >> > >> Sam > >> > >>> Message: 1 > >>> Date: Thu, 30 Jul 2009 11:54:12 +0200 > >>> From: Emmanuel Paradis <[email protected]> > >>> Subject: Re: [R-sig-phylo] plot.phylo downwards/leftwards > >>> To: Janet Young <[email protected]> > >>> Cc: [email protected] > >>> Message-ID: <[email protected]> > >>> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > >>> format="flowed" > >>> > >>> Hi Janet, > >>> > >>> The bug comes from the fact that it is tough to determine the space > >>> required by the labels when some are (very) long. In fact, even the > >>> default plot is truncated on its right-hand side. > >>> > >>> I'll try to improve this and take the opportunity to clean-up the > >>> code of plot.phylo, so if you have suggestions or reports of little > >>> annoyances, please share them. > >>> > >>> EP > -- > Emmanuel Paradis > IRD, Montpellier, France > ph: +33 (0)4 67 16 64 47 > fax: +33 (0)4 67 16 64 40 > http://ape.mpl.ird.fr/ _________________________________________________________________ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
