Hi Agustin,
The problem seems to be the space between the genus and the species
names. Try this:
require(ape)
require(geiger)
tree-read.tree(text=
Calyptommatus_leiolepis:0.0168, Calyptommatus_nicterus:0.0099):0.0242
,Calyptommatus_sinebrachiatus:0.038):0.0724
,(Scriptosaura_catimbau:0.022,Nothobachia_ablephara:0.0309):0.0648):0.0659
,Procellosaurinus_erythrocercus:0.0235,
Procellosaurinus_tetradactylus:0.0259):0.0462
,Vanzosaura_rubricauda:0.072):0.142
,Micrablepharus_maximiliani:0.863):0.0225
,Psilopthalmus_paeminosus:0.193):0.0131);)
rgb(red=0, green=0, blue=0, alpha=100, max=255)
plot(tree,use.edge.length = T, font=4,tip.col=black, bg=transparent,
cex=1.5,edge.color = 'cyan',edge.width = 3)
Marcio
On Sun, Aug 19, 2012 at 8:19 PM, Agus Camacho agus.cama...@gmail.com wrote:
Dear list,
Im trying to plot a coloured tree with transparent background, to do that,
im using the following script:
require(ape)
require(geiger)
tree - read.tree(text=
Calyptommatus leiolepis:0.0168, Calyptommatus nicterus:0.0099):0.0242
,Calyptommatus sinebrachiatus:0.038):0.0724
,(Scriptosaura catimbau:0.022,Nothobachia ablephara:0.0309):0.0648):0.0659
,Procellosaurinus erythrocercus:0.0235,Procellosaurinus
tetradactylus:0.0259):0.0462
,Vanzosaura rubricauda:0.072):0.142
,Micrablepharus maximiliani:0.863):0.0225
,Psilopthalmus paeminosus:0.193):0.0131);)
rgb(red=0, green=0, blue=0, alpha=100, max=255)
plot(tree,use.edge.length = T, font=4,tip.col=black, bg=transparent,
cex=1.5,edge.color = 'cyan',edge.width = 3)
However, when I plot that, it does not appear transparent background and it
also plots together the species name and the genus.
Anybody knows how to do that?
Thanks in advance!
Agus
--
Agustín Camacho Guerrero.
Doutorando em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.
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--
Marcio R. Pie
Departamento de Zoologia
Universidade Federal do Paraná
Caixa Postal 19020
81531-980 Curitiba - PR - Brasil
Phone:+55(41) 3361-1558
FAX: +55(41) 3266-2042
http://piegroup.wordpress.com/
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