Dear R-sig-phylo users,
Im trygin to use the cool phenogram (Revell's phytools) to plot two graphs
together.
The code to do that comes below.
1. Id like to adjust the margins of the figure and the position of the
names so I can avoid the names getting cropped by the margins of the figure
2. id like to save it to tiff and 600ppi, but when i try using tiff(), as i
do for other graphs, but the figure gets totally deformed. The export
option also does not allow to set resolution.
Thanks Liam for your recent info. I decided to post this to the list so
others migth also give a hint.
Cheers
Agus
#tree for plotting
tree <- read.tree(text="
((((C.leiolepis:0.0168, C.nicterus:0.0099):0.0242
,C.sinebrachiatus:0.024):0.0724
,(S.catimbau:0.0652,N.ablephara:0.0309):0.0648):0.0659
,((((P.erythrocercus:0.0235,P.tetradactylus:0.0259):0.0462
,V.rubricauda:0.072):0.142
,M.maximiliani:0.1463):0.0225
,P.paeminosus:0.1093):0.0131);")
tree$tip.label<-gsub("\\.","\\. ",tree$tip.label)
# first create plotting area
tiff("tp&ctmax.tif",width=5.5, height=7, unit="cm", res=600,
compression="lzw")
plot.new(); par(mar=c(2.5,4,0,2))
par(mfrow=c(2,1))
par(usr=c(-0.04,1.04,-5,1.04*length(tree$tip.label)))
source('C:/Users/Agus/Desktop/Curso de analise compartiva em R/phenogram.R')
# first paint tree
tree<-paintSubTree(tree,node=16,state="2",stem=T)
cols<-setNames(c("blue","red"),1:2)
# define variable and names
tp=seq(1:10)
names(tp)=tree$tip.label
# plot
phenogram(tree,tp,
xlab="",
ylab="preferred temperature (ºC)",
colors=cols,
ftype="i",
spread.labels=TRUE,
spread.cost=c(1,0.4),
link=0.2,offset=0,
)
# first paint tree
tree<-paintSubTree(tree,node=16,state="2",stem=T)
cols<-setNames(c("blue","red"),1:2)
# define variables
ctmax=seq(1:10)
names(ctmax)=tree$tip.label
phenogram(tree,ctmax,
xlab="branch length ",
ylab="CTMAX (ºC)",
colors=cols,
ftype="i",
spread.labels=TRUE,
spread.cost=c(1,0.4),
link=0.2,offset=0,
)
cols<-setNames(c("blue","red"),c("snake-like", "lacertoid"))
dev.off()
--
Agustín Camacho Guerrero.
Doutor 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.
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
