Hello,
I have a question about margins when plotting an unrooted tree
(type="unrooted") with the 'ape' package ver. 1.7. When I plot
an unrooted
tree with:
no.margin=TRUE
it seems that the margins are still there. It appears to be only when
type="unrooted".
I'm plotting multiple plots using layout() and would like to be able to get
rid of the margins or if the margins are not there, have the plot take up
more of the plotting region. Below is an example of one of the trees.
cat("(((((R3:500.0,R4:500.0):439.0,L._amplexicaule:500.0):494.8,((W4:500.0,R1:500.0):499.0,
W2:500.0):500.0):495.8,(W5:500.0,R2:500.0):491.8):500.0,W1:500.0);",
file = "clustal.tre", sep = "\n")
clustal.tree4 <- read.tree("clustal.tre")
plot(clustal.tree4, type="unrooted", no.margin=TRUE,
font=c(1,1,3,1,1,1,1,1,1))
unlink("clustal.tre")
text.lab < -c(99.2,99.0,87.8,100.0,99.8,98.4)
node.lab <- c(3:8)
nodelabels(text=text.lab, node=node.lab, cex=.7)
Any help or general suggestions are greatly appreciated,
Thanks, Jerry
Graduate Student, Missouri State University
R 2.2.0 Windows XP
I figured out my problem. I just used locator() to find where I wanted my x.lim and y.lim, and set them manually. Jerry>Hello,> I have a question about margins when plotting an unrooted tree >(type="unrooted") with >the 'ape' package ver. 1.7. When I plot an unrooted >tree with: no.margin=TRUE it seems that the margins are still there. It >appears to be only when type="unrooted". I'm plotting multiple plots using >layout() and would like to be able to get rid of the margins or if >the >margins are not there, have the plot take up more of the plotting region. >Below is an example >of one of the trees.>cat("(((((R3:500.0,R4:500.0):439.0,L._amplexicaule:500.0):494.8,((W4:500.0,R1:500.0):499.0, > >W2:500.0):500.0):495.8,(W5:500.0,R2:500.0):491.8):500.0,W1:500.0);", file >= "clustal.tre", sep >= "\n") clustal.tree4 <- read.tree("clustal.tre") >plot(clustal.tree4, type="unrooted", no.margin=TRUE, > >font=c(1,1,3,1,1,1,1,1,1)) unlink("clustal.tre") text.lab < >-c(99.2,99.0,87.8,100.0,99.8,98.4) node.lab <- c(3:8) >nodelabels(text=text.lab, node=node.lab, cex=.7)