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
Quoting Janet Young <[email protected]>:
Hi,
I think I've found a very minor display bug in ape's plot.phylo when a
tree contains long tip name(s).
My tree looks great if I use direction="rightwards" or "upwards", but
if I use leftwards or downwards, part of the tree including the root
isn't displayed (it looks like it's been truncated by the margin).
It's a problem whether I work on Mac or linux.
Here's some code that demonstrates the problem:
#####################
#read in a simple example tree, as in plot.phylo help doc:
### An extract from Sibley and Ahlquist (1990)
cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",
"Athene_noctua:7.3):6.3,Tyto_alba:13.5);", file = "ex.tre", sep = "\n")
tree.owls <- read.tree("ex.tre")
plot(tree.owls)
unlink("ex.tre") # delete the file "ex.tre"
#now, give one tip a silly long label
mytree<-tree.owls
mytree$tip.label[2]<-"Asio_otusAsio_otusAsio_otusAsio_otusAsio_otusAsio_otusAsio_otusAsio_otusAsio_otusAsio_otusAsio_otusAsio_otus"
#plot the tree
plot(mytree,direction="leftwards") #tree display is truncated
plot(mytree,direction="downwards") #tree display is truncated
plot(mytree,direction="rightwards") #OK
plot(mytree,direction="upwards") #OK
#####################
I'm not actually displaying the tip names on my tree, so I'll just
substitute them for something very short to avoid the problem, but I
thought you'd want to know what I found.
thanks very much,
Janet Young
-------------------------------------------------------------------
Dr. Janet Young (Trask lab)
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., C3-168,
P.O. Box 19024, Seattle, WA 98109-1024, USA.
tel: (206) 667 1471 fax: (206) 667 6524
email: jayoung ...at... fhcrc.org
http://www.fhcrc.org/labs/trask/
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