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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