This is a bug & it is apparently here:
if (is.character(alp))
tmp <- max(xx.tips) * 1.5
This line tells R to give 50% of the total tree height (or 1/3 of the
plotting width) for labels if optimization of the amount of space to
leave for labels fails (which makes is.character(alp) evaluate to TRUE);
however that optimization is irrelevant if no labels are to be plotted!
If this were changed to:
if (is.character(alp)&&show.tip.label)
tmp <- max(xx.tips) * 1.5
then the correct function appears to be restored.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected]
blog: http://blog.phytools.org
On 6/18/2015 1:04 PM, David Bapst wrote:
Hi all,
I was plotting some trees with obscenely long taxon names (long story)
and found an odd plotting artifact that leaves white-space when
show.tip.labels=FALSE, as if the plot was trying make room for the
extraordinarily long tip labels, even though they wouldn't be plotted.
I'm using R version 3.2.0 and ape 3.3.
Here's some reproducible code:
##################################
library(ape)
tree<-rcoal(1000)
tree1<-tree
tree1$tip.label<-paste0("a_really_long_obnoxious_very_very_long",
"_when_is_it_going_to_end_name_are_we_there_yet_maybe",
"okay_lets_do_this",1:1000)
tree2<-tree
tree2$tip.label<-paste0("a_long_name",1:1000)
plot(tree1, show.tip.label=FALSE)
#####################################
And we can see the plot of tree1 pushes the tips back, leaving a lot
of white space to the right. The curious thing is, plots for tree and
tree2 with its slightly longer name look identical, with the same
amount of whitespace.
##################################
plot(tree, show.tip.label=FALSE)
plot(tree2, show.tip.label=FALSE)
##################################
So there's some threshold to the length of the tip labels to produce
this white space.
For reasons not entirely clear to me, this issue inconsistently
appears when various layouts are used.
#######################################
#has it:
layout(matrix(1:4,2,2))
plot(tree,show.tip.label=FALSE)
plot(tree1,show.tip.label=FALSE)
plot(tree2,show.tip.label=FALSE)
plot(tree,show.tip.label=FALSE)
#doesn't has it
layout(1:4)
plot(tree,show.tip.label=FALSE)
plot(tree1,show.tip.label=FALSE)
plot(tree2,show.tip.label=FALSE)
plot(tree,show.tip.label=FALSE)
#######################################
Perhaps that suggests some clue to this odd behavior.
Apologies for all the emails lately!
Cheers,
-Dave
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