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
--
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701
http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html
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