[Phylobase-devl] What I did with my summer vacation -- phylobase plotting

David Orme d.orme at imperial.ac.uk
Thu Aug 7 10:58:04 CEST 2008

Hi Peter,

That all looks fantastic. I noticed a couple of things running the  

- The data plotted in the 'treePlot(geospiza, tip.plot.fun = ff)'  
example seems to be random - it certainly is randomised with respect  
to the tips and it looks like the values are as well. I've plotted two  
calls in the attached pdf to show what I mean

- Oddly, the 'treePlot(geospiza, tip.plot.fun = 'density')' example  
seems to have a weird bug. In successive calls of the same example,  
the density plots shift between the correct place at the tips and  
appearing half way down the tree. Even odder, I only get this  
behaviour in a Quartz window - it plots correctly to a pdf for both  
calls, as you can see!

- For some reason, plotting any treePlot to a pdf leads with a blank  
page, as you can also see!

Mac OS 10.5.3, R 2.7.1, ape 2.1.3, phylobase r. 270


 > pdf("~/Desktop/treePlotQuestions.pdf")
 > treePlot(geospiza, tip.plot.fun = ff)
 > treePlot(geospiza, tip.plot.fun = ff)
 > treePlot(geospiza, tip.plot.fun = 'density')
 > treePlot(geospiza, tip.plot.fun = 'density')
 > dev.off()

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