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

David Orme d.orme at imperial.ac.uk
Fri Aug 8 10:18:44 CEST 2008


>> That all looks fantastic. I noticed a couple of things running the  
>> examples:
>> - 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
> Yes, this was a bit of trickier on my part.  grid.points() with no
> parameters plots random data.  The function ff() takes a parameter x,
> which is the data associated with a tip, but I didn't pass it on in
> the example.

Ah - I did come to suspect that after I e-mailed!
>> - 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!
> I tried to replicate this, e.g. calling treePlot(geospiza,
> tip.plot.fun = 'density') several times in a row and couldn't get it
> on my quartz window, strange.  If you see it again, could you save the
> window and send it to me?  Sounds kinda like a quartz bug.

I can't now replicate it! I will keep an eye out for a recurrence and  
copy it to you if I see it...

On a new question - how do these functions cope with multiple plots on  
a page. I tried using par(mfrow=c(2,1))  before plotting the density  
plots and found that the tree plots across both panels but the density  
plots respect the plot division. See below for a demonstration -  
probably best to avoid mfrow and mfcol with grid graphics, I guess!

>> - For some reason, plotting any treePlot to a pdf leads with a  
>> blank page,
>> as you can also see!
> What I got initially was two pages of plots as expected then a blank
> page, a density plot, a blank page and the density plot.  I've made
> some changes, and now I get a blank page when a density plot is called
> for the first time but not afterwards.  I'm at a loss for why this is
> happening, but I suspect it is related to the gridBase package.
>>> 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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