[BioC] makeGOGraph internode distance

[Loren Engrav]

Thank you

I am learning two things, how to use R/Bioconductor and how to do the email
Bear with me please, I will learn both

David Bodanis in E=mc^2 when discussing geezers doing research said, geezers
may have good ideas, that is not the problem, their problem is that they are
afraid to take risk, entering the R/Bioconductor email fray demonstrates
that I can take risk

And I may have a work around that is better than any solution

Save graph as postscript
Open in Illustrator
Scale 400%
Rotate labels 45 degrees
Set font to 6point
And voila, a nice big induced GO tree
Never mind if I will ever understand the tree, it is the process, not the
result

But as for the problem

>you probably have more nodes than you can easily render on the available
plotting device

True
length(go2tree.leaves) returned 428 nodes

>You could make it larger

I have tried this, but failed, am sorry
Like I tried
> par (pin = c(100,100))
> plot (xctree)
It say Error in plot.new() : plot region too large
So I try
> par (pin = c(50,50))
> plot (xctree)
It say Error in plot.new() : plot region too large
Etc, etc, etc
Till I choose > par (pin = c(10,10))
Which is pretty much where I started
So I clearly do not know how to make it larger, am sorry

> how would you know that the tree has changed?
Open them in Illustrator at 400% scale and I cannot see significant
difference

>You should read the Rgraphviz vignette
I have read that so much that I have almost memorized it, but I could not
make it solve this problem, am sorry

>You may find that you would rather use graphviz
>You could investigate the use of the imageMap function (geneplotter)

True but, I think the combo of makeGOGraph (from genes) and xctree.leaves
[1:428]  and GOGraph (from leaves trimmed of junk) and Illustrator is
extremely powerful to make a big GO tree, is in fact pawerful enough, again
never mind if I ever understand the biology, it is process not result

I see you wrote both, cool, you might add to the documentation something
about large trees and to finish the study for LARGE trees the user might do
makeGOGraph, get the nodes, cull the junk, plot them up with GOGraph, and
load them up into Illustrator to wrap it up

which I will now do for MF

Thank you

Loren Engrav, MD
Univ Washington