On Thu, Feb 16, 2012 at 10:10 AM, Tim Triche, Jr. <tim.triche@gmail.com>wrote:

> seconding this, I did not know about Gviz, but with GRanges and rtracklayer
> it seems like an obvious choice.
> have been playing with ggbio lately as well, very cool but has some issues
> with ggplot2 dev (don't we all?  Hadley...)
>

Hi  Tim,

You are right, I have been working on the update based on ggplot2-dev and
also with some API and functionality change in ggbio recently in git,
should be released to bioc-dev after March 1st, I guess March 1st is
Hadley's plan to release ggplot2 0.9. Sorry for the inconvenience so far...
ggbio is designed in different way and serve different purpose, it's highly
depend on and extend ggplot2 which make it general in the manner of grammar
of graphics, also full of add-on features and it works most directly for
core classes in bioconductor instead of bring a new constructor or class. I
made lots of update(layout, geoms...) compared to the first release so far,
probably need to rewrite or update the whole vignette again, please feel
free to test ggbio again after March 1st on bioc-dev repos.

btw: Gviz looks cool ~  I didn't know about it either, thanks a lot, Martin.

thanks

Tengfei

>
> thank you for the pointers, this is great.
>
>
> On Thu, Feb 16, 2012 at 2:47 AM, Steve Lianoglou <
> mailinglist.honeypot@gmail.com> wrote:
>
> > Hah!
> >
> > On Thu, Feb 16, 2012 at 1:11 AM, Martin Morgan <mtmorgan@fhcrc.org>
> wrote:
> >
> > > http://bioconductor.org/packages/release/bioc/html/ggbio.html
> > >
> > > and the Gvis vignette (if you're willing to use the 'devel' version of
> R
> > and
> > > Bioconductor)
> > >
> > >  http://bioconductor.org/packages/2.10/bioc/html/Gviz.html
> >
> > These packages are seriously cool!
> >
> > -steve
> >
> > --
> > Steve Lianoglou
> > Graduate Student: Computational Systems Biology
> >  | Memorial Sloan-Kettering Cancer Center
> >  | Weill Medical College of Cornell University
> > Contact Info: http://cbio.mskcc.org/~lianos/contact
> >
> > _______________________________________________
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> >
>
>
>
> --
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper<
> http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>
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-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274

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