[BioC] plotting GO output as pie charts

[Sean Davis]

On 5/22/06 12:07 PM, "Celine Carret" <ckc at sanger.ac.uk> wrote:

> Hi everybody,
> I was wondering if there was a simple function allowing me to do this,
> plotting a GO-output search from ensembl into a pie-chart?
> I looked at biomaRt but the main problem I'm facing here is actually
> calling ensembl database as my Institute doesn't allow me to do so
> through R (I'm working on a farm nodes Linux 64), but also I couldn't
> actually find anywhere such a function in the package.
> So I took out my list of Human affyID I'm interested in, and used
> biomart directly on the web of Ensembl to fetch all the GO IDs
> associated... Now I'd like to plot those, and preferentially in a "user
> defined" fashion (by selecting the GO categories I want my genes to
> separate into, the end idea would be to compare several lists, for the
> same categories...)

You may want to look at the GOstats, GO, Category, and annotate packages in
bioconductor.  Affy gets a great deal of "special treatment" in the
microarray community because of its popularity; Bioconductor includes the
annotation packages for most of the affy arrays and these annotation
packages typically have GO mappings.  The R function pie() makes pie charts.

Sean