[BioC] [Geneanswers] About the meaning of colours in networks

[Enrico Ferrero]

Hi,

I'm using the GeneAnswers package and its geneAnswersConceptRelation 
function to display Gene Ontology enrichments for my lists of genes in 
the form of connected networks.

I find the output very informative but I'm having a hard time in 
understanding what the sizes of circles and the colours of cirlces and 
arrows in the network represent.

My guess is that the intensity of red in circles reflects the adjusted 
p-value of the enrichment while the size could be proportional to the 
number of the genes associated with that term. Also I have no clue about 
what is the meaning of the different colours of the arrows connecting 
the circles (I've stumpled upon grey, light blue, orange and purple so far).

I can't find anything in the package documentation, so I was wondering 
if somebody could point me to the right docs.

Thanks very much.
Best,
-- 

Enrico Ferrero
PhD Student
Steve Russell Lab - Department of Genetics
FlyChip - Cambridge Systems Biology Centre
University of Cambridge

e.ferrero at gen.cam.ac.uk
http://flypress.gen.cam.ac.uk/